src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.event.*;
  25
  26 import jalview.schemes.*;
  27
  28 public class GAlignFrame extends JInternalFrame
  29 {
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  31
  32   protected JMenu fileMenu = new JMenu();
  33
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35
  36   protected JMenu editMenu = new JMenu();
  37
  38   protected JMenu viewMenu = new JMenu();
  39
  40   protected JMenu colourMenu = new JMenu();
  41
  42   protected JMenu calculateMenu = new JMenu();
  43
  44   protected JMenu webService = new JMenu();
  45
  46   protected JMenuItem webServiceNoServices;
  47
  48   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  49
  50   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  51
  52   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  53
  54   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  55
  56   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  57
  58   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  59
  60   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  61
  62   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  63
  64   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  65
  66   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  67
  68   protected JMenuItem sortIDMenuItem = new JMenuItem();
  69
  70   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  71
  72   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  73
  74   protected JMenu sortByAnnotScore = new JMenu();
  75
  76   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  77
  78   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  79
  80   protected JMenuItem PCAMenuItem = new JMenuItem();
  81
  82   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  83
  84   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  85
  86   BorderLayout borderLayout1 = new BorderLayout();
  87
  88   public JLabel statusBar = new JLabel();
  89
  90   protected JMenuItem saveAs = new JMenuItem();
  91
  92   protected JMenu outputTextboxMenu = new JMenu();
  93
  94   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  95
  96   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  97
  98   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  99
 100   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 115
 116   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 117
 118   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 119
 120   // protected JRadioButtonMenuItem covariationColour = new
 121   // JRadioButtonMenuItem();
 122
 123   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 124
 125   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 126
 127   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 128
 129   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 130
 131   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 132
 133   JMenuItem htmlMenuItem = new JMenuItem();
 134
 135   JMenuItem overviewMenuItem = new JMenuItem();
 136
 137   protected JMenuItem undoMenuItem = new JMenuItem();
 138
 139   protected JMenuItem redoMenuItem = new JMenuItem();
 140
 141   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 142
 143   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 144
 145   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 146
 147   JMenuItem printMenuItem = new JMenuItem();
 148
 149   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 150
 151   JMenuItem findMenuItem = new JMenuItem();
 152
 153   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 154
 155   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 156
 157   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 158
 159   JMenuItem deleteGroups = new JMenuItem();
 160
 161   JMenuItem delete = new JMenuItem();
 162
 163   JMenuItem copy = new JMenuItem();
 164
 165   JMenuItem cut = new JMenuItem();
 166
 167   JMenu pasteMenu = new JMenu();
 168
 169   JMenuItem pasteNew = new JMenuItem();
 170
 171   JMenuItem pasteThis = new JMenuItem();
 172
 173   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 174
 175   JMenuItem createPNG = new JMenuItem();
 176
 177   protected JMenuItem font = new JMenuItem();
 178
 179   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 180
 181   JMenuItem epsFile = new JMenuItem();
 182
 183   JMenuItem LoadtreeMenuItem = new JMenuItem();
 184
 185   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 186
 187   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 188
 189   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 190
 191   protected JMenuItem modifyPID = new JMenuItem();
 192
 193   protected JMenuItem modifyConservation = new JMenuItem();
 194
 195   protected JMenu sortByTreeMenu = new JMenu();
 196
 197   protected JMenu sort = new JMenu();
 198
 199   protected JMenu calculateTree = new JMenu();
 200
 201   JMenu jMenu2 = new JMenu();
 202
 203   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 204
 205   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 206
 207   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 208
 209   protected ButtonGroup colours = new ButtonGroup();
 210
 211   JMenuItem vamsasStore = new JMenuItem();
 212
 213   protected JMenuItem showTranslation = new JMenuItem();
 214
 215   protected JMenuItem extractScores = new JMenuItem();
 216
 217   protected JMenu showProducts = new JMenu();
 218
 219   public JMenuItem featureSettings = new JMenuItem();
 220
 221   JMenuItem fetchSequence = new JMenuItem();
 222
 223   JMenuItem annotationColour = new JMenuItem();
 224
 225   JMenuItem rnahelicesColour = new JMenuItem();
 226
 227   JMenuItem associatedData = new JMenuItem();
 228
 229   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 230
 231   JMenu addSequenceMenu = new JMenu();
 232
 233   JMenuItem addFromFile = new JMenuItem();
 234
 235   JMenuItem addFromText = new JMenuItem();
 236
 237   JMenuItem addFromURL = new JMenuItem();
 238
 239   JMenuItem exportAnnotations = new JMenuItem();
 240
 241   JMenuItem exportFeatures = new JMenuItem();
 242
 243   protected JPanel statusPanel = new JPanel();
 244
 245   GridLayout gridLayout1 = new GridLayout();
 246
 247   JMenu jMenu3 = new JMenu();
 248
 249   JMenuItem showAllSeqs = new JMenuItem();
 250
 251   JMenuItem showAllColumns = new JMenuItem();
 252
 253   JMenu hideMenu = new JMenu();
 254
 255   JMenuItem hideSelSequences = new JMenuItem();
 256
 257   JMenuItem hideSelColumns = new JMenuItem();
 258
 259   JMenuItem hideAllButSelection = new JMenuItem();
 260
 261   JMenuItem hideAllSelection = new JMenuItem();
 262
 263   JMenuItem showAllhidden = new JMenuItem();
 264
 265   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 266
 267   JMenuItem invertColSel = new JMenuItem();
 268
 269   protected JTabbedPane tabbedPane = new JTabbedPane();
 270
 271   JMenuItem save = new JMenuItem();
 272
 273   protected JMenuItem reload = new JMenuItem();
 274
 275   JMenuItem newView = new JMenuItem();
 276
 277   JMenuItem textColour = new JMenuItem();
 278
 279   JMenu formatMenu = new JMenu();
 280
 281   JMenu selectMenu = new JMenu();
 282
 283   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 284
 285   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 286
 287   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 288
 289   protected JMenuItem gatherViews = new JMenuItem();
 290
 291   protected JMenuItem expandViews = new JMenuItem();
 292
 293   JMenuItem pageSetup = new JMenuItem();
 294
 295   JMenuItem alignmentProperties = new JMenuItem();
 296
 297   JMenu tooltipSettingsMenu = new JMenu();
 298
 299   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 300
 301   private JMenuItem justifyRightMenuItem = new JMenuItem();
 302
 303   JMenu autoAnnMenu = new JMenu();
 304
 305   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 306
 307   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 308
 309   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 310
 311   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 312
 313   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 314
 315   private JMenuItem grpsFromSelection = new JMenuItem();
 316
 317   public GAlignFrame()
 318   {
 319     try
 320     {
 321       jbInit();
 322       setJMenuBar(alignFrameMenuBar);
 323
 324       // dynamically fill save as menu with available formats
 325       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 326       {
 327         JMenuItem item = new JMenuItem(
 328                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 329
 330         item.addActionListener(new java.awt.event.ActionListener()
 331         {
 332           public void actionPerformed(ActionEvent e)
 333           {
 334             outputText_actionPerformed(e);
 335           }
 336         });
 337
 338         outputTextboxMenu.add(item);
 339       }
 340     } catch (Exception e)
 341     {
 342     }
 343
 344     if (!new jalview.util.Platform().isAMac())
 345     {
 346       closeMenuItem.setMnemonic('C');
 347       outputTextboxMenu.setMnemonic('T');
 348       undoMenuItem.setMnemonic('Z');
 349       redoMenuItem.setMnemonic('0');
 350       copy.setMnemonic('C');
 351       cut.setMnemonic('U');
 352       pasteMenu.setMnemonic('P');
 353       reload.setMnemonic('R');
 354     }
 355
 356     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 357     {
 358       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 359               .getUserColourSchemes().keys();
 360
 361       while (userColours.hasMoreElements())
 362       {
 363         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 364                 userColours.nextElement().toString());
 365         radioItem.setName("USER_DEFINED");
 366         radioItem.addMouseListener(new MouseAdapter()
 367         {
 368           public void mousePressed(MouseEvent evt)
 369           {
 370             if (evt.isControlDown()
 371                     || SwingUtilities.isRightMouseButton(evt))
 372             {
 373               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 374
 375               int option = JOptionPane.showInternalConfirmDialog(
 376                       jalview.gui.Desktop.desktop,
 377                       "Remove from default list?",
