src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
 150   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 151
 152   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 153
 154   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 155
 156   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 157
 158   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 159
 160   JMenuItem htmlMenuItem = new JMenuItem();
 161
 162   JMenuItem overviewMenuItem = new JMenuItem();
 163
 164   protected JMenuItem undoMenuItem = new JMenuItem();
 165
 166   protected JMenuItem redoMenuItem = new JMenuItem();
 167
 168   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 169
 170   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 171
 172   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 173
 174   JMenuItem printMenuItem = new JMenuItem();
 175
 176   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 177
 178   JMenuItem findMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 185
 186   JMenuItem deleteGroups = new JMenuItem();
 187
 188   JMenuItem delete = new JMenuItem();
 189
 190   JMenuItem copy = new JMenuItem();
 191
 192   JMenuItem cut = new JMenuItem();
 193
 194   JMenu pasteMenu = new JMenu();
 195
 196   JMenuItem pasteNew = new JMenuItem();
 197
 198   JMenuItem pasteThis = new JMenuItem();
 199
 200   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 201
 202   JMenuItem createPNG = new JMenuItem();
 203
 204   protected JMenuItem font = new JMenuItem();
 205
 206   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 207
 208   JMenuItem epsFile = new JMenuItem();
 209
 210   JMenuItem LoadtreeMenuItem = new JMenuItem();
 211
 212   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 213
 214   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 215
 216   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 217
 218   protected JMenuItem modifyPID = new JMenuItem();
 219
 220   protected JMenuItem modifyConservation = new JMenuItem();
 221
 222   protected JMenu sortByTreeMenu = new JMenu();
 223
 224   protected JMenu sort = new JMenu();
 225
 226   protected JMenu calculateTree = new JMenu();
 227
 228   JMenu jMenu2 = new JMenu();
 229
 230   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 231
 232   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 233
 234   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 235
 236   protected ButtonGroup colours = new ButtonGroup();
 237
 238   JMenuItem vamsasStore = new JMenuItem();
 239
 240   protected JMenuItem showTranslation = new JMenuItem();
 241
 242   protected JMenuItem extractScores = new JMenuItem();
 243
 244   protected JMenu showProducts = new JMenu();
 245
 246   public JMenuItem openFeatureSettings = new JMenuItem();
 247
 248   JMenuItem fetchSequence = new JMenuItem();
 249
 250   JMenuItem annotationColour = new JMenuItem();
 251
 252   protected JMenuItem rnahelicesColour = new JMenuItem();
 253
 254   JMenuItem associatedData = new JMenuItem();
 255
 256   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 257
 258   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 259
 260   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 261
 262   JMenu addSequenceMenu = new JMenu();
 263
 264   JMenuItem addFromFile = new JMenuItem();
 265
 266   JMenuItem addFromText = new JMenuItem();
 267
 268   JMenuItem addFromURL = new JMenuItem();
 269
 270   JMenuItem exportAnnotations = new JMenuItem();
 271
 272   JMenuItem exportFeatures = new JMenuItem();
 273
 274   protected JPanel statusPanel = new JPanel();
 275
 276   GridLayout gridLayout1 = new GridLayout();
 277
 278   JMenu jMenu3 = new JMenu();
 279
 280   JMenuItem showAllSeqs = new JMenuItem();
 281
 282   JMenuItem showAllColumns = new JMenuItem();
 283
 284   JMenu hideMenu = new JMenu();
 285
 286   JMenuItem hideSelSequences = new JMenuItem();
 287
 288   JMenuItem hideSelColumns = new JMenuItem();
 289
 290   JMenuItem hideAllButSelection = new JMenuItem();
 291
 292   JMenuItem hideAllSelection = new JMenuItem();
 293
 294   JMenuItem showAllhidden = new JMenuItem();
 295
 296   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 297
 298   JMenuItem invertColSel = new JMenuItem();
 299
 300   protected JTabbedPane tabbedPane = new JTabbedPane();
 301
 302   JMenuItem save = new JMenuItem();
 303
 304   protected JMenuItem reload = new JMenuItem();
 305
 306   JMenuItem newView = new JMenuItem();
 307
 308   JMenuItem textColour = new JMenuItem();
 309
 310   JMenu formatMenu = new JMenu();
 311
 312   JMenu selectMenu = new JMenu();
 313
 314   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 315
 316   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 317
 318   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 319
 320   protected JMenuItem gatherViews = new JMenuItem();
 321
 322   protected JMenuItem expandViews = new JMenuItem();
 323
 324   JMenuItem pageSetup = new JMenuItem();
 325
 326   JMenuItem alignmentProperties = new JMenuItem();
 327
 328   JMenu tooltipSettingsMenu = new JMenu();
 329
 330   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 331
 332   private JMenuItem justifyRightMenuItem = new JMenuItem();
 333
 334   JMenu autoAnnMenu = new JMenu();
 335
 336   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 337
 338   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 339
 340   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 341
 342   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 343
 344   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 345
 346   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 347
 348   private JMenuItem grpsFromSelection = new JMenuItem();
 349
 350   public GAlignFrame()
 351   {
 352     try
 353     {
 354       jbInit();
 355       setJMenuBar(alignFrameMenuBar);
 356
 357       // dynamically fill save as menu with available formats
 358       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 359       {
 360         JMenuItem item = new JMenuItem(
 361                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 362
 363         item.addActionListener(new java.awt.event.ActionListener()
 364         {
 365           public void actionPerformed(ActionEvent e)
 366           {
 367             outputText_actionPerformed(e);
 368           }
 369         });
 370
 371         outputTextboxMenu.add(item);
 372       }
 373     } catch (Exception e)
 374     {
 375     }
 376
 377     if (!new jalview.util.Platform().isAMac())
 378     {
 379       closeMenuItem.setMnemonic('C');
 380       outputTextboxMenu.setMnemonic('T');
 381       undoMenuItem.setMnemonic('Z');
 382       redoMenuItem.setMnemonic('0');
 383       copy.setMnemonic('C');
 384       cut.setMnemonic('U');
 385       pasteMenu.setMnemonic('P');
 386       reload.setMnemonic('R');
 387     }
 388
 389     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 390     {
 391       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 392               .getUserColourSchemes().keys();
 393
 394       while (userColours.hasMoreElements())
 395       {
 396         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 397                 userColours.nextElement().toString());
 398         radioItem.setName("USER_DEFINED");
 399         radioItem.addMouseListener(new MouseAdapter()
 400         {
 401           public void mousePressed(MouseEvent evt)
 402           {
 403             if (evt.isControlDown()
 404                     || SwingUtilities.isRightMouseButton(evt))
 405             {
 406               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 407
 408               int option = JOptionPane.showInternalConfirmDialog(
 409                       jalview.gui.Desktop.desktop,
 410                       "Remove from default list?",
 411                       "Remove user defined colour",
 412                       JOptionPane.YES_NO_OPTION);
 413               if (option == JOptionPane.YES_OPTION)
 414               {
 415                 jalview.gui.UserDefinedColours
