src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.schemes.*;
  28
  29 public class GAlignFrame extends JInternalFrame
  30 {
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  32
  33   protected JMenu fileMenu = new JMenu();
  34
  35   protected JMenuItem closeMenuItem = new JMenuItem();
  36
  37   protected JMenu editMenu = new JMenu();
  38
  39   protected JMenu viewMenu = new JMenu();
  40
  41   protected JMenu colourMenu = new JMenu();
  42
  43   protected JMenu calculateMenu = new JMenu();
  44
  45   protected JMenu webService = new JMenu();
  46
  47   protected JMenuItem webServiceNoServices;
  48
  49   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  50
  51   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  52
  53   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  54
  55   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  56
  57   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  58
  59   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  60
  61   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  62
  63   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  64
  65   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  66
  67   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  68
  69   protected JMenuItem sortIDMenuItem = new JMenuItem();
  70
  71   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  72
  73   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  74
  75   protected JMenu sortByAnnotScore = new JMenu();
  76
  77   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  78
  79   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  80
  81   protected JMenuItem PCAMenuItem = new JMenuItem();
  82
  83   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  84
  85   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  86
  87   BorderLayout borderLayout1 = new BorderLayout();
  88
  89   public JLabel statusBar = new JLabel();
  90
  91   protected JMenuItem saveAs = new JMenuItem();
  92
  93   protected JMenu outputTextboxMenu = new JMenu();
  94
  95   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  96
  97   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  98
  99   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 112
 113   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 114
 115   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 116
 117   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 118
 119   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 120
 121   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 122
 123   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 124
 125   public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
 126
 127   JMenuItem htmlMenuItem = new JMenuItem();
 128
 129   JMenuItem overviewMenuItem = new JMenuItem();
 130
 131   protected JMenuItem undoMenuItem = new JMenuItem();
 132
 133   protected JMenuItem redoMenuItem = new JMenuItem();
 134
 135   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 136
 137   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 138
 139   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 140
 141   JMenuItem printMenuItem = new JMenuItem();
 142
 143   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 144
 145   JMenuItem findMenuItem = new JMenuItem();
 146
 147   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 148
 149   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 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   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 200   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected ButtonGroup colours = new ButtonGroup();
 203
 204   JMenuItem vamsasStore = new JMenuItem();
 205
 206   protected JMenuItem showTranslation = new JMenuItem();
 207
 208   protected JMenuItem extractScores = new JMenuItem();
 209
 210   protected JMenu showProducts = new JMenu();
 211
 212   public JMenuItem featureSettings = new JMenuItem();
 213
 214   JMenuItem fetchSequence = new JMenuItem();
 215
 216   JMenuItem annotationColour = new JMenuItem();
 217
 218   JMenuItem associatedData = new JMenuItem();
 219
 220   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 221
 222   JMenu addSequenceMenu = new JMenu();
 223
 224   JMenuItem addFromFile = new JMenuItem();
 225
 226   JMenuItem addFromText = new JMenuItem();
 227
 228   JMenuItem addFromURL = new JMenuItem();
 229
 230   JMenuItem exportAnnotations = new JMenuItem();
 231
 232   JMenuItem exportFeatures = new JMenuItem();
 233
 234   protected JPanel statusPanel = new JPanel();
 235
 236   GridLayout gridLayout1 = new GridLayout();
 237
 238   JMenu jMenu3 = new JMenu();
 239
 240   JMenuItem showAllSeqs = new JMenuItem();
 241
 242   JMenuItem showAllColumns = new JMenuItem();
 243
 244   JMenu hideMenu = new JMenu();
 245
 246   JMenuItem hideSelSequences = new JMenuItem();
 247