 378                       "Remove user defined colour",
 379                       JOptionPane.YES_NO_OPTION);
 380               if (option == JOptionPane.YES_OPTION)
 381               {
 382                 jalview.gui.UserDefinedColours
 383                         .removeColourFromDefaults(radioItem.getText());
 384                 colourMenu.remove(radioItem);
 385               }
 386               else
 387               {
 388                 radioItem.addActionListener(new ActionListener()
 389                 {
 390                   public void actionPerformed(ActionEvent evt)
 391                   {
 392                     userDefinedColour_actionPerformed(evt);
 393                   }
 394                 });
 395               }
 396             }
 397           }
 398         });
 399         radioItem.addActionListener(new ActionListener()
 400         {
 401           public void actionPerformed(ActionEvent evt)
 402           {
 403             userDefinedColour_actionPerformed(evt);
 404           }
 405         });
 406         colourMenu.insert(radioItem, 15);
 407         colours.add(radioItem);
 408       }
 409     }
 410     colours.add(noColourmenuItem);
 411     colours.add(clustalColour);
 412     colours.add(zappoColour);
 413     colours.add(taylorColour);
 414     colours.add(hydrophobicityColour);
 415     colours.add(helixColour);
 416     colours.add(strandColour);
 417     colours.add(turnColour);
 418     colours.add(buriedColour);
 419     colours.add(userDefinedColour);
 420     colours.add(PIDColour);
 421     colours.add(BLOSUM62Colour);
 422     colours.add(nucleotideColour);
 423     colours.add(purinePyrimidineColour);
 424     // colours.add(covariationColour);
 425
 426     setColourSelected(jalview.bin.Cache
 427             .getDefault("DEFAULT_COLOUR", "None"));
 428
 429   }
 430
 431   public void setColourSelected(String defaultColour)
 432   {
 433
 434     if (defaultColour != null)
 435     {
 436       int index = ColourSchemeProperty
 437               .getColourIndexFromName(defaultColour);
 438
 439       switch (index)
 440       {
 441       case ColourSchemeProperty.CLUSTAL:
 442         clustalColour.setSelected(true);
 443
 444         break;
 445
 446       case ColourSchemeProperty.BLOSUM:
 447         BLOSUM62Colour.setSelected(true);
 448
 449         break;
 450
 451       case ColourSchemeProperty.PID:
 452         PIDColour.setSelected(true);
 453
 454         break;
 455
 456       case ColourSchemeProperty.ZAPPO:
 457         zappoColour.setSelected(true);
 458
 459         break;
 460
 461       case ColourSchemeProperty.TAYLOR:
 462         taylorColour.setSelected(true);
 463         break;
 464
 465       case ColourSchemeProperty.HYDROPHOBIC:
 466         hydrophobicityColour.setSelected(true);
 467
 468         break;
 469
 470       case ColourSchemeProperty.HELIX:
 471         helixColour.setSelected(true);
 472
 473         break;
 474
 475       case ColourSchemeProperty.STRAND:
 476         strandColour.setSelected(true);
 477
 478         break;
 479
 480       case ColourSchemeProperty.TURN:
 481         turnColour.setSelected(true);
 482
 483         break;
 484
 485       case ColourSchemeProperty.BURIED:
 486         buriedColour.setSelected(true);
 487
 488         break;
 489
 490       case ColourSchemeProperty.NUCLEOTIDE:
 491         nucleotideColour.setSelected(true);
 492
 493         break;
 494
 495       case ColourSchemeProperty.PURINEPYRIMIDINE:
 496         purinePyrimidineColour.setSelected(true);
 497
 498         break;
 499       /*
 500        * case ColourSchemeProperty.COVARIATION:
 501        * covariationColour.setSelected(true);
 502        *
 503        * break;
 504        */
 505       case ColourSchemeProperty.USER_DEFINED:
 506         userDefinedColour.setSelected(true);
 507
 508         break;
 509       case ColourSchemeProperty.NONE:
 510       default:
 511         noColourmenuItem.setSelected(true);
 512         break;
 513
 514       }
 515     }
 516
 517   }
 518
 519   private void jbInit() throws Exception
 520   {
 521     fileMenu.setText("File");
 522     saveAs.setText("Save As...");
 523     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 524             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 525                     .getMenuShortcutKeyMask()
 526                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 527     saveAs.addActionListener(new ActionListener()
 528     {
 529       public void actionPerformed(ActionEvent e)
 530       {
 531         saveAs_actionPerformed(e);
 532       }
 533     });
 534     closeMenuItem.setText("Close");
 535     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 536             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 537                     .getMenuShortcutKeyMask(), false));
 538     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 539     {
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         closeMenuItem_actionPerformed(false);
 543       }
 544     });
 545     editMenu.setText("Edit");
 546     viewMenu.setText("View");
 547     colourMenu.setText("Colour");
 548     calculateMenu.setText("Calculate");
 549     webService.setText("Web Service");
 550     selectAllSequenceMenuItem.setText("Select All");
 551     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 552             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 553                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 554     selectAllSequenceMenuItem
 555             .addActionListener(new java.awt.event.ActionListener()
 556             {
 557               public void actionPerformed(ActionEvent e)
 558               {
 559                 selectAllSequenceMenuItem_actionPerformed(e);
 560               }
 561             });
 562     deselectAllSequenceMenuItem.setText("Deselect All");
 563     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 564             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 565     deselectAllSequenceMenuItem
 566             .addActionListener(new java.awt.event.ActionListener()
 567             {
 568               public void actionPerformed(ActionEvent e)
 569               {
 570                 deselectAllSequenceMenuItem_actionPerformed(e);
 571               }
 572             });
 573     invertSequenceMenuItem.setText("Invert Sequence Selection");
 574     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 575             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 576                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 577     invertSequenceMenuItem
 578             .addActionListener(new java.awt.event.ActionListener()
 579             {
 580               public void actionPerformed(ActionEvent e)
 581               {
 582                 invertSequenceMenuItem_actionPerformed(e);
 583               }
 584             });
 585     grpsFromSelection.setText("Make Groups for selection");
 586     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 587     {
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         makeGrpsFromSelection_actionPerformed(e);
 591       }
 592     });
 593
 594     remove2LeftMenuItem.setText("Remove Left");
 595     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 596             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 597                     .getMenuShortcutKeyMask(), false));
 598     remove2LeftMenuItem
 599             .addActionListener(new java.awt.event.ActionListener()
 600             {
 601               public void actionPerformed(ActionEvent e)
 602               {
 603                 remove2LeftMenuItem_actionPerformed(e);
 604               }
 605             });
 606     remove2RightMenuItem.setText("Remove Right");
 607     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 608             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 609                     .getMenuShortcutKeyMask(), false));
 610     remove2RightMenuItem
 611             .addActionListener(new java.awt.event.ActionListener()
 612             {
 613               public void actionPerformed(ActionEvent e)
 614               {
 615                 remove2RightMenuItem_actionPerformed(e);
 616               }
 617             });
 618     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 619     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 620             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 621                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 622     removeGappedColumnMenuItem
 623             .addActionListener(new java.awt.event.ActionListener()
 624             {
 625               public void actionPerformed(ActionEvent e)
 626               {
 627                 removeGappedColumnMenuItem_actionPerformed(e);
 628               }
 629             });
 630     removeAllGapsMenuItem.setText("Remove All Gaps");
 631     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 632             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 633                     .getDefaultToolkit().getMenuShortcutKeyMask()
 634                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 635     removeAllGapsMenuItem
 636             .addActionListener(new java.awt.event.ActionListener()
 637             {
 638               public void actionPerformed(ActionEvent e)
 639               {
 640                 removeAllGapsMenuItem_actionPerformed(e);
 641               }
 642             });
 643     justifyLeftMenuItem.setText("Left Justify Alignment");
 644     justifyLeftMenuItem
 645             .addActionListener(new java.awt.event.ActionListener()
 646             {
 647               public void actionPerformed(ActionEvent e)
 648               {
 649                 justifyLeftMenuItem_actionPerformed(e);
 650               }
 651             });
 652     justifyRightMenuItem.setText("Right Justify Alignment");
 653     justifyRightMenuItem
 654             .addActionListener(new java.awt.event.ActionListener()
 655             {
 656               public void actionPerformed(ActionEvent e)
 657               {
 658                 justifyRightMenuItem_actionPerformed(e);
 659               }
 660             });