 416                         .removeColourFromDefaults(radioItem.getText());
 417                 colourMenu.remove(radioItem);
 418               }
 419               else
 420               {
 421                 radioItem.addActionListener(new ActionListener()
 422                 {
 423                   public void actionPerformed(ActionEvent evt)
 424                   {
 425                     userDefinedColour_actionPerformed(evt);
 426                   }
 427                 });
 428               }
 429             }
 430           }
 431         });
 432         radioItem.addActionListener(new ActionListener()
 433         {
 434           public void actionPerformed(ActionEvent evt)
 435           {
 436             userDefinedColour_actionPerformed(evt);
 437           }
 438         });
 439         colourMenu.insert(radioItem, 15);
 440         colours.add(radioItem);
 441       }
 442     }
 443     colours.add(noColourmenuItem);
 444     colours.add(clustalColour);
 445     colours.add(zappoColour);
 446     colours.add(taylorColour);
 447     colours.add(hydrophobicityColour);
 448     colours.add(helixColour);
 449     colours.add(strandColour);
 450     colours.add(turnColour);
 451     colours.add(buriedColour);
 452     colours.add(userDefinedColour);
 453     colours.add(PIDColour);
 454     colours.add(BLOSUM62Colour);
 455     colours.add(nucleotideColour);
 456     colours.add(purinePyrimidineColour);
 457     // colours.add(covariationColour);
 458     colours.add(tcoffeeColour);
 459     colours.add(RNAInteractionColour);
 460     setColourSelected(jalview.bin.Cache
 461             .getDefault("DEFAULT_COLOUR", "None"));
 462
 463   }
 464
 465   public void setColourSelected(String defaultColour)
 466   {
 467
 468     if (defaultColour != null)
 469     {
 470       int index = ColourSchemeProperty
 471               .getColourIndexFromName(defaultColour);
 472
 473       switch (index)
 474       {
 475       case ColourSchemeProperty.CLUSTAL:
 476         clustalColour.setSelected(true);
 477
 478         break;
 479
 480       case ColourSchemeProperty.BLOSUM:
 481         BLOSUM62Colour.setSelected(true);
 482
 483         break;
 484
 485       case ColourSchemeProperty.PID:
 486         PIDColour.setSelected(true);
 487
 488         break;
 489
 490       case ColourSchemeProperty.ZAPPO:
 491         zappoColour.setSelected(true);
 492
 493         break;
 494
 495       case ColourSchemeProperty.TAYLOR:
 496         taylorColour.setSelected(true);
 497         break;
 498
 499       case ColourSchemeProperty.HYDROPHOBIC:
 500         hydrophobicityColour.setSelected(true);
 501
 502         break;
 503
 504       case ColourSchemeProperty.HELIX:
 505         helixColour.setSelected(true);
 506
 507         break;
 508
 509       case ColourSchemeProperty.STRAND:
 510         strandColour.setSelected(true);
 511
 512         break;
 513
 514       case ColourSchemeProperty.TURN:
 515         turnColour.setSelected(true);
 516
 517         break;
 518
 519       case ColourSchemeProperty.BURIED:
 520         buriedColour.setSelected(true);
 521
 522         break;
 523
 524       case ColourSchemeProperty.NUCLEOTIDE:
 525         nucleotideColour.setSelected(true);
 526
 527         break;
 528
 529       case ColourSchemeProperty.TCOFFEE:
 530         tcoffeeColour.setSelected(true);
 531         break;
 532
 533       case ColourSchemeProperty.PURINEPYRIMIDINE:
 534         purinePyrimidineColour.setSelected(true);
 535
 536         break;
 537
 538       case ColourSchemeProperty.RNAINTERACTION:
 539           RNAInteractionColour.setSelected(true);
 540
 541           break;
 542       /*
 543        * case ColourSchemeProperty.COVARIATION:
 544        * covariationColour.setSelected(true);
 545        *
 546        * break;
 547        */
 548       case ColourSchemeProperty.USER_DEFINED:
 549         userDefinedColour.setSelected(true);
 550
 551         break;
 552       case ColourSchemeProperty.NONE:
 553       default:
 554         noColourmenuItem.setSelected(true);
 555         break;
 556
 557       }
 558     }
 559
 560   }
 561
 562   private void jbInit() throws Exception
 563   {
 564     fileMenu.setText("File");
 565     saveAs.setText("Save As...");
 566     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 567             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 568                     .getMenuShortcutKeyMask()
 569                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 570     saveAs.addActionListener(new ActionListener()
 571     {
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         saveAs_actionPerformed(e);
 575       }
 576     });
 577     closeMenuItem.setText("Close");
 578     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 579             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 580                     .getMenuShortcutKeyMask(), false));
 581     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 582     {
 583       public void actionPerformed(ActionEvent e)
 584       {
 585         closeMenuItem_actionPerformed(false);
 586       }
 587     });
 588     editMenu.setText("Edit");
 589     viewMenu.setText("View");
 590     colourMenu.setText("Colour");
 591     calculateMenu.setText("Calculate");
 592     webService.setText("Web Service");
 593     selectAllSequenceMenuItem.setText("Select All");
 594     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 595             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 596                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 597     selectAllSequenceMenuItem
 598             .addActionListener(new java.awt.event.ActionListener()
 599             {
 600               public void actionPerformed(ActionEvent e)
 601               {
 602                 selectAllSequenceMenuItem_actionPerformed(e);
 603               }
 604             });
 605     deselectAllSequenceMenuItem.setText("Deselect All");
 606     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 607             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 608     deselectAllSequenceMenuItem
 609             .addActionListener(new java.awt.event.ActionListener()
 610             {
 611               public void actionPerformed(ActionEvent e)
 612               {
 613                 deselectAllSequenceMenuItem_actionPerformed(e);
 614               }
 615             });
 616     invertSequenceMenuItem.setText("Invert Sequence Selection");
 617     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 618             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 619                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 620     invertSequenceMenuItem
 621             .addActionListener(new java.awt.event.ActionListener()
 622             {
 623               public void actionPerformed(ActionEvent e)
 624               {
 625                 invertSequenceMenuItem_actionPerformed(e);
 626               }
 627             });
 628     grpsFromSelection.setText("Make Groups for selection");
 629     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 630     {
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         makeGrpsFromSelection_actionPerformed(e);
 634       }
 635     });
 636
 637     remove2LeftMenuItem.setText("Remove Left");
 638     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 639             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 640                     .getMenuShortcutKeyMask(), false));
 641     remove2LeftMenuItem
 642             .addActionListener(new java.awt.event.ActionListener()
 643             {
 644               public void actionPerformed(ActionEvent e)
 645               {
 646                 remove2LeftMenuItem_actionPerformed(e);
 647               }
 648             });
 649     remove2RightMenuItem.setText("Remove Right");
 650     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 651             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 652                     .getMenuShortcutKeyMask(), false));
