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