 661     viewBoxesMenuItem.setText("Boxes");
 662     viewBoxesMenuItem.setState(true);
 663     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 664     {
 665       public void actionPerformed(ActionEvent e)
 666       {
 667         viewBoxesMenuItem_actionPerformed(e);
 668       }
 669     });
 670     viewTextMenuItem.setText("Text");
 671     viewTextMenuItem.setState(true);
 672     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 673     {
 674       public void actionPerformed(ActionEvent e)
 675       {
 676         viewTextMenuItem_actionPerformed(e);
 677       }
 678     });
 679     showNonconservedMenuItem.setText("Show nonconserved");
 680     showNonconservedMenuItem.setState(false);
 681     showNonconservedMenuItem
 682             .addActionListener(new java.awt.event.ActionListener()
 683             {
 684               public void actionPerformed(ActionEvent e)
 685               {
 686                 showUnconservedMenuItem_actionPerformed(e);
 687               }
 688             });
 689     sortPairwiseMenuItem.setText("by Pairwise Identity");
 690     sortPairwiseMenuItem
 691             .addActionListener(new java.awt.event.ActionListener()
 692             {
 693               public void actionPerformed(ActionEvent e)
 694               {
 695                 sortPairwiseMenuItem_actionPerformed(e);
 696               }
 697             });
 698     sortIDMenuItem.setText("by ID");
 699     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 700     {
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         sortIDMenuItem_actionPerformed(e);
 704       }
 705     });
 706     sortLengthMenuItem.setText("By Length");
 707     sortLengthMenuItem
 708             .addActionListener(new java.awt.event.ActionListener()
 709             {
 710               public void actionPerformed(ActionEvent e)
 711               {
 712                 sortLengthMenuItem_actionPerformed(e);
 713               }
 714             });
 715     sortGroupMenuItem.setText("by Group");
 716     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 717     {
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         sortGroupMenuItem_actionPerformed(e);
 721       }
 722     });
 723     removeRedundancyMenuItem.setText("Remove Redundancy...");
 724     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 725             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 726                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 727     removeRedundancyMenuItem
 728             .addActionListener(new java.awt.event.ActionListener()
 729             {
 730               public void actionPerformed(ActionEvent e)
 731               {
 732                 removeRedundancyMenuItem_actionPerformed(e);
 733               }
 734             });
 735     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 736     pairwiseAlignmentMenuItem
 737             .addActionListener(new java.awt.event.ActionListener()
 738             {
 739               public void actionPerformed(ActionEvent e)
 740               {
 741                 pairwiseAlignmentMenuItem_actionPerformed(e);
 742               }
 743             });
 744     PCAMenuItem.setText("Principal Component Analysis");
 745     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 746     {
 747       public void actionPerformed(ActionEvent e)
 748       {
 749         PCAMenuItem_actionPerformed(e);
 750       }
 751     });
 752     averageDistanceTreeMenuItem
 753             .setText("Average Distance Using % Identity");
 754     averageDistanceTreeMenuItem
 755             .addActionListener(new java.awt.event.ActionListener()
 756             {
 757               public void actionPerformed(ActionEvent e)
 758               {
 759                 averageDistanceTreeMenuItem_actionPerformed(e);
 760               }
 761             });
 762     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 763     neighbourTreeMenuItem
 764             .addActionListener(new java.awt.event.ActionListener()
 765             {
 766               public void actionPerformed(ActionEvent e)
 767               {
 768                 neighbourTreeMenuItem_actionPerformed(e);
 769               }
 770             });
 771     this.getContentPane().setLayout(borderLayout1);
 772     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 773     statusBar.setBackground(Color.white);
 774     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 775     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 776     statusBar.setText("Status bar");
 777     outputTextboxMenu.setText("Output to Textbox");
 778     clustalColour.setText("Clustalx");
 779
 780     clustalColour.addActionListener(new java.awt.event.ActionListener()
 781     {
 782       public void actionPerformed(ActionEvent e)
 783       {
 784         clustalColour_actionPerformed(e);
 785       }
 786     });
 787     zappoColour.setText("Zappo");
 788     zappoColour.addActionListener(new java.awt.event.ActionListener()
 789     {
 790       public void actionPerformed(ActionEvent e)
 791       {
 792         zappoColour_actionPerformed(e);
 793       }
 794     });
 795     taylorColour.setText("Taylor");
 796     taylorColour.addActionListener(new java.awt.event.ActionListener()
 797     {
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         taylorColour_actionPerformed(e);
 801       }
 802     });
 803     hydrophobicityColour.setText("Hydrophobicity");
 804     hydrophobicityColour
 805             .addActionListener(new java.awt.event.ActionListener()
 806             {
 807               public void actionPerformed(ActionEvent e)
 808               {
 809                 hydrophobicityColour_actionPerformed(e);
 810               }
 811             });
 812     helixColour.setText("Helix Propensity");
 813     helixColour.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       public void actionPerformed(ActionEvent e)
 816       {
 817         helixColour_actionPerformed(e);
 818       }
 819     });
 820     strandColour.setText("Strand Propensity");
 821     strandColour.addActionListener(new java.awt.event.ActionListener()
 822     {
 823       public void actionPerformed(ActionEvent e)
 824       {
 825         strandColour_actionPerformed(e);
 826       }
 827     });
 828     turnColour.setText("Turn Propensity");
 829     turnColour.addActionListener(new java.awt.event.ActionListener()
 830     {
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         turnColour_actionPerformed(e);
 834       }
 835     });
 836     buriedColour.setText("Buried Index");
 837     buriedColour.addActionListener(new java.awt.event.ActionListener()
 838     {
 839       public void actionPerformed(ActionEvent e)
 840       {
 841         buriedColour_actionPerformed(e);
 842       }
 843     });
 844     userDefinedColour.setText("User Defined...");
 845     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 846     {
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         userDefinedColour_actionPerformed(e);
 850       }
 851     });
 852     PIDColour.setText("Percentage Identity");
 853     PIDColour.addActionListener(new java.awt.event.ActionListener()
 854     {
 855       public void actionPerformed(ActionEvent e)
 856       {
 857         PIDColour_actionPerformed(e);
 858       }
 859     });
 860     BLOSUM62Colour.setText("BLOSUM62 Score");
 861     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 862     {
 863       public void actionPerformed(ActionEvent e)
 864       {
 865         BLOSUM62Colour_actionPerformed(e);
 866       }
 867     });
 868     nucleotideColour.setText("Nucleotide");
 869     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 870     {
 871       public void actionPerformed(ActionEvent e)
 872       {
 873         nucleotideColour_actionPerformed(e);
 874       }
 875     });
 876
 877     purinePyrimidineColour.setText("Purine/Pyrimidine");
 878     purinePyrimidineColour
 879             .addActionListener(new java.awt.event.ActionListener()
 880             {
 881               public void actionPerformed(ActionEvent e)
 882               {
 883                 purinePyrimidineColour_actionPerformed(e);
 884               }
 885             });
 886     /*
 887      * covariationColour.setText("Covariation");
 888      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
 889      * public void actionPerformed(ActionEvent e) {
 890      * covariationColour_actionPerformed(e); } });
 891      */
 892
 893     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 894     avDistanceTreeBlosumMenuItem
 895             .addActionListener(new java.awt.event.ActionListener()
 896             {
 897               public void actionPerformed(ActionEvent e)
 898               {
 899                 avTreeBlosumMenuItem_actionPerformed(e);
 900               }
 901             });
 902     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 903     njTreeBlosumMenuItem
 904             .addActionListener(new java.awt.event.ActionListener()
 905             {
 906               public void actionPerformed(ActionEvent e)
 907               {
 908                 njTreeBlosumMenuItem_actionPerformed(e);
 909               }
 910             });
 911     annotationPanelMenuItem.setActionCommand("");
 912     annotationPanelMenuItem.setText("Show Annotations");
 913     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 914             "SHOW_ANNOTATIONS", true));
 915     annotationPanelMenuItem
 916             .addActionListener(new java.awt.event.ActionListener()
 917             {
 918               public void actionPerformed(ActionEvent e)
 919               {
 920                 annotationPanelMenuItem_actionPerformed(e);
 921               }
 922             });
 923     colourTextMenuItem.setText("Colour Text");
 924     colourTextMenuItem
 925             .addActionListener(new java.awt.event.ActionListener()
 926             {
 927               public void actionPerformed(ActionEvent e)
 928               {
 929                 colourTextMenuItem_actionPerformed(e);
 930               }
 931             });
 932     htmlMenuItem.setText("HTML");
 933     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         htmlMenuItem_actionPerformed(e);