 653     remove2RightMenuItem
 654             .addActionListener(new java.awt.event.ActionListener()
 655             {
 656               public void actionPerformed(ActionEvent e)
 657               {
 658                 remove2RightMenuItem_actionPerformed(e);
 659               }
 660             });
 661     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 662     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 663             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 664                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 665     removeGappedColumnMenuItem
 666             .addActionListener(new java.awt.event.ActionListener()
 667             {
 668               public void actionPerformed(ActionEvent e)
 669               {
 670                 removeGappedColumnMenuItem_actionPerformed(e);
 671               }
 672             });
 673     removeAllGapsMenuItem.setText("Remove All Gaps");
 674     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 675             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 676                     .getDefaultToolkit().getMenuShortcutKeyMask()
 677                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 678     removeAllGapsMenuItem
 679             .addActionListener(new java.awt.event.ActionListener()
 680             {
 681               public void actionPerformed(ActionEvent e)
 682               {
 683                 removeAllGapsMenuItem_actionPerformed(e);
 684               }
 685             });
 686     justifyLeftMenuItem.setText("Left Justify Alignment");
 687     justifyLeftMenuItem
 688             .addActionListener(new java.awt.event.ActionListener()
 689             {
 690               public void actionPerformed(ActionEvent e)
 691               {
 692                 justifyLeftMenuItem_actionPerformed(e);
 693               }
 694             });
 695     justifyRightMenuItem.setText("Right Justify Alignment");
 696     justifyRightMenuItem
 697             .addActionListener(new java.awt.event.ActionListener()
 698             {
 699               public void actionPerformed(ActionEvent e)
 700               {
 701                 justifyRightMenuItem_actionPerformed(e);
 702               }
 703             });
 704     viewBoxesMenuItem.setText("Boxes");
 705     viewBoxesMenuItem.setState(true);
 706     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 707     {
 708       public void actionPerformed(ActionEvent e)
 709       {
 710         viewBoxesMenuItem_actionPerformed(e);
 711       }
 712     });
 713     viewTextMenuItem.setText("Text");
 714     viewTextMenuItem.setState(true);
 715     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 716     {
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         viewTextMenuItem_actionPerformed(e);
 720       }
 721     });
 722     showNonconservedMenuItem.setText("Show nonconserved");
 723     showNonconservedMenuItem.setState(false);
 724     showNonconservedMenuItem
 725             .addActionListener(new java.awt.event.ActionListener()
 726             {
 727               public void actionPerformed(ActionEvent e)
 728               {
 729                 showUnconservedMenuItem_actionPerformed(e);
 730               }
 731             });
 732     sortPairwiseMenuItem.setText("by Pairwise Identity");
 733     sortPairwiseMenuItem
 734             .addActionListener(new java.awt.event.ActionListener()
 735             {
 736               public void actionPerformed(ActionEvent e)
 737               {
 738                 sortPairwiseMenuItem_actionPerformed(e);
 739               }
 740             });
 741     sortIDMenuItem.setText("by ID");
 742     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 743     {
 744       public void actionPerformed(ActionEvent e)
 745       {
 746         sortIDMenuItem_actionPerformed(e);
 747       }
 748     });
 749     sortLengthMenuItem.setText("By Length");
 750     sortLengthMenuItem
 751             .addActionListener(new java.awt.event.ActionListener()
 752             {
 753               public void actionPerformed(ActionEvent e)
 754               {
 755                 sortLengthMenuItem_actionPerformed(e);
 756               }
 757             });
 758     sortGroupMenuItem.setText("by Group");
 759     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 760     {
 761       public void actionPerformed(ActionEvent e)
 762       {
 763         sortGroupMenuItem_actionPerformed(e);
 764       }
 765     });
 766     removeRedundancyMenuItem.setText("Remove Redundancy...");
 767     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 768             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 769                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 770     removeRedundancyMenuItem
 771             .addActionListener(new java.awt.event.ActionListener()
 772             {
 773               public void actionPerformed(ActionEvent e)
 774               {
 775                 removeRedundancyMenuItem_actionPerformed(e);
 776               }
 777             });
 778     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 779     pairwiseAlignmentMenuItem
 780             .addActionListener(new java.awt.event.ActionListener()
 781             {
 782               public void actionPerformed(ActionEvent e)
 783               {
 784                 pairwiseAlignmentMenuItem_actionPerformed(e);
 785               }
 786             });
 787     PCAMenuItem.setText("Principal Component Analysis");
 788     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 789     {
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         PCAMenuItem_actionPerformed(e);
 793       }
 794     });
 795     averageDistanceTreeMenuItem
 796             .setText("Average Distance Using % Identity");
 797     averageDistanceTreeMenuItem
 798             .addActionListener(new java.awt.event.ActionListener()
 799             {
 800               public void actionPerformed(ActionEvent e)
 801               {
 802                 averageDistanceTreeMenuItem_actionPerformed(e);
 803               }
 804             });
 805     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 806     neighbourTreeMenuItem
 807             .addActionListener(new java.awt.event.ActionListener()
 808             {
 809               public void actionPerformed(ActionEvent e)
 810               {
 811                 neighbourTreeMenuItem_actionPerformed(e);
 812               }
 813             });
 814     this.getContentPane().setLayout(borderLayout1);
 815     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 816     alignFrameMenuBar.setBackground(Color.lightGray);
 817     statusBar.setBackground(Color.white);
 818     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 819     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 820     statusBar.setText("Status bar");
 821     outputTextboxMenu.setText("Output to Textbox");
 822     clustalColour.setText("Clustalx");
 823
 824     clustalColour.addActionListener(new java.awt.event.ActionListener()
 825     {
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         clustalColour_actionPerformed(e);
 829       }
 830     });
 831     zappoColour.setText("Zappo");
 832     zappoColour.addActionListener(new java.awt.event.ActionListener()
 833     {
 834       public void actionPerformed(ActionEvent e)
 835       {
 836         zappoColour_actionPerformed(e);
 837       }
 838     });
 839     taylorColour.setText("Taylor");
 840     taylorColour.addActionListener(new java.awt.event.ActionListener()
 841     {
 842       public void actionPerformed(ActionEvent e)
 843       {
 844         taylorColour_actionPerformed(e);
 845       }
 846     });
 847     hydrophobicityColour.setText("Hydrophobicity");
 848     hydrophobicityColour
 849             .addActionListener(new java.awt.event.ActionListener()
 850             {
 851               public void actionPerformed(ActionEvent e)
 852               {
 853                 hydrophobicityColour_actionPerformed(e);