 248   JMenuItem hideSelColumns = new JMenuItem();
 249
 250   JMenuItem hideAllButSelection = new JMenuItem();
 251
 252   JMenuItem hideAllSelection = new JMenuItem();
 253
 254   JMenuItem showAllhidden = new JMenuItem();
 255
 256   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 257
 258   JMenuItem invertColSel = new JMenuItem();
 259
 260   protected JTabbedPane tabbedPane = new JTabbedPane();
 261
 262   JMenuItem save = new JMenuItem();
 263
 264   protected JMenuItem reload = new JMenuItem();
 265
 266   JMenuItem newView = new JMenuItem();
 267
 268   JMenuItem textColour = new JMenuItem();
 269
 270   JMenu formatMenu = new JMenu();
 271
 272   JMenu selectMenu = new JMenu();
 273
 274   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 275
 276   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 277
 278   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 279
 280   protected JMenuItem gatherViews = new JMenuItem();
 281
 282   protected JMenuItem expandViews = new JMenuItem();
 283
 284   JMenuItem pageSetup = new JMenuItem();
 285
 286   JMenuItem alignmentProperties = new JMenuItem();
 287
 288   JMenu tooltipSettingsMenu = new JMenu();
 289
 290   private JMenuItem justifyLeftMenuItem=new JMenuItem();
 291
 292   private JMenuItem justifyRightMenuItem=new JMenuItem();
 293
 294   JMenu autoAnnMenu = new JMenu();
 295   protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
 296   protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
 297   protected JCheckBoxMenuItem showConsensusHistogram=new JCheckBoxMenuItem();
 298   protected JCheckBoxMenuItem showSequenceLogo=new JCheckBoxMenuItem();
 299   protected JCheckBoxMenuItem applyAutoAnnotationSettings=new JCheckBoxMenuItem();
 300
 301   private JMenuItem grpsFromSelection = new JMenuItem();
 302   public GAlignFrame()
 303   {
 304     try
 305     {
 306       jbInit();
 307       setJMenuBar(alignFrameMenuBar);
 308
 309       // dynamically fill save as menu with available formats
 310       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 311       {
 312         JMenuItem item = new JMenuItem(
 313                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 314
 315         item.addActionListener(new java.awt.event.ActionListener()
 316         {
 317           public void actionPerformed(ActionEvent e)
 318           {
 319             outputText_actionPerformed(e);
 320           }
 321         });
 322
 323         outputTextboxMenu.add(item);
 324       }
 325     } catch (Exception e)
 326     {
 327     }
 328
 329     if (!new jalview.util.Platform().isAMac())
 330     {
 331       closeMenuItem.setMnemonic('C');
 332       outputTextboxMenu.setMnemonic('T');
 333       undoMenuItem.setMnemonic('Z');
 334       redoMenuItem.setMnemonic('0');
 335       copy.setMnemonic('C');
 336       cut.setMnemonic('U');
 337       pasteMenu.setMnemonic('P');
 338       reload.setMnemonic('R');
 339     }
 340
 341     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 342     {
 343       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 344               .getUserColourSchemes().keys();
 345
 346       while (userColours.hasMoreElements())
 347       {
 348         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 349                 userColours.nextElement().toString());
 350         radioItem.setName("USER_DEFINED");
 351         radioItem.addMouseListener(new MouseAdapter()
 352         {
 353           public void mousePressed(MouseEvent evt)
 354           {
 355             if (evt.isControlDown()
 356                     || SwingUtilities.isRightMouseButton(evt))
 357             {
 358               radioItem
 359                       .removeActionListener(radioItem.getActionListeners()[0]);
 360
 361               int option = JOptionPane.showInternalConfirmDialog(
 362                       jalview.gui.Desktop.desktop,
 363                       "Remove from default list?",
 364                       "Remove user defined colour",
 365                       JOptionPane.YES_NO_OPTION);
 366               if (option == JOptionPane.YES_OPTION)
 367               {
 368                 jalview.gui.UserDefinedColours
 369                         .removeColourFromDefaults(radioItem.getText());
 370                 colourMenu.remove(radioItem);
 371               }
 372               else
 373               {
 374                 radioItem.addActionListener(new ActionListener()
 375                 {
 376                   public void actionPerformed(ActionEvent evt)
 377                   {
 378                     userDefinedColour_actionPerformed(evt);
 379                   }
 380                 });
 381               }
 382             }
 383           }
 384         });
 385         radioItem.addActionListener(new ActionListener()
 386         {
 387           public void actionPerformed(ActionEvent evt)