 938       }
 939     });
 940     overviewMenuItem.setText("Overview Window");
 941     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 942     {
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         overviewMenuItem_actionPerformed(e);
 946       }
 947     });
 948     undoMenuItem.setEnabled(false);
 949     undoMenuItem.setText("Undo");
 950     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 951             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 952                     .getMenuShortcutKeyMask(), false));
 953     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 954     {
 955       public void actionPerformed(ActionEvent e)
 956       {
 957         undoMenuItem_actionPerformed(e);
 958       }
 959     });
 960     redoMenuItem.setEnabled(false);
 961     redoMenuItem.setText("Redo");
 962     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 963             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 964                     .getMenuShortcutKeyMask(), false));
 965     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 966     {
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         redoMenuItem_actionPerformed(e);
 970       }
 971     });
 972     conservationMenuItem.setText("By Conservation");
 973     conservationMenuItem
 974             .addActionListener(new java.awt.event.ActionListener()
 975             {
 976               public void actionPerformed(ActionEvent e)
 977               {
 978                 conservationMenuItem_actionPerformed(e);
 979               }
 980             });
 981     noColourmenuItem.setText("None");
 982     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         noColourmenuItem_actionPerformed(e);
 987       }
 988     });
 989     wrapMenuItem.setText("Wrap");
 990     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 991     {
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         wrapMenuItem_actionPerformed(e);
 995       }
 996     });
 997     printMenuItem.setText("Print ...");
 998     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 999             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1000                     .getMenuShortcutKeyMask(), false));
1001     printMenuItem.addActionListener(new java.awt.event.ActionListener()
1002     {
1003       public void actionPerformed(ActionEvent e)
1004       {
1005         printMenuItem_actionPerformed(e);
1006       }
1007     });
1008     renderGapsMenuItem.setText("Show Gaps");
1009     renderGapsMenuItem.setState(true);
1010     renderGapsMenuItem
1011             .addActionListener(new java.awt.event.ActionListener()
1012             {
1013               public void actionPerformed(ActionEvent e)
1014               {
1015                 renderGapsMenuItem_actionPerformed(e);
1016               }
1017             });
1018     findMenuItem.setText("Find...");
1019     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1020             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1021                     .getMenuShortcutKeyMask(), false));
1022     findMenuItem.addActionListener(new java.awt.event.ActionListener()
1023     {
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         findMenuItem_actionPerformed(e);
1027       }
1028     });
1029     abovePIDThreshold.setText("Above Identity Threshold");
1030     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         abovePIDThreshold_actionPerformed(e);
1035       }
1036     });
1037     showSeqFeatures.setText("Show Sequence Features");
1038     showSeqFeatures.addActionListener(new ActionListener()
1039     {
1040       public void actionPerformed(ActionEvent actionEvent)
1041       {
1042         showSeqFeatures_actionPerformed(actionEvent);
1043       }
1044     });
1045     /*
1046      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1047      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1048      * void actionPerformed(ActionEvent actionEvent) {
1049      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1050      */
1051     showDbRefsMenuitem.setText("Show Database Refs");
1052     showDbRefsMenuitem.addActionListener(new ActionListener()
1053     {
1054
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         showDbRefs_actionPerformed(e);
1058       }
1059
1060     });
1061     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1062     showNpFeatsMenuitem.addActionListener(new ActionListener()
1063     {
1064
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         showNpFeats_actionPerformed(e);
1068       }
1069
1070     });
1071     showGroupConservation.setText("Group Conservation");
1072     showGroupConservation.addActionListener(new ActionListener()
1073     {
1074
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         showGroupConservation_actionPerformed(e);
1078       }
1079
1080     });
1081
1082     showGroupConsensus.setText("Group Consensus");
1083     showGroupConsensus.addActionListener(new ActionListener()
1084     {
1085
1086       public void actionPerformed(ActionEvent e)
1087       {
1088         showGroupConsensus_actionPerformed(e);
1089       }
1090
1091     });
1092     showConsensusHistogram.setText("Show Consensus Histogram");
1093     showConsensusHistogram.addActionListener(new ActionListener()
1094     {
1095
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         showConsensusHistogram_actionPerformed(e);
1099       }
1100
1101     });
1102     showSequenceLogo.setText("Show Consensus Logo");
1103     showSequenceLogo.addActionListener(new ActionListener()
1104     {
1105
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         showSequenceLogo_actionPerformed(e);
1109       }
1110
1111     });
1112     applyAutoAnnotationSettings.setText("Apply to all groups");
1113     applyAutoAnnotationSettings.setState(false);
1114     applyAutoAnnotationSettings.setVisible(true);
1115     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1116     {
1117
1118       public void actionPerformed(ActionEvent e)
1119       {
1120         applyAutoAnnotationSettings_actionPerformed(e);
1121       }
1122
1123     });
1124
1125     nucleotideColour.setText("Nucleotide");
1126     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1127     {
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         nucleotideColour_actionPerformed(e);
1131       }
1132     });
1133     deleteGroups.setText("Undefine groups");
1134     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1135             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1136                     .getMenuShortcutKeyMask(), false));
1137     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1138     {
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         deleteGroups_actionPerformed(e);
1142       }
1143     });
1144     copy.setText("Copy");
1145     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1146             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1147                     .getMenuShortcutKeyMask(), false));
1148
1149     copy.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       public void actionPerformed(ActionEvent e)
1152       {
1153         copy_actionPerformed(e);
1154       }
1155     });
1156     cut.setText("Cut");
1157     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1158             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1159                     .getMenuShortcutKeyMask(), false));
1160     cut.addActionListener(new java.awt.event.ActionListener()
1161     {
1162       public void actionPerformed(ActionEvent e)
1163       {
1164         cut_actionPerformed(e);
1165       }
1166     });
1167     delete.setText("Delete");
1168     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1169             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1170     delete.addActionListener(new java.awt.event.ActionListener()
1171     {
1172       public void actionPerformed(ActionEvent e)
1173       {
1174         delete_actionPerformed(e);
1175       }
1176     });
1177     pasteMenu.setText("Paste");
1178     pasteNew.setText("To New Alignment");
1179     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1180             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1181                     .getMenuShortcutKeyMask()
1182                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1183     pasteNew.addActionListener(new java.awt.event.ActionListener()
1184     {
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         pasteNew_actionPerformed(e);
1188       }
1189     });
1190     pasteThis.setText("Add To This Alignment");
1191     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1192             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1193                     .getMenuShortcutKeyMask(), false));
1194     pasteThis.addActionListener(new java.awt.event.ActionListener()
1195     {
1196       public void actionPerformed(ActionEvent e)
1197       {
1198         pasteThis_actionPerformed(e);
1199       }
1200     });
1201     applyToAllGroups.setText("Apply Colour To All Groups");
1202     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1203     {
1204       public void actionPerformed(ActionEvent e)
1205       {
1206         applyToAllGroups_actionPerformed(e);
1207       }
1208     });
1209     createPNG.addActionListener(new java.awt.event.ActionListener()
1210     {
1211       public void actionPerformed(ActionEvent e)
1212       {
1213         createPNG(null);
1214       }
1215     });
1216     createPNG.setActionCommand("Save As PNG Image");
1217     createPNG.setText("PNG");
1218     font.setText("Font...");
1219     font.addActionListener(new java.awt.event.ActionListener()
1220     {
1221       public void actionPerformed(ActionEvent e)
1222       {
1223         font_actionPerformed(e);
1224       }
1225     });
1226
1227     seqLimits.setText("Show Sequence Limits");
1228     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1229     seqLimits.addActionListener(new java.awt.event.ActionListener()
1230     {
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         seqLimit_actionPerformed(e);
1234       }
1235     });
1236     epsFile.setText("EPS");
1237     epsFile.addActionListener(new java.awt.event.ActionListener()