 854               }
 855             });
 856     helixColour.setText("Helix Propensity");
 857     helixColour.addActionListener(new java.awt.event.ActionListener()
 858     {
 859       public void actionPerformed(ActionEvent e)
 860       {
 861         helixColour_actionPerformed(e);
 862       }
 863     });
 864     strandColour.setText("Strand Propensity");
 865     strandColour.addActionListener(new java.awt.event.ActionListener()
 866     {
 867       public void actionPerformed(ActionEvent e)
 868       {
 869         strandColour_actionPerformed(e);
 870       }
 871     });
 872     turnColour.setText("Turn Propensity");
 873     turnColour.addActionListener(new java.awt.event.ActionListener()
 874     {
 875       public void actionPerformed(ActionEvent e)
 876       {
 877         turnColour_actionPerformed(e);
 878       }
 879     });
 880     buriedColour.setText("Buried Index");
 881     buriedColour.addActionListener(new java.awt.event.ActionListener()
 882     {
 883       public void actionPerformed(ActionEvent e)
 884       {
 885         buriedColour_actionPerformed(e);
 886       }
 887     });
 888     userDefinedColour.setText("User Defined...");
 889     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 890     {
 891       public void actionPerformed(ActionEvent e)
 892       {
 893         userDefinedColour_actionPerformed(e);
 894       }
 895     });
 896     PIDColour.setText("Percentage Identity");
 897     PIDColour.addActionListener(new java.awt.event.ActionListener()
 898     {
 899       public void actionPerformed(ActionEvent e)
 900       {
 901         PIDColour_actionPerformed(e);
 902       }
 903     });
 904     BLOSUM62Colour.setText("BLOSUM62 Score");
 905     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 906     {
 907       public void actionPerformed(ActionEvent e)
 908       {
 909         BLOSUM62Colour_actionPerformed(e);
 910       }
 911     });
 912     nucleotideColour.setText("Nucleotide");
 913     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 914     {
 915       public void actionPerformed(ActionEvent e)
 916       {
 917         nucleotideColour_actionPerformed(e);
 918       }
 919     });
 920
 921     purinePyrimidineColour.setText("Purine/Pyrimidine");
 922     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
 923             {
 924               public void actionPerformed(ActionEvent e)
 925               {
 926                 purinePyrimidineColour_actionPerformed(e);
 927               }
 928             });
 929
 930     RNAInteractionColour.setText("RNA Interaction type");
 931     RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
 932             {
 933               public void actionPerformed(ActionEvent e)
 934               {
 935                   RNAInteractionColour_actionPerformed(e);
 936               }
 937             });
 938     /*
 939      * covariationColour.setText("Covariation");
 940      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 941      * public void actionPerformed(ActionEvent e) {
 942      * covariationColour_actionPerformed(e); } });
 943      */
 944
 945     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 946     avDistanceTreeBlosumMenuItem
 947             .addActionListener(new java.awt.event.ActionListener()
 948             {
 949               public void actionPerformed(ActionEvent e)
 950               {
 951                 avTreeBlosumMenuItem_actionPerformed(e);
 952               }
 953             });
 954     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 955     njTreeBlosumMenuItem
 956             .addActionListener(new java.awt.event.ActionListener()
 957             {
 958               public void actionPerformed(ActionEvent e)
 959               {
 960                 njTreeBlosumMenuItem_actionPerformed(e);
 961               }
 962             });
 963     annotationPanelMenuItem.setActionCommand("");
 964     annotationPanelMenuItem.setText("Show Annotations");
 965     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 966             "SHOW_ANNOTATIONS", true));
 967     annotationPanelMenuItem
 968             .addActionListener(new java.awt.event.ActionListener()
 969             {
 970               public void actionPerformed(ActionEvent e)
 971               {
 972                 annotationPanelMenuItem_actionPerformed(e);
 973               }
 974             });
 975     colourTextMenuItem.setText("Colour Text");
 976     colourTextMenuItem
 977             .addActionListener(new java.awt.event.ActionListener()
 978             {
 979               public void actionPerformed(ActionEvent e)
 980               {
 981                 colourTextMenuItem_actionPerformed(e);
 982               }
 983             });
 984     htmlMenuItem.setText("HTML");
 985     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 986     {
 987       public void actionPerformed(ActionEvent e)
 988       {
 989         htmlMenuItem_actionPerformed(e);
 990       }
 991     });
 992     overviewMenuItem.setText("Overview Window");
 993     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 994     {
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         overviewMenuItem_actionPerformed(e);
 998       }
 999     });
1000     undoMenuItem.setEnabled(false);
1001     undoMenuItem.setText("Undo");
1002     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1004                     .getMenuShortcutKeyMask(), false));
1005     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1006     {
1007       public void actionPerformed(ActionEvent e)
1008       {
1009         undoMenuItem_actionPerformed(e);
1010       }
1011     });
1012     redoMenuItem.setEnabled(false);
1013     redoMenuItem.setText("Redo");
1014     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1015             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1016                     .getMenuShortcutKeyMask(), false));
1017     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1018     {
1019       public void actionPerformed(ActionEvent e)
1020       {
1021         redoMenuItem_actionPerformed(e);
1022       }
1023     });
1024     conservationMenuItem.setText("By Conservation");
1025     conservationMenuItem
1026             .addActionListener(new java.awt.event.ActionListener()
1027             {
1028               public void actionPerformed(ActionEvent e)
1029               {
1030                 conservationMenuItem_actionPerformed(e);
1031               }
1032             });
1033     noColourmenuItem.setText("None");
1034     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1035     {
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         noColourmenuItem_actionPerformed(e);
1039       }
1040     });
1041     wrapMenuItem.setText("Wrap");
1042     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1043     {
1044       public void actionPerformed(ActionEvent e)
1045       {
1046         wrapMenuItem_actionPerformed(e);
1047       }
1048     });
1049     printMenuItem.setText("Print ...");
1050     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1051             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1052                     .getMenuShortcutKeyMask(), false));
1053     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         printMenuItem_actionPerformed(e);
1058       }
1059     });
1060     renderGapsMenuItem.setText("Show Gaps");
1061     renderGapsMenuItem.setState(true);
1062     renderGapsMenuItem
1063             .addActionListener(new java.awt.event.ActionListener()
1064             {
1065               public void actionPerformed(ActionEvent e)
1066               {
1067                 renderGapsMenuItem_actionPerformed(e);
1068               }
1069             });
1070     findMenuItem.setText("Find...");
1071     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1072             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1073                     .getMenuShortcutKeyMask(), false));
1074     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1075     {