 388           {
 389             userDefinedColour_actionPerformed(evt);
 390           }
 391         });
 392         colourMenu.insert(radioItem, 15);
 393         colours.add(radioItem);
 394       }
 395     }
 396     colours.add(noColourmenuItem);
 397     colours.add(clustalColour);
 398     colours.add(zappoColour);
 399     colours.add(taylorColour);
 400     colours.add(hydrophobicityColour);
 401     colours.add(helixColour);
 402     colours.add(strandColour);
 403     colours.add(turnColour);
 404     colours.add(buriedColour);
 405     colours.add(userDefinedColour);
 406     colours.add(PIDColour);
 407     colours.add(BLOSUM62Colour);
 408     colours.add(nucleotideColour);
 409
 410     setColourSelected(jalview.bin.Cache
 411             .getDefault("DEFAULT_COLOUR", "None"));
 412
 413   }
 414
 415   public void setColourSelected(String defaultColour)
 416   {
 417
 418     if (defaultColour != null)
 419     {
 420       int index = ColourSchemeProperty
 421               .getColourIndexFromName(defaultColour);
 422
 423       switch (index)
 424       {
 425       case ColourSchemeProperty.NONE:
 426         noColourmenuItem.setSelected(true);
 427         break;
 428       case ColourSchemeProperty.CLUSTAL:
 429         clustalColour.setSelected(true);
 430
 431         break;
 432
 433       case ColourSchemeProperty.BLOSUM:
 434         BLOSUM62Colour.setSelected(true);
 435
 436         break;
 437
 438       case ColourSchemeProperty.PID:
 439         PIDColour.setSelected(true);
 440
 441         break;
 442
 443       case ColourSchemeProperty.ZAPPO:
 444         zappoColour.setSelected(true);
 445
 446         break;
 447
 448       case ColourSchemeProperty.TAYLOR:
 449         taylorColour.setSelected(true);
 450         break;
 451
 452       case ColourSchemeProperty.HYDROPHOBIC:
 453         hydrophobicityColour.setSelected(true);
 454
 455         break;
 456
 457       case ColourSchemeProperty.HELIX:
 458         helixColour.setSelected(true);
 459
 460         break;
 461
 462       case ColourSchemeProperty.STRAND:
 463         strandColour.setSelected(true);
 464
 465         break;
 466
 467       case ColourSchemeProperty.TURN:
 468         turnColour.setSelected(true);
 469
 470         break;
 471
 472       case ColourSchemeProperty.BURIED:
 473         buriedColour.setSelected(true);
 474
 475         break;
 476
 477       case ColourSchemeProperty.NUCLEOTIDE:
 478         nucleotideColour.setSelected(true);
 479
 480         break;
 481
 482       case ColourSchemeProperty.USER_DEFINED:
 483         userDefinedColour.setSelected(true);
 484
 485         break;
 486       }
 487     }
 488
 489   }
 490
 491   private void jbInit() throws Exception
 492   {
 493     fileMenu.setText("File");
 494     saveAs.setText("Save As...");
 495     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 496             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 497                     .getMenuShortcutKeyMask()
 498                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 499     saveAs.addActionListener(new ActionListener()
 500     {
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         saveAs_actionPerformed(e);
 504       }
 505     });
 506     closeMenuItem.setText("Close");
 507     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 508             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 509                     .getMenuShortcutKeyMask(), false));
 510     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 511     {
 512       public void actionPerformed(ActionEvent e)
 513       {
 514         closeMenuItem_actionPerformed(false);
 515       }
 516     });
 517     editMenu.setText("Edit");
 518     viewMenu.setText("View");
 519     colourMenu.setText("Colour");
 520     calculateMenu.setText("Calculate");
 521     webService.setText("Web Service");
 522     selectAllSequenceMenuItem.setText("Select All");
 523     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 524             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 525                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 526     selectAllSequenceMenuItem
 527             .addActionListener(new java.awt.event.ActionListener()
 528             {
 529               public void actionPerformed(ActionEvent e)
 530               {
 531                 selectAllSequenceMenuItem_actionPerformed(e);
 532               }
 533             });
 534     deselectAllSequenceMenuItem.setText("Deselect All");
 535     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 536             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 537     deselectAllSequenceMenuItem
 538             .addActionListener(new java.awt.event.ActionListener()
 539             {
 540               public void actionPerformed(ActionEvent e)
 541               {