1238     {
1239       public void actionPerformed(ActionEvent e)
1240       {
1241         createEPS(null);
1242       }
1243     });
1244     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1245     LoadtreeMenuItem.setText("Load Associated Tree");
1246     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1247     {
1248       public void actionPerformed(ActionEvent e)
1249       {
1250         LoadtreeMenuItem_actionPerformed(e);
1251       }
1252     });
1253     scaleAbove.setVisible(false);
1254     scaleAbove.setText("Scale Above");
1255     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1256     {
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         scaleAbove_actionPerformed(e);
1260       }
1261     });
1262     scaleLeft.setVisible(false);
1263     scaleLeft.setSelected(true);
1264     scaleLeft.setText("Scale Left");
1265     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1266     {
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         scaleLeft_actionPerformed(e);
1270       }
1271     });
1272     scaleRight.setVisible(false);
1273     scaleRight.setSelected(true);
1274     scaleRight.setText("Scale Right");
1275     scaleRight.addActionListener(new java.awt.event.ActionListener()
1276     {
1277       public void actionPerformed(ActionEvent e)
1278       {
1279         scaleRight_actionPerformed(e);
1280       }
1281     });
1282     centreColumnLabelsMenuItem.setVisible(true);
1283     centreColumnLabelsMenuItem.setState(false);
1284     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1285     centreColumnLabelsMenuItem
1286             .addActionListener(new java.awt.event.ActionListener()
1287             {
1288               public void actionPerformed(ActionEvent e)
1289               {
1290                 centreColumnLabels_actionPerformed(e);
1291               }
1292             });
1293     followHighlightMenuItem.setVisible(true);
1294     followHighlightMenuItem.setState(true);
1295     followHighlightMenuItem.setText("Automatic Scrolling");
1296     followHighlightMenuItem.addActionListener(new ActionListener()
1297     {
1298
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         followHighlight_actionPerformed();
1302       }
1303
1304     });
1305
1306     modifyPID.setText("Modify Identity Threshold...");
1307     modifyPID.addActionListener(new java.awt.event.ActionListener()
1308     {
1309       public void actionPerformed(ActionEvent e)
1310       {
1311         modifyPID_actionPerformed(e);
1312       }
1313     });
1314     modifyConservation.setText("Modify Conservation Threshold...");
1315     modifyConservation
1316             .addActionListener(new java.awt.event.ActionListener()
1317             {
1318               public void actionPerformed(ActionEvent e)
1319               {
1320                 modifyConservation_actionPerformed(e);
1321               }
1322             });
1323     sortByTreeMenu.setText("By Tree Order");
1324     sort.setText("Sort");
1325     sort.addMenuListener(new MenuListener()
1326     {
1327       public void menuSelected(MenuEvent e)
1328       {
1329         buildTreeMenu();
1330       }
1331
1332       public void menuDeselected(MenuEvent e)
1333       {
1334       }
1335
1336       public void menuCanceled(MenuEvent e)
1337       {
1338       }
1339     });
1340     sortByAnnotScore.setText("by Score");
1341     sort.add(sortByAnnotScore);
1342     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1343     {
1344
1345       public void menuCanceled(MenuEvent e)
1346       {
1347       }
1348
1349       public void menuDeselected(MenuEvent e)
1350       {
1351       }
1352
1353       public void menuSelected(MenuEvent e)
1354       {
1355         buildSortByAnnotationScoresMenu();
1356       }
1357     });
1358     sortByAnnotScore.setVisible(false);
1359
1360     calculateTree.setText("Calculate Tree");
1361
1362     jMenu2.setText("Export Image");
1363     padGapsMenuitem.setText("Pad Gaps");
1364     padGapsMenuitem.setState(jalview.bin.Cache
1365             .getDefault("PAD_GAPS", false));
1366     padGapsMenuitem.addActionListener(new ActionListener()
1367     {
1368       public void actionPerformed(ActionEvent e)
1369       {
1370         padGapsMenuitem_actionPerformed(e);
1371       }
1372     });
1373     vamsasStore.setVisible(false);
1374     vamsasStore.setText("VAMSAS store");
1375     vamsasStore.addActionListener(new ActionListener()
1376     {
1377       public void actionPerformed(ActionEvent e)
1378       {
1379         vamsasStore_actionPerformed(e);
1380       }
1381     });
1382     showTranslation.setText("Translate cDNA");
1383     showTranslation.addActionListener(new ActionListener()
1384     {
1385       public void actionPerformed(ActionEvent e)
1386       {
1387         showTranslation_actionPerformed(e);
1388       }
1389     });
1390     extractScores.setText("Extract Scores...");
1391     extractScores.addActionListener(new ActionListener()
1392     {
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         extractScores_actionPerformed(e);
1396       }
1397     });
1398     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1399     // score extraction
1400     showProducts.setText("Get Cross References");
1401     /*
1402      * showProducts.addActionListener(new ActionListener() {
1403      *
1404      * public void actionPerformed(ActionEvent e) {
1405      * showProducts_actionPerformed(e); } });
1406      */
1407     featureSettings.setText("Feature Settings...");
1408     featureSettings.addActionListener(new ActionListener()
1409     {
1410       public void actionPerformed(ActionEvent e)
1411       {
1412         featureSettings_actionPerformed(e);
1413       }
1414     });
1415     fetchSequence.setText("Fetch Sequence(s)...");
1416     fetchSequence.addActionListener(new ActionListener()
1417     {
1418       public void actionPerformed(ActionEvent e)
1419       {
1420         fetchSequence_actionPerformed(e);
1421       }
1422     });
1423
1424     annotationColour.setText("By Annotation...");
1425     annotationColour.addActionListener(new ActionListener()
1426     {
1427       public void actionPerformed(ActionEvent e)
1428       {
1429         annotationColour_actionPerformed(e);
1430       }
1431     });
1432
1433     rnahelicesColour.setText("By RNA helices");
1434     rnahelicesColour.addActionListener(new ActionListener()
1435     {
1436       public void actionPerformed(ActionEvent e)
1437       {
1438         rnahelicesColour_actionPerformed(e);
1439       }
1440     });
1441
1442     associatedData.setText("Load Features / Annotations");
1443     associatedData.addActionListener(new ActionListener()
1444     {
1445       public void actionPerformed(ActionEvent e)
1446       {
1447         associatedData_actionPerformed(e);
1448       }
1449     });
1450     autoCalculate.setText("Autocalculate Consensus");
1451     autoCalculate.setState(jalview.bin.Cache.getDefault(
1452             "AUTO_CALC_CONSENSUS", true));
1453     autoCalculate.addActionListener(new ActionListener()
1454     {
1455       public void actionPerformed(ActionEvent e)
1456       {
1457         autoCalculate_actionPerformed(e);
1458       }
1459     });
1460     addSequenceMenu.setText("Add Sequences");
1461     addFromFile.setText("From File");
1462     addFromFile.addActionListener(new ActionListener()
1463     {
1464       public void actionPerformed(ActionEvent e)
1465       {
1466         addFromFile_actionPerformed(e);
1467       }
1468     });
1469     addFromText.setText("From Textbox");
1470     addFromText.addActionListener(new ActionListener()
1471     {
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         addFromText_actionPerformed(e);
1475       }
1476     });
1477     addFromURL.setText("From URL");
1478     addFromURL.addActionListener(new ActionListener()
1479     {
1480       public void actionPerformed(ActionEvent e)
1481       {
1482         addFromURL_actionPerformed(e);
1483       }
1484     });
1485     exportFeatures.setText("Export Features...");
1486     exportFeatures.addActionListener(new ActionListener()
1487     {
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         exportFeatures_actionPerformed(e);
1491       }
1492     });
1493     exportAnnotations.setText("Export Annotations...");
1494     exportAnnotations.addActionListener(new ActionListener()
1495     {
1496       public void actionPerformed(ActionEvent e)
1497       {
1498         exportAnnotations_actionPerformed(e);
1499       }
1500     });
1501     statusPanel.setLayout(gridLayout1);
1502     jMenu3.setText("Show");
1503     showAllSeqs.setText("All Sequences");
1504     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1505     showAllSeqs.addActionListener(new ActionListener()
1506     {
1507       public void actionPerformed(ActionEvent e)
1508       {
1509         showAllSeqs_actionPerformed(e);
1510       }
1511     });
1512     showAllColumns.setText("All Columns");
1513     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1514     showAllColumns.addActionListener(new ActionListener()
1515     {
1516       public void actionPerformed(ActionEvent e)
1517       {
1518         showAllColumns_actionPerformed(e);
1519       }
1520     });
1521     hideMenu.setText("Hide");
1522     hideSelSequences.setText("Selected Sequences");
1523     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1524     hideSelSequences.addActionListener(new ActionListener()
1525     {
1526       public void actionPerformed(ActionEvent e)
1527       {
1528         hideSelSequences_actionPerformed(e);
1529       }
1530     });
1531     hideSelColumns.setText("Selected Columns");
1532     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1533     hideSelColumns.addActionListener(new ActionListener()
1534     {
1535       public void actionPerformed(ActionEvent e)
1536       {
1537         hideSelColumns_actionPerformed(e);
1538       }
1539     });
1540     hideAllSelection.setText("Selected Region");
1541     hideAllSelection.addActionListener(new ActionListener()
1542     {
1543       public void actionPerformed(ActionEvent e)
1544       {
1545         hideAllSelection_actionPerformed(e);
1546       }
1547     });
1548     // TODO: should be hidden if no selection exists.