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         findMenuItem_actionPerformed(e);
1079       }
1080     });
1081     abovePIDThreshold.setText("Above Identity Threshold");
1082     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1083     {
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         abovePIDThreshold_actionPerformed(e);
1087       }
1088     });
1089     showSeqFeatures.setText("Show Sequence Features");
1090     showSeqFeatures.addActionListener(new ActionListener()
1091     {
1092       public void actionPerformed(ActionEvent actionEvent)
1093       {
1094         showSeqFeatures_actionPerformed(actionEvent);
1095       }
1096     });
1097     /*
1098      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1099      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1100      * void actionPerformed(ActionEvent actionEvent) {
1101      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1102      */
1103     showDbRefsMenuitem.setText("Show Database Refs");
1104     showDbRefsMenuitem.addActionListener(new ActionListener()
1105     {
1106
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         showDbRefs_actionPerformed(e);
1110       }
1111
1112     });
1113     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1114     showNpFeatsMenuitem.addActionListener(new ActionListener()
1115     {
1116
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         showNpFeats_actionPerformed(e);
1120       }
1121
1122     });
1123     showGroupConservation.setText("Group Conservation");
1124     showGroupConservation.addActionListener(new ActionListener()
1125     {
1126
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         showGroupConservation_actionPerformed(e);
1130       }
1131
1132     });
1133
1134     showGroupConsensus.setText("Group Consensus");
1135     showGroupConsensus.addActionListener(new ActionListener()
1136     {
1137
1138       public void actionPerformed(ActionEvent e)
1139       {
1140         showGroupConsensus_actionPerformed(e);
1141       }
1142
1143     });
1144     showConsensusHistogram.setText("Show Consensus Histogram");
1145     showConsensusHistogram.addActionListener(new ActionListener()
1146     {
1147
1148       public void actionPerformed(ActionEvent e)
1149       {
1150         showConsensusHistogram_actionPerformed(e);
1151       }
1152
1153     });
1154     showSequenceLogo.setText("Show Consensus Logo");
1155     showSequenceLogo.addActionListener(new ActionListener()
1156     {
1157
1158       public void actionPerformed(ActionEvent e)
1159       {
1160         showSequenceLogo_actionPerformed(e);
1161       }
1162
1163     });
1164     normaliseSequenceLogo.setText("Normalise Consensus Logo");
1165     normaliseSequenceLogo.addActionListener(new ActionListener()
1166     {
1167
1168       public void actionPerformed(ActionEvent e)
1169       {
1170         normaliseSequenceLogo_actionPerformed(e);
1171       }
1172
1173     });
1174     applyAutoAnnotationSettings.setText("Apply to all groups");
1175     applyAutoAnnotationSettings.setState(false);
1176     applyAutoAnnotationSettings.setVisible(true);
1177     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1178     {
1179
1180       public void actionPerformed(ActionEvent e)
1181       {
1182         applyAutoAnnotationSettings_actionPerformed(e);
1183       }
1184
1185     });
1186
1187     nucleotideColour.setText("Nucleotide");
1188     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1189     {
1190       public void actionPerformed(ActionEvent e)
1191       {
1192         nucleotideColour_actionPerformed(e);
1193       }
1194     });
1195
1196     tcoffeeColour.setText("T-Coffee scores");
1197     tcoffeeColour.setEnabled(false);
1198     tcoffeeColour.addActionListener( new ActionListener() {
1199
1200                 @Override
1201                 public void actionPerformed(ActionEvent e) {
1202                         tcoffeeColorScheme_actionPerformed(e);
1203                 }
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.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
1537     sortByTree.setState(jalview.bin.Cache.getDefault(
1538             "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.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
1549     listenToViewSelections.setState(false);
1550     listenToViewSelections.addActionListener(new ActionListener()
1551     {
1552       public void actionPerformed(ActionEvent e)
1553       {
1554         listenToViewSelections_actionPerformed(e);
1555       }
1556     });
1557
1558     addSequenceMenu.setText("Add Sequences");
1559     addFromFile.setText("From File");
1560     addFromFile.addActionListener(new ActionListener()
1561     {
1562       public void actionPerformed(ActionEvent e)
1563       {
1564         addFromFile_actionPerformed(e);
1565       }
1566     });
1567     addFromText.setText("From Textbox");
1568     addFromText.addActionListener(new ActionListener()
1569     {
1570       public void actionPerformed(ActionEvent e)
1571       {
1572         addFromText_actionPerformed(e);
1573       }
1574     });
1575     addFromURL.setText("From URL");
1576     addFromURL.addActionListener(new ActionListener()
1577     {
1578       public void actionPerformed(ActionEvent e)
1579       {
1580         addFromURL_actionPerformed(e);
1581       }
1582     });
1583     exportFeatures.setText("Export Features...");
1584     exportFeatures.addActionListener(new ActionListener()
1585     {
1586       public void actionPerformed(ActionEvent e)
1587       {
1588         exportFeatures_actionPerformed(e);
1589       }
1590     });
1591     exportAnnotations.setText("Export Annotations...");
1592     exportAnnotations.addActionListener(new ActionListener()
1593     {
1594       public void actionPerformed(ActionEvent e)
1595       {
1596         exportAnnotations_actionPerformed(e);
1597       }
1598     });
1599     statusPanel.setLayout(gridLayout1);
1600     jMenu3.setText("Show");
1601     showAllSeqs.setText("All Sequences");
1602     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1603     showAllSeqs.addActionListener(new ActionListener()
1604     {
1605       public void actionPerformed(ActionEvent e)
1606       {
1607         showAllSeqs_actionPerformed(e);
1608       }
1609     });
1610     showAllColumns.setText("All Columns");
1611     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1612     showAllColumns.addActionListener(new ActionListener()
1613     {
1614       public void actionPerformed(ActionEvent e)
1615       {
1616         showAllColumns_actionPerformed(e);
1617       }
1618     });
1619     hideMenu.setText("Hide");
1620     hideSelSequences.setText("Selected Sequences");
1621     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1622     hideSelSequences.addActionListener(new ActionListener()
1623     {
1624       public void actionPerformed(ActionEvent e)
1625       {
1626         hideSelSequences_actionPerformed(e);
1627       }
1628     });
1629     hideSelColumns.setText("Selected Columns");
1630     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1631     hideSelColumns.addActionListener(new ActionListener()
1632     {
1633       public void actionPerformed(ActionEvent e)
1634       {
1635         hideSelColumns_actionPerformed(e);
1636       }
1637     });
1638     hideAllSelection.setText("Selected Region");
1639     hideAllSelection.addActionListener(new ActionListener()
1640     {
1641       public void actionPerformed(ActionEvent e)
1642       {
1643         hideAllSelection_actionPerformed(e);
1644       }
1645     });
1646     // TODO: should be hidden if no selection exists.
1647     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1648     hideAllButSelection.addActionListener(new ActionListener()
1649     {
1650       public void actionPerformed(ActionEvent e)
1651       {
1652         hideAllButSelection_actionPerformed(e);
1653       }
1654     });
1655     showAllhidden.setText("All Sequences and Columns");
1656     showAllhidden
1657             .setToolTipText("H toggles visibility of hidden or selected regions.");
1658     showAllhidden.addActionListener(new ActionListener()
1659     {
1660       public void actionPerformed(ActionEvent e)
1661       {
1662         showAllhidden_actionPerformed(e);
1663       }
1664     });
1665
1666     hiddenMarkers.setText("Show Hidden Markers");
1667     hiddenMarkers.addActionListener(new ActionListener()
1668     {
1669       public void actionPerformed(ActionEvent e)
1670       {
1671         hiddenMarkers_actionPerformed(e);
1672       }
1673     });
1674     invertColSel.setText("Invert Column Selection");
1675     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1676             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1677                     .getMenuShortcutKeyMask()
1678                     | java.awt.event.KeyEvent.ALT_MASK, false));
1679     invertColSel.addActionListener(new ActionListener()
1680     {
1681       public void actionPerformed(ActionEvent e)
1682       {
1683         invertColSel_actionPerformed(e);
1684       }
1685     });
1686     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1687     {
1688       public void stateChanged(ChangeEvent evt)
1689       {
1690         JTabbedPane pane = (JTabbedPane) evt.getSource();
1691         int sel = pane.getSelectedIndex();
1692         tabSelectionChanged(sel);
1693       }
1694     });
1695     tabbedPane.addMouseListener(new MouseAdapter()
1696     {
1697       public void mousePressed(MouseEvent e)
1698       {
1699         tabbedPane_mousePressed(e);
1700       }
1701     });
1702     tabbedPane.addFocusListener(new FocusAdapter()
1703     {
1704       public void focusGained(FocusEvent e)
1705       {
1706         tabbedPane_focusGained(e);
1707       }
1708     });
1709     save.setText("Save");
1710     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1711             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1712                     .getMenuShortcutKeyMask(), false));
1713     save.addActionListener(new ActionListener()
1714     {
1715       public void actionPerformed(ActionEvent e)
1716       {
1717         save_actionPerformed(e);
1718       }
1719     });
1720     reload.setEnabled(false);
1721     reload.setText("Reload");
1722     reload.addActionListener(new ActionListener()
1723     {
1724       public void actionPerformed(ActionEvent e)
1725       {
1726         reload_actionPerformed(e);
1727       }
1728     });
1729     newView.setText("New View");
1730     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1731             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1732                     .getMenuShortcutKeyMask(), false));
1733     newView.addActionListener(new ActionListener()
1734     {
1735       public void actionPerformed(ActionEvent e)
1736       {
1737         newView_actionPerformed(e);
1738       }
1739     });
1740     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1741             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1742     textColour.setText("Colour Text ...");
1743     textColour.addActionListener(new ActionListener()
1744     {
1745       public void actionPerformed(ActionEvent e)
1746       {
1747         textColour_actionPerformed(e);
1748       }
1749     });
1750     formatMenu.setText("Format");
1751     selectMenu.setText("Select");
1752     idRightAlign.setText("Right Align Sequence Id");
1753     idRightAlign.addActionListener(new ActionListener()
1754     {
1755       public void actionPerformed(ActionEvent e)
1756       {
1757         idRightAlign_actionPerformed(e);
1758       }
1759     });
1760     gatherViews.setEnabled(false);
1761     gatherViews.setText("Gather Views");
1762     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1763             java.awt.event.KeyEvent.VK_G, 0, false));
1764     gatherViews.addActionListener(new ActionListener()
1765     {
1766       public void actionPerformed(ActionEvent e)
1767       {
1768         gatherViews_actionPerformed(e);
1769       }
1770     });
1771     expandViews.setEnabled(false);
1772     expandViews.setText("Expand Views");
1773     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1774             java.awt.event.KeyEvent.VK_X, 0, false));
1775     expandViews.addActionListener(new ActionListener()
1776     {
1777       public void actionPerformed(ActionEvent e)
1778       {
1779         expandViews_actionPerformed(e);
1780       }
1781     });
1782     pageSetup.setText("Page Setup ...");
1783     pageSetup.addActionListener(new ActionListener()
1784     {
1785       public void actionPerformed(ActionEvent e)
1786       {
1787         pageSetup_actionPerformed(e);
1788       }
1789     });
1790     alignmentProperties.setText("Alignment Properties...");
1791     alignmentProperties.addActionListener(new ActionListener()
1792     {
1793       public void actionPerformed(ActionEvent actionEvent)
1794       {
1795         alignmentProperties();
1796       }
1797     });
1798     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1799     autoAnnMenu.setText("Autocalculated Annotation");
1800     alignFrameMenuBar.add(fileMenu);
1801     alignFrameMenuBar.add(editMenu);
1802     alignFrameMenuBar.add(selectMenu);
1803     alignFrameMenuBar.add(viewMenu);
1804     alignFrameMenuBar.add(formatMenu);
1805     alignFrameMenuBar.add(colourMenu);
1806     alignFrameMenuBar.add(calculateMenu);
1807     alignFrameMenuBar.add(webService);
1808     fileMenu.add(fetchSequence);
1809     fileMenu.add(addSequenceMenu);
1810     fileMenu.add(reload);
1811     fileMenu.addSeparator();
1812     fileMenu.add(vamsasStore);
1813     fileMenu.add(save);
1814     fileMenu.add(saveAs);
1815     fileMenu.add(outputTextboxMenu);
1816     fileMenu.add(pageSetup);
1817     fileMenu.add(printMenuItem);
1818     fileMenu.addSeparator();
1819     fileMenu.add(jMenu2);
1820     fileMenu.add(exportFeatures);
1821     fileMenu.add(exportAnnotations);
1822     fileMenu.add(LoadtreeMenuItem);
1823     fileMenu.add(associatedData);
1824     fileMenu.addSeparator();
1825     fileMenu.add(closeMenuItem);
1826     editMenu.add(undoMenuItem);
1827     editMenu.add(redoMenuItem);
1828     editMenu.add(cut);
1829     editMenu.add(copy);
1830     editMenu.add(pasteMenu);
1831     editMenu.add(delete);
1832     editMenu.addSeparator();
1833     editMenu.add(remove2LeftMenuItem);
1834     editMenu.add(remove2RightMenuItem);
1835     editMenu.add(removeGappedColumnMenuItem);
1836     editMenu.add(removeAllGapsMenuItem);
1837     editMenu.add(removeRedundancyMenuItem);
1838     editMenu.addSeparator();
1839     // dont add these yet in the CVS build - they cannot be undone!
1840     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1841     // editMenu.add(justifyLeftMenuItem);
1842     // editMenu.add(justifyRightMenuItem);
1843     // editMenu.addSeparator();
1844     editMenu.add(padGapsMenuitem);
1845     viewMenu.add(newView);
1846     viewMenu.add(expandViews);
1847     viewMenu.add(gatherViews);
1848     viewMenu.addSeparator();
1849     viewMenu.add(jMenu3);
1850     viewMenu.add(hideMenu);
1851     viewMenu.addSeparator();
1852     viewMenu.add(followHighlightMenuItem);
1853     viewMenu.add(annotationPanelMenuItem);
1854     autoAnnMenu.add(applyAutoAnnotationSettings);
1855     autoAnnMenu.add(showConsensusHistogram);
1856     autoAnnMenu.add(showSequenceLogo);
1857     autoAnnMenu.add(normaliseSequenceLogo);
1858     autoAnnMenu.addSeparator();
1859     autoAnnMenu.add(showGroupConservation);
1860     autoAnnMenu.add(showGroupConsensus);
1861     viewMenu.add(autoAnnMenu);
1862     viewMenu.addSeparator();
1863     viewMenu.add(showSeqFeatures);
1864     // viewMenu.add(showSeqFeaturesHeight);
1865
1866     viewMenu.add(openFeatureSettings);
1867     tooltipSettingsMenu.add(showDbRefsMenuitem);
1868     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1869     viewMenu.add(tooltipSettingsMenu);
1870     viewMenu.addSeparator();
1871     viewMenu.add(alignmentProperties);
1872     viewMenu.addSeparator();
1873     viewMenu.add(overviewMenuItem);
1874     colourMenu.add(applyToAllGroups);