1549     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1550     hideAllButSelection.addActionListener(new ActionListener()
1551     {
1552       public void actionPerformed(ActionEvent e)
1553       {
1554         hideAllButSelection_actionPerformed(e);
1555       }
1556     });
1557     showAllhidden.setText("All Sequences and Columns");
1558     showAllhidden
1559             .setToolTipText("H toggles visibility of hidden or selected regions.");
1560     showAllhidden.addActionListener(new ActionListener()
1561     {
1562       public void actionPerformed(ActionEvent e)
1563       {
1564         showAllhidden_actionPerformed(e);
1565       }
1566     });
1567
1568     hiddenMarkers.setText("Show Hidden Markers");
1569     hiddenMarkers.addActionListener(new ActionListener()
1570     {
1571       public void actionPerformed(ActionEvent e)
1572       {
1573         hiddenMarkers_actionPerformed(e);
1574       }
1575     });
1576     invertColSel.setText("Invert Column Selection");
1577     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1578             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1579                     .getMenuShortcutKeyMask()
1580                     | java.awt.event.KeyEvent.ALT_MASK, false));
1581     invertColSel.addActionListener(new ActionListener()
1582     {
1583       public void actionPerformed(ActionEvent e)
1584       {
1585         invertColSel_actionPerformed(e);
1586       }
1587     });
1588     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1589     {
1590       public void stateChanged(ChangeEvent evt)
1591       {
1592         JTabbedPane pane = (JTabbedPane) evt.getSource();
1593         int sel = pane.getSelectedIndex();
1594         tabSelectionChanged(sel);
1595       }
1596     });
1597     tabbedPane.addMouseListener(new MouseAdapter()
1598     {
1599       public void mousePressed(MouseEvent e)
1600       {
1601         tabbedPane_mousePressed(e);
1602       }
1603     });
1604     tabbedPane.addFocusListener(new FocusAdapter()
1605     {
1606       public void focusGained(FocusEvent e)
1607       {
1608         tabbedPane_focusGained(e);
1609       }
1610     });
1611     save.setText("Save");
1612     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1613             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1614                     .getMenuShortcutKeyMask(), false));
1615     save.addActionListener(new ActionListener()
1616     {
1617       public void actionPerformed(ActionEvent e)
1618       {
1619         save_actionPerformed(e);
1620       }
1621     });
1622     reload.setEnabled(false);
1623     reload.setText("Reload");
1624     reload.addActionListener(new ActionListener()
1625     {
1626       public void actionPerformed(ActionEvent e)
1627       {
1628         reload_actionPerformed(e);
1629       }
1630     });
1631     newView.setText("New View");
1632     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1633             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1634                     .getMenuShortcutKeyMask(), false));
1635     newView.addActionListener(new ActionListener()
1636     {
1637       public void actionPerformed(ActionEvent e)
1638       {
1639         newView_actionPerformed(e);
1640       }
1641     });
1642     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1643             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1644     textColour.setText("Colour Text ...");
1645     textColour.addActionListener(new ActionListener()
1646     {
1647       public void actionPerformed(ActionEvent e)
1648       {
1649         textColour_actionPerformed(e);
1650       }
1651     });
1652     formatMenu.setText("Format");
1653     selectMenu.setText("Select");
1654     idRightAlign.setText("Right Align Sequence Id");
1655     idRightAlign.addActionListener(new ActionListener()
1656     {
1657       public void actionPerformed(ActionEvent e)
1658       {
1659         idRightAlign_actionPerformed(e);
1660       }
1661     });
1662     gatherViews.setEnabled(false);
1663     gatherViews.setText("Gather Views");
1664     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1665             java.awt.event.KeyEvent.VK_G, 0, false));
1666     gatherViews.addActionListener(new ActionListener()
1667     {
1668       public void actionPerformed(ActionEvent e)
1669       {
1670         gatherViews_actionPerformed(e);
1671       }
1672     });
1673     expandViews.setEnabled(false);
1674     expandViews.setText("Expand Views");
1675     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1676             java.awt.event.KeyEvent.VK_X, 0, false));
1677     expandViews.addActionListener(new ActionListener()
1678     {
1679       public void actionPerformed(ActionEvent e)
1680       {
1681         expandViews_actionPerformed(e);
1682       }
1683     });
1684     pageSetup.setText("Page Setup ...");
1685     pageSetup.addActionListener(new ActionListener()
1686     {
1687       public void actionPerformed(ActionEvent e)
1688       {
1689         pageSetup_actionPerformed(e);
1690       }
1691     });
1692     alignmentProperties.setText("Alignment Properties...");
1693     alignmentProperties.addActionListener(new ActionListener()
1694     {
1695       public void actionPerformed(ActionEvent actionEvent)
1696       {
1697         alignmentProperties();
1698       }
1699     });
1700     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1701     autoAnnMenu.setText("Autocalculated Annotation");
1702     alignFrameMenuBar.add(fileMenu);
1703     alignFrameMenuBar.add(editMenu);
1704     alignFrameMenuBar.add(selectMenu);
1705     alignFrameMenuBar.add(viewMenu);
1706     alignFrameMenuBar.add(formatMenu);
1707     alignFrameMenuBar.add(colourMenu);
1708     alignFrameMenuBar.add(calculateMenu);
1709     alignFrameMenuBar.add(webService);
1710     fileMenu.add(fetchSequence);
1711     fileMenu.add(addSequenceMenu);
1712     fileMenu.add(reload);
1713     fileMenu.addSeparator();
1714     fileMenu.add(vamsasStore);
1715     fileMenu.add(save);
1716     fileMenu.add(saveAs);
1717     fileMenu.add(outputTextboxMenu);
1718     fileMenu.add(pageSetup);
1719     fileMenu.add(printMenuItem);
1720     fileMenu.addSeparator();
1721     fileMenu.add(jMenu2);
1722     fileMenu.add(exportFeatures);
1723     fileMenu.add(exportAnnotations);
1724     fileMenu.add(LoadtreeMenuItem);
1725     fileMenu.add(associatedData);
1726     fileMenu.addSeparator();
1727     fileMenu.add(closeMenuItem);
1728     editMenu.add(undoMenuItem);
1729     editMenu.add(redoMenuItem);
1730     editMenu.add(cut);
1731     editMenu.add(copy);
1732     editMenu.add(pasteMenu);
1733     editMenu.add(delete);
1734     editMenu.addSeparator();
1735     editMenu.add(remove2LeftMenuItem);
1736     editMenu.add(remove2RightMenuItem);
1737     editMenu.add(removeGappedColumnMenuItem);
1738     editMenu.add(removeAllGapsMenuItem);
1739     editMenu.add(removeRedundancyMenuItem);
1740     editMenu.addSeparator();
1741     // dont add these yet in the CVS build - they cannot be undone!