1875     colourMenu.add(textColour);
1876     colourMenu.addSeparator();
1877     colourMenu.add(noColourmenuItem);
1878     colourMenu.add(clustalColour);
1879     colourMenu.add(BLOSUM62Colour);
1880     colourMenu.add(PIDColour);
1881     colourMenu.add(zappoColour);
1882     colourMenu.add(taylorColour);
1883     colourMenu.add(hydrophobicityColour);
1884     colourMenu.add(helixColour);
1885     colourMenu.add(strandColour);
1886     colourMenu.add(turnColour);
1887     colourMenu.add(buriedColour);
1888     colourMenu.add(nucleotideColour);
1889     colourMenu.add(purinePyrimidineColour);
1890     colourMenu.add(RNAInteractionColour);
1891     // colourMenu.add(covariationColour);
1892     colourMenu.add(tcoffeeColour);
1893     colourMenu.add(userDefinedColour);
1894     colourMenu.addSeparator();
1895     colourMenu.add(conservationMenuItem);
1896     colourMenu.add(modifyConservation);
1897     colourMenu.add(abovePIDThreshold);
1898     colourMenu.add(modifyPID);
1899     colourMenu.add(annotationColour);
1900     colourMenu.add(rnahelicesColour);
1901     calculateMenu.add(sort);
1902     calculateMenu.add(calculateTree);
1903     calculateMenu.addSeparator();
1904     calculateMenu.add(pairwiseAlignmentMenuItem);
1905     calculateMenu.add(PCAMenuItem);
1906     calculateMenu.addSeparator();
1907     calculateMenu.add(showTranslation);
1908     calculateMenu.add(showProducts);
1909     calculateMenu.add(autoCalculate);
1910     calculateMenu.add(sortByTree);
1911     calculateMenu.addSeparator();
1912     calculateMenu.add(extractScores);
1913     webServiceNoServices = new JMenuItem("<No Services>");
1914     webService.add(webServiceNoServices);
1915     pasteMenu.add(pasteNew);
1916     pasteMenu.add(pasteThis);
1917     sort.add(sortIDMenuItem);
1918     sort.add(sortLengthMenuItem);
1919     sort.add(sortGroupMenuItem);
1920     sort.add(sortPairwiseMenuItem);
1921     sort.add(sortByTreeMenu);
1922     calculateTree.add(averageDistanceTreeMenuItem);
1923     calculateTree.add(neighbourTreeMenuItem);
1924     calculateTree.add(avDistanceTreeBlosumMenuItem);
1925     calculateTree.add(njTreeBlosumMenuItem);
1926     jMenu2.add(htmlMenuItem);
1927     jMenu2.add(epsFile);
1928     jMenu2.add(createPNG);
1929     addSequenceMenu.add(addFromFile);
1930     addSequenceMenu.add(addFromText);
1931     addSequenceMenu.add(addFromURL);
1932     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1933     statusPanel.add(statusBar, null);
1934     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1935     jMenu3.add(showAllColumns);
1936     jMenu3.add(showAllSeqs);
1937     jMenu3.add(showAllhidden);
1938     hideMenu.add(hideSelColumns);
1939     hideMenu.add(hideSelSequences);
1940     hideMenu.add(hideAllSelection);
1941     hideMenu.add(hideAllButSelection);
1942
1943     formatMenu.add(font);
1944     formatMenu.addSeparator();
1945     formatMenu.add(wrapMenuItem);
1946     formatMenu.add(scaleAbove);
1947     formatMenu.add(scaleLeft);
1948     formatMenu.add(scaleRight);
1949     formatMenu.add(seqLimits);
1950     formatMenu.add(idRightAlign);
1951     formatMenu.add(hiddenMarkers);
1952     formatMenu.add(viewBoxesMenuItem);
1953     formatMenu.add(viewTextMenuItem);
1954     formatMenu.add(colourTextMenuItem);
1955     formatMenu.add(renderGapsMenuItem);
1956     formatMenu.add(centreColumnLabelsMenuItem);
1957     formatMenu.add(showNonconservedMenuItem);
1958     selectMenu.add(findMenuItem);
1959     selectMenu.addSeparator();
1960     selectMenu.add(selectAllSequenceMenuItem);
1961     selectMenu.add(deselectAllSequenceMenuItem);
1962     selectMenu.add(invertSequenceMenuItem);
1963     selectMenu.add(invertColSel);
1964     selectMenu.add(deleteGroups);
1965     selectMenu.add(grpsFromSelection);
1966     // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
1967     //selectMenu.addSeparator();
1968     //selectMenu.add(listenToViewSelections);
1969   }
1970
1971   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
1972   {
1973     // TODO Auto-generated method stub
1974
1975   }
1976
1977   protected void listenToViewSelections_actionPerformed(ActionEvent e)
1978   {
1979     // TODO Auto-generated method stub
1980
1981   }
1982
1983   protected void showAllhidden_actionPerformed(ActionEvent e)
1984   {
1985     // TODO Auto-generated method stub
1986
1987   }
1988
1989   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1990   {
1991     // TODO Auto-generated method stub
1992
1993   }
1994
1995   protected void hideAllSelection_actionPerformed(ActionEvent e)
1996   {
1997     // TODO Auto-generated method stub
1998
1999   }
2000
2001   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2002   {
2003     // TODO Auto-generated method stub
2004
2005   }
2006
2007   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2008   {
2009     // TODO Auto-generated method stub
2010
2011   }
2012
2013   protected void showSequenceLogo_actionPerformed(ActionEvent e)
2014   {
2015     // TODO Auto-generated method stub
2016
2017   }
2018
2019   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2020   {
2021     // TODO Auto-generated method stub
2022
2023   }
2024
2025   protected void showGroupConsensus_actionPerformed(ActionEvent e)
2026   {
2027     // TODO Auto-generated method stub
2028
2029   }
2030
2031   protected void showGroupConservation_actionPerformed(ActionEvent e)
2032   {
2033     // TODO Auto-generated method stub
2034
2035   }
2036
2037   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2038   {
2039     // TODO Auto-generated method stub
2040
2041   }
2042
2043   protected void showSeqFeaturesHeight_actionPerformed(
2044           ActionEvent actionEvent)
2045   {
2046     // TODO Auto-generated method stub
2047
2048   }
2049
2050   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2051   {
2052     // TODO Auto-generated method stub
2053
2054   }
2055
2056   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2057   {
2058     // TODO Auto-generated method stub
2059
2060   }
2061
2062   protected void followHighlight_actionPerformed()
2063   {
2064     // TODO Auto-generated method stub
2065
2066   }
2067
2068   protected void showNpFeats_actionPerformed(ActionEvent e)
2069   {
2070     // TODO Auto-generated method stub
2071
2072   }
2073
2074   protected void showDbRefs_actionPerformed(ActionEvent e)
2075   {
2076     // TODO Auto-generated method stub
2077
2078   }
2079
2080   protected void centreColumnLabels_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void showProducts_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void buildSortByAnnotationScoresMenu()
2089   {
2090   }
2091
2092   protected void extractScores_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   protected void outputText_actionPerformed(ActionEvent e)
2097   {
2098   }
2099
2100   public void addFromFile_actionPerformed(ActionEvent e)
2101   {
2102
2103   }
2104
2105   public void addFromText_actionPerformed(ActionEvent e)
2106   {
2107
2108   }
2109
2110   public void addFromURL_actionPerformed(ActionEvent e)
2111   {
2112
2113   }
2114
2115   public void exportFeatures_actionPerformed(ActionEvent e)
2116   {
2117
2118   }
2119
2120   public void exportAnnotations_actionPerformed(ActionEvent e)
2121   {
2122
2123   }
2124
2125   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2126   {
2127   }
2128
2129   protected void closeMenuItem_actionPerformed(boolean b)
2130   {
2131   }
2132
2133   protected void redoMenuItem_actionPerformed(ActionEvent e)
2134   {
2135   }
2136
2137   protected void undoMenuItem_actionPerformed(ActionEvent e)
2138   {
2139   }
2140
2141   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2142   {
2143   }
2144
2145   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2146   {
2147   }
2148
2149   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2150   {
2151   }
2152
2153   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2154   {
2155   }
2156
2157   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2158   {
2159   }
2160