1742     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1743     // editMenu.add(justifyLeftMenuItem);
1744     // editMenu.add(justifyRightMenuItem);
1745     // editMenu.addSeparator();
1746     editMenu.add(padGapsMenuitem);
1747     viewMenu.add(newView);
1748     viewMenu.add(expandViews);
1749     viewMenu.add(gatherViews);
1750     viewMenu.addSeparator();
1751     viewMenu.add(jMenu3);
1752     viewMenu.add(hideMenu);
1753     viewMenu.addSeparator();
1754     viewMenu.add(followHighlightMenuItem);
1755     viewMenu.add(annotationPanelMenuItem);
1756     autoAnnMenu.add(applyAutoAnnotationSettings);
1757     autoAnnMenu.add(showConsensusHistogram);
1758     autoAnnMenu.add(showSequenceLogo);
1759     autoAnnMenu.addSeparator();
1760     autoAnnMenu.add(showGroupConservation);
1761     autoAnnMenu.add(showGroupConsensus);
1762     viewMenu.add(autoAnnMenu);
1763     viewMenu.addSeparator();
1764     viewMenu.add(showSeqFeatures);
1765     // viewMenu.add(showSeqFeaturesHeight);
1766
1767     viewMenu.add(featureSettings);
1768     tooltipSettingsMenu.add(showDbRefsMenuitem);
1769     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1770     viewMenu.add(tooltipSettingsMenu);
1771     viewMenu.addSeparator();
1772     viewMenu.add(alignmentProperties);
1773     viewMenu.addSeparator();
1774     viewMenu.add(overviewMenuItem);
1775     colourMenu.add(applyToAllGroups);
1776     colourMenu.add(textColour);
1777     colourMenu.addSeparator();
1778     colourMenu.add(noColourmenuItem);
1779     colourMenu.add(clustalColour);
1780     colourMenu.add(BLOSUM62Colour);
1781     colourMenu.add(PIDColour);
1782     colourMenu.add(zappoColour);
1783     colourMenu.add(taylorColour);
1784     colourMenu.add(hydrophobicityColour);
1785     colourMenu.add(helixColour);
1786     colourMenu.add(strandColour);
1787     colourMenu.add(turnColour);
1788     colourMenu.add(buriedColour);
1789     colourMenu.add(nucleotideColour);
1790     colourMenu.add(purinePyrimidineColour);
1791     // colourMenu.add(covariationColour);
1792     colourMenu.add(userDefinedColour);
1793     colourMenu.addSeparator();
1794     colourMenu.add(conservationMenuItem);
1795     colourMenu.add(modifyConservation);
1796     colourMenu.add(abovePIDThreshold);
1797     colourMenu.add(modifyPID);
1798     colourMenu.add(annotationColour);
1799     colourMenu.add(rnahelicesColour);
1800     calculateMenu.add(sort);
1801     calculateMenu.add(calculateTree);
1802     calculateMenu.addSeparator();
1803     calculateMenu.add(pairwiseAlignmentMenuItem);
1804     calculateMenu.add(PCAMenuItem);
1805     calculateMenu.addSeparator();
1806     calculateMenu.add(showTranslation);
1807     calculateMenu.add(showProducts);
1808     calculateMenu.add(autoCalculate);
1809     calculateMenu.addSeparator();
1810     calculateMenu.add(extractScores);
1811     webServiceNoServices = new JMenuItem("<No Services>");
1812     webService.add(webServiceNoServices);
1813     pasteMenu.add(pasteNew);
1814     pasteMenu.add(pasteThis);
1815     sort.add(sortIDMenuItem);
1816     sort.add(sortLengthMenuItem);
1817     sort.add(sortGroupMenuItem);
1818     sort.add(sortPairwiseMenuItem);
1819     sort.add(sortByTreeMenu);
1820     calculateTree.add(averageDistanceTreeMenuItem);
1821     calculateTree.add(neighbourTreeMenuItem);
1822     calculateTree.add(avDistanceTreeBlosumMenuItem);
1823     calculateTree.add(njTreeBlosumMenuItem);
1824     jMenu2.add(htmlMenuItem);
1825     jMenu2.add(epsFile);
1826     jMenu2.add(createPNG);
1827     addSequenceMenu.add(addFromFile);
1828     addSequenceMenu.add(addFromText);
1829     addSequenceMenu.add(addFromURL);
1830     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1831     statusPanel.add(statusBar, null);
1832     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1833     jMenu3.add(showAllColumns);
1834     jMenu3.add(showAllSeqs);
1835     jMenu3.add(showAllhidden);
1836     hideMenu.add(hideSelColumns);
1837     hideMenu.add(hideSelSequences);
1838     hideMenu.add(hideAllSelection);
1839     hideMenu.add(hideAllButSelection);
1840
1841     formatMenu.add(font);
1842     formatMenu.addSeparator();
1843     formatMenu.add(wrapMenuItem);
1844     formatMenu.add(scaleAbove);
1845     formatMenu.add(scaleLeft);
1846     formatMenu.add(scaleRight);
1847     formatMenu.add(seqLimits);
1848     formatMenu.add(idRightAlign);
1849     formatMenu.add(hiddenMarkers);
1850     formatMenu.add(viewBoxesMenuItem);
1851     formatMenu.add(viewTextMenuItem);
1852     formatMenu.add(colourTextMenuItem);
1853     formatMenu.add(renderGapsMenuItem);
1854     formatMenu.add(centreColumnLabelsMenuItem);
1855     formatMenu.add(showNonconservedMenuItem);
1856     selectMenu.add(findMenuItem);
1857     selectMenu.addSeparator();
1858     selectMenu.add(selectAllSequenceMenuItem);
1859     selectMenu.add(deselectAllSequenceMenuItem);
1860     selectMenu.add(invertSequenceMenuItem);
1861     selectMenu.add(invertColSel);
1862     selectMenu.add(deleteGroups);
1863     selectMenu.add(grpsFromSelection);
1864   }
1865
1866   protected void showAllhidden_actionPerformed(ActionEvent e)
1867   {
1868     // TODO Auto-generated method stub
1869
1870   }
1871
1872   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1873   {
1874     // TODO Auto-generated method stub
1875
1876   }
1877
1878   protected void hideAllSelection_actionPerformed(ActionEvent e)
1879   {
1880     // TODO Auto-generated method stub
1881
1882   }
1883
1884   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1885   {
1886     // TODO Auto-generated method stub
1887
1888   }
1889
1890   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1891   {
1892     // TODO Auto-generated method stub
1893
1894   }
1895
1896   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1897   {
1898     // TODO Auto-generated method stub
1899
1900   }
1901
1902   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1903   {
1904     // TODO Auto-generated method stub
1905
1906   }
1907
1908   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1909   {
1910     // TODO Auto-generated method stub
1911
1912   }
1913
1914   protected void showGroupConservation_actionPerformed(ActionEvent e)
1915   {
1916     // TODO Auto-generated method stub
1917
1918   }
1919
1920   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1921   {
1922     // TODO Auto-generated method stub
1923
1924   }
1925
1926   protected void showSeqFeaturesHeight_actionPerformed(
1927           ActionEvent actionEvent)
1928   {
1929     // TODO Auto-generated method stub
1930
1931   }
1932
1933   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1934   {
1935     // TODO Auto-generated method stub
1936
1937   }
1938
1939   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1940   {
1941     // TODO Auto-generated method stub
1942
1943   }
1944
1945   protected void followHighlight_actionPerformed()
1946   {
1947     // TODO Auto-generated method stub
1948
1949   }
1950
1951   protected void showNpFeats_actionPerformed(ActionEvent e)
1952   {
1953     // TODO Auto-generated method stub
1954
1955   }
1956
1957   protected void showDbRefs_actionPerformed(ActionEvent e)
1958   {
1959     // TODO Auto-generated method stub
1960
1961   }
1962
1963   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1964   {
1965   }
1966
1967   protected void showProducts_actionPerformed(ActionEvent e)
1968   {
1969   }
1970
1971   protected void buildSortByAnnotationScoresMenu()
1972   {
1973   }
1974
1975   protected void extractScores_actionPerformed(ActionEvent e)
1976   {
1977   }
1978
1979   protected void outputText_actionPerformed(ActionEvent e)
1980   {
1981   }
1982
1983   public void addFromFile_actionPerformed(ActionEvent e)
1984   {
1985
1986   }
1987
1988   public void addFromText_actionPerformed(ActionEvent e)
1989   {
1990
1991   }
1992
1993   public void addFromURL_actionPerformed(ActionEvent e)
1994   {
1995
1996   }
1997
1998   public void exportFeatures_actionPerformed(ActionEvent e)
1999   {
2000
2001   }
2002