2161   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2162   {
2163   }
2164
2165   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2166   {
2167   }
2168
2169   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2170   {
2171   }
2172
2173   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2174   {
2175   }
2176
2177   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2178   {
2179   }
2180
2181   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2182   {
2183   }
2184
2185   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2186   {
2187   }
2188
2189   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2190   {
2191   }
2192
2193   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2210   {
2211   }
2212
2213   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2214   {
2215   }
2216
2217   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2218   {
2219   }
2220
2221   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2222   {
2223   }
2224
2225   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2226   {
2227   }
2228
2229   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2230   {
2231   }
2232
2233   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2234   {
2235   }
2236
2237   protected void clustalColour_actionPerformed(ActionEvent e)
2238   {
2239   }
2240
2241   protected void zappoColour_actionPerformed(ActionEvent e)
2242   {
2243   }
2244
2245   protected void taylorColour_actionPerformed(ActionEvent e)
2246   {
2247   }
2248
2249   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2250   {
2251   }
2252
2253   protected void helixColour_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void strandColour_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void turnColour_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void buriedColour_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void userDefinedColour_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void PIDColour_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289
2290   /*
2291    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2292    */
2293
2294   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2295   {
2296   }
2297
2298   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2299   {
2300   }
2301
2302   protected void printMenuItem_actionPerformed(ActionEvent e)
2303   {
2304   }
2305
2306   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2307   {
2308   }
2309
2310   protected void findMenuItem_actionPerformed(ActionEvent e)
2311   {
2312   }
2313
2314   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2315   {
2316   }
2317
2318   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2319   {
2320   }
2321
2322   protected void nucleotideColour_actionPerformed(ActionEvent e)
2323   {
2324   }
2325
2326   protected void deleteGroups_actionPerformed(ActionEvent e)
2327   {
2328   }
2329
2330   protected void copy_actionPerformed(ActionEvent e)
2331   {
2332   }
2333
2334   protected void cut_actionPerformed(ActionEvent e)
2335   {
2336   }
2337
2338   protected void delete_actionPerformed(ActionEvent e)
2339   {
2340   }
2341
2342   protected void pasteNew_actionPerformed(ActionEvent e)
2343   {
2344   }
2345
2346   protected void pasteThis_actionPerformed(ActionEvent e)
2347   {
2348   }
2349
2350   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2351   {
2352   }
2353
2354   public void createPNG(java.io.File f)
2355   {
2356   }
2357
2358   protected void font_actionPerformed(ActionEvent e)
2359   {
2360   }
2361
2362   protected void seqLimit_actionPerformed(ActionEvent e)
2363   {
2364   }
2365
2366   public void seqDBRef_actionPerformed(ActionEvent e)
2367   {
2368
2369   }
2370
2371   public void createEPS(java.io.File f)
2372   {
2373   }
2374
2375   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2376   {
2377
2378   }
2379
2380   /**
2381    * Template method to handle the 'load T-Coffee scores' menu event.
2382    * <p>
2383    * Subclasses override this method to provide a custom action.
2384    *
2385    * @param event The raised event
2386    */
2387   protected void loadScores_actionPerformed(ActionEvent event) {
2388
2389   }
2390
2391
2392   /**
2393    * Template method to handle the 'Color T-Coffee scores' menu event.
2394    * <p>
2395    * Subclasses override this method to provide a custom action.
2396    *
2397    * @param event The raised event
2398    */
2399   protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
2400
2401   }
2402
2403
2404   protected void jpred_actionPerformed(ActionEvent e)
2405   {
2406   }
2407
2408   protected void scaleAbove_actionPerformed(ActionEvent e)
2409   {
2410   }
2411
2412   protected void scaleLeft_actionPerformed(ActionEvent e)
2413   {
2414   }
2415
2416   protected void scaleRight_actionPerformed(ActionEvent e)
2417   {
2418   }
2419
2420   protected void modifyPID_actionPerformed(ActionEvent e)
2421   {
2422   }
2423
2424   protected void modifyConservation_actionPerformed(ActionEvent e)
2425   {
2426   }
2427
2428   protected void saveAs_actionPerformed(ActionEvent e)
2429   {
2430   }
2431
2432   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2433   {
2434   }
2435
2436   public void vamsasStore_actionPerformed(ActionEvent e)
2437   {
2438
2439   }
2440
2441   public void vamsasLoad_actionPerformed(ActionEvent e)
2442   {
2443
2444   }
2445
2446   public void showTranslation_actionPerformed(ActionEvent e)
2447   {
2448
2449   }
2450
2451   public void featureSettings_actionPerformed(ActionEvent e)
2452   {
2453
2454   }
2455
2456   public void fetchSequence_actionPerformed(ActionEvent e)
2457   {
2458
2459   }
2460
2461   public void smoothFont_actionPerformed(ActionEvent e)
2462   {
2463
2464   }
2465
2466   public void annotationColour_actionPerformed(ActionEvent e)
2467   {
2468
2469   }
2470
2471   public void rnahelicesColour_actionPerformed(ActionEvent e)
2472   {
2473
2474   }
2475
2476   public void associatedData_actionPerformed(ActionEvent e)
2477   {
2478
2479   }
2480
2481   public void autoCalculate_actionPerformed(ActionEvent e)
2482   {
2483
2484   }
2485
2486   public void sortByTreeOption_actionPerformed(ActionEvent e)
2487   {
2488
2489   }
2490
2491   public void showAllSeqs_actionPerformed(ActionEvent e)
2492   {
2493
2494   }
2495
2496   public void showAllColumns_actionPerformed(ActionEvent e)
2497   {
2498
2499   }
2500
2501   public void hideSelSequences_actionPerformed(ActionEvent e)
2502   {
2503
2504   }
2505
2506   public void hideSelColumns_actionPerformed(ActionEvent e)
2507   {
2508
2509   }
2510
2511   public void hiddenMarkers_actionPerformed(ActionEvent e)
2512   {
2513
2514   }
2515
2516   public void findPdbId_actionPerformed(ActionEvent e)
2517   {
2518
2519   }
2520
2521   public void enterPdbId_actionPerformed(ActionEvent e)
2522   {
2523
2524   }
2525
2526   public void pdbFile_actionPerformed(ActionEvent e)
2527   {
2528
2529   }
2530
2531   public void invertColSel_actionPerformed(ActionEvent e)
2532   {
2533
2534   }
2535
2536   public void tabSelectionChanged(int sel)
2537   {
2538
2539   }
2540
2541   public void tabbedPane_mousePressed(MouseEvent e)
2542   {
2543
2544   }
2545
2546   public void tabbedPane_focusGained(FocusEvent e)
2547   {
2548     requestFocus();
2549   }
2550
2551   public void save_actionPerformed(ActionEvent e)
2552   {
2553
2554   }
2555
2556   public void reload_actionPerformed(ActionEvent e)
2557   {
2558
2559   }
2560
2561   public void newView_actionPerformed(ActionEvent e)
2562   {
2563
2564   }
2565
2566   public void textColour_actionPerformed(ActionEvent e)
2567   {
2568
2569   }
2570
2571   public void idRightAlign_actionPerformed(ActionEvent e)
2572   {
2573
2574   }
2575
2576   public void expandViews_actionPerformed(ActionEvent e)
2577   {
2578
2579   }
2580
2581   public void gatherViews_actionPerformed(ActionEvent e)
2582   {
2583
2584   }
2585
2586   public void buildTreeMenu()
2587   {
2588
2589   }
2590
2591   public void pageSetup_actionPerformed(ActionEvent e)
2592   {
2593
2594   }
2595
2596   public void alignmentProperties()
2597   {
2598
2599   }
2600 }