2003   public void exportAnnotations_actionPerformed(ActionEvent e)
2004   {
2005
2006   }
2007
2008   protected void htmlMenuItem_actionPerformed(ActionEvent e)
2009   {
2010   }
2011
2012   protected void closeMenuItem_actionPerformed(boolean b)
2013   {
2014   }
2015
2016   protected void redoMenuItem_actionPerformed(ActionEvent e)
2017   {
2018   }
2019
2020   protected void undoMenuItem_actionPerformed(ActionEvent e)
2021   {
2022   }
2023
2024   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2025   {
2026   }
2027
2028   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2029   {
2030   }
2031
2032   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2033   {
2034   }
2035
2036   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2037   {
2038   }
2039
2040   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2041   {
2042   }
2043
2044   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2045   {
2046   }
2047
2048   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2049   {
2050   }
2051
2052   protected void wrapMenuItem_actionPerformed(ActionEvent e)
2053   {
2054   }
2055
2056   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2057   {
2058   }
2059
2060   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2061   {
2062   }
2063
2064   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2069   {
2070   }
2071
2072   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2097   {
2098   }
2099
2100   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2109   {
2110   }
2111
2112   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2113   {
2114   }
2115
2116   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2117   {
2118   }
2119
2120   protected void clustalColour_actionPerformed(ActionEvent e)
2121   {
2122   }
2123
2124   protected void zappoColour_actionPerformed(ActionEvent e)
2125   {
2126   }
2127
2128   protected void taylorColour_actionPerformed(ActionEvent e)
2129   {
2130   }
2131
2132   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2133   {
2134   }
2135
2136   protected void helixColour_actionPerformed(ActionEvent e)
2137   {
2138   }
2139
2140   protected void strandColour_actionPerformed(ActionEvent e)
2141   {
2142   }
2143
2144   protected void turnColour_actionPerformed(ActionEvent e)
2145   {
2146   }
2147
2148   protected void buriedColour_actionPerformed(ActionEvent e)
2149   {
2150   }
2151
2152   protected void userDefinedColour_actionPerformed(ActionEvent e)
2153   {
2154   }
2155
2156   protected void PIDColour_actionPerformed(ActionEvent e)
2157   {
2158   }
2159
2160   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2161   {
2162   }
2163
2164   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2165   {
2166   }
2167
2168   /*
2169    * protected void covariationColour_actionPerformed(ActionEvent e) { }
2170    */
2171
2172   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2173   {
2174   }
2175
2176   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2177   {
2178   }
2179
2180   protected void printMenuItem_actionPerformed(ActionEvent e)
2181   {
2182   }
2183
2184   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2185   {
2186   }
2187
2188   protected void findMenuItem_actionPerformed(ActionEvent e)
2189   {
2190   }
2191
2192   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2193   {
2194   }
2195
2196   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2197   {
2198   }
2199
2200   protected void nucleotideColour_actionPerformed(ActionEvent e)
2201   {
2202   }
2203
2204   protected void deleteGroups_actionPerformed(ActionEvent e)
2205   {
2206   }
2207
2208   protected void copy_actionPerformed(ActionEvent e)
2209   {
2210   }
2211
2212   protected void cut_actionPerformed(ActionEvent e)
2213   {
2214   }
2215
2216   protected void delete_actionPerformed(ActionEvent e)
2217   {
2218   }
2219
2220   protected void pasteNew_actionPerformed(ActionEvent e)
2221   {
2222   }
2223
2224   protected void pasteThis_actionPerformed(ActionEvent e)
2225   {
2226   }
2227
2228   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2229   {
2230   }
2231
2232   public void createPNG(java.io.File f)
2233   {
2234   }
2235
2236   protected void font_actionPerformed(ActionEvent e)
2237   {
2238   }
2239
2240   protected void seqLimit_actionPerformed(ActionEvent e)
2241   {
2242   }
2243
2244   public void seqDBRef_actionPerformed(ActionEvent e)
2245   {
2246
2247   }
2248
2249   public void createEPS(java.io.File f)
2250   {
2251   }
2252
2253   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2254   {
2255   }
2256
2257   protected void jpred_actionPerformed(ActionEvent e)
2258   {
2259   }
2260
2261   protected void scaleAbove_actionPerformed(ActionEvent e)
2262   {
2263   }
2264
2265   protected void scaleLeft_actionPerformed(ActionEvent e)
2266   {
2267   }
2268
2269   protected void scaleRight_actionPerformed(ActionEvent e)
2270   {
2271   }
2272
2273   protected void modifyPID_actionPerformed(ActionEvent e)
2274   {
2275   }
2276
2277   protected void modifyConservation_actionPerformed(ActionEvent e)
2278   {
2279   }
2280
2281   protected void saveAs_actionPerformed(ActionEvent e)
2282   {
2283   }
2284
2285   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2286   {
2287   }
2288
2289   public void vamsasStore_actionPerformed(ActionEvent e)
2290   {
2291
2292   }
2293
2294   public void vamsasLoad_actionPerformed(ActionEvent e)
2295   {
2296
2297   }
2298
2299   public void showTranslation_actionPerformed(ActionEvent e)
2300   {
2301
2302   }
2303
2304   public void featureSettings_actionPerformed(ActionEvent e)
2305   {
2306
2307   }
2308
2309   public void fetchSequence_actionPerformed(ActionEvent e)
2310   {
2311
2312   }
2313
2314   public void smoothFont_actionPerformed(ActionEvent e)
2315   {
2316
2317   }
2318
2319   public void annotationColour_actionPerformed(ActionEvent e)
2320   {
2321
2322   }
2323
2324   public void rnahelicesColour_actionPerformed(ActionEvent e)
2325   {
2326
2327   }
2328
2329   public void associatedData_actionPerformed(ActionEvent e)
2330   {
2331
2332   }
2333
2334   public void autoCalculate_actionPerformed(ActionEvent e)
2335   {
2336
2337   }
2338
2339   public void showAllSeqs_actionPerformed(ActionEvent e)
2340   {
2341
2342   }
2343
2344   public void showAllColumns_actionPerformed(ActionEvent e)
2345   {
2346
2347   }
2348
2349   public void hideSelSequences_actionPerformed(ActionEvent e)
2350   {
2351
2352   }
2353
2354   public void hideSelColumns_actionPerformed(ActionEvent e)
2355   {
2356
2357   }
2358
2359   public void hiddenMarkers_actionPerformed(ActionEvent e)
2360   {
2361
2362   }
2363
2364   public void findPdbId_actionPerformed(ActionEvent e)
2365   {
2366
2367   }
2368
2369   public void enterPdbId_actionPerformed(ActionEvent e)
2370   {
2371
2372   }
2373
2374   public void pdbFile_actionPerformed(ActionEvent e)
2375   {
2376
2377   }
2378
2379   public void invertColSel_actionPerformed(ActionEvent e)
2380   {
2381
2382   }
2383
2384   public void tabSelectionChanged(int sel)
2385   {
2386
2387   }
2388
2389   public void tabbedPane_mousePressed(MouseEvent e)
2390   {
2391
2392   }
2393
2394   public void tabbedPane_focusGained(FocusEvent e)
2395   {
2396     requestFocus();
2397   }
2398
2399   public void save_actionPerformed(ActionEvent e)
2400   {
2401
2402   }
2403
2404   public void reload_actionPerformed(ActionEvent e)
2405   {
2406
2407   }
2408
2409   public void newView_actionPerformed(ActionEvent e)
2410   {
2411
2412   }
2413
2414   public void textColour_actionPerformed(ActionEvent e)
2415   {
2416
2417   }
2418
2419   public void idRightAlign_actionPerformed(ActionEvent e)
2420   {
2421
2422   }
2423
2424   public void expandViews_actionPerformed(ActionEvent e)
2425   {
2426
2427   }
2428
2429   public void gatherViews_actionPerformed(ActionEvent e)
2430   {
2431
2432   }
2433
2434   public void buildTreeMenu()
2435   {
2436
2437   }
2438
2439   public void pageSetup_actionPerformed(ActionEvent e)
2440   {
2441
2442   }
2443
2444   public void alignmentProperties()
2445   {
2446
2447   }
2448 }