 542                 deselectAllSequenceMenuItem_actionPerformed(e);
 543               }
 544             });
 545     invertSequenceMenuItem.setText("Invert Sequence Selection");
 546     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 547             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 548                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 549     invertSequenceMenuItem
 550             .addActionListener(new java.awt.event.ActionListener()
 551             {
 552               public void actionPerformed(ActionEvent e)
 553               {
 554                 invertSequenceMenuItem_actionPerformed(e);
 555               }
 556             });
 557     grpsFromSelection.setText("Make Groups for selection");
 558     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 559     {
 560       public void actionPerformed(ActionEvent e)
 561       {
 562         makeGrpsFromSelection_actionPerformed(e);
 563       }
 564     });
 565
 566     remove2LeftMenuItem.setText("Remove Left");
 567     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 568             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 569                     .getMenuShortcutKeyMask(), false));
 570     remove2LeftMenuItem
 571             .addActionListener(new java.awt.event.ActionListener()
 572             {
 573               public void actionPerformed(ActionEvent e)
 574               {
 575                 remove2LeftMenuItem_actionPerformed(e);
 576               }
 577             });
 578     remove2RightMenuItem.setText("Remove Right");
 579     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 580             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 581                     .getMenuShortcutKeyMask(), false));
 582     remove2RightMenuItem
 583             .addActionListener(new java.awt.event.ActionListener()
 584             {
 585               public void actionPerformed(ActionEvent e)
 586               {
 587                 remove2RightMenuItem_actionPerformed(e);
 588               }
 589             });
 590     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 591     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 592             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 593                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 594     removeGappedColumnMenuItem
 595             .addActionListener(new java.awt.event.ActionListener()
 596             {
 597               public void actionPerformed(ActionEvent e)
 598               {
 599                 removeGappedColumnMenuItem_actionPerformed(e);
 600               }
 601             });
 602     removeAllGapsMenuItem.setText("Remove All Gaps");
 603     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 604             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 605                     .getDefaultToolkit().getMenuShortcutKeyMask()
 606                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 607     removeAllGapsMenuItem
 608             .addActionListener(new java.awt.event.ActionListener()
 609             {
 610               public void actionPerformed(ActionEvent e)
 611               {
 612                 removeAllGapsMenuItem_actionPerformed(e);
 613               }
 614             });
 615     justifyLeftMenuItem.setText("Left Justify Alignment");
 616     justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 617     {
 618         public void actionPerformed(ActionEvent e)
 619         {
 620           justifyLeftMenuItem_actionPerformed(e);
 621         }
 622     });
 623     justifyRightMenuItem.setText("Right Justify Alignment");
 624     justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
 625     {
 626         public void actionPerformed(ActionEvent e)
 627         {
 628           justifyRightMenuItem_actionPerformed(e);
 629         }
 630     });
 631     viewBoxesMenuItem.setText("Boxes");
 632     viewBoxesMenuItem.setState(true);
 633     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 634     {
 635       public void actionPerformed(ActionEvent e)
 636       {
 637         viewBoxesMenuItem_actionPerformed(e);
 638       }
 639     });
 640     viewTextMenuItem.setText("Text");
 641     viewTextMenuItem.setState(true);
 642     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 643     {
 644       public void actionPerformed(ActionEvent e)
 645       {
 646         viewTextMenuItem_actionPerformed(e);
 647       }
 648     });
 649     showUnconservedMenuItem.setText("Show Unconserved");
 650     showUnconservedMenuItem.setState(false);
 651     showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
 652     {
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         showUnconservedMenuItem_actionPerformed(e);
 656       }
 657     });
 658     sortPairwiseMenuItem.setText("by Pairwise Identity");
 659     sortPairwiseMenuItem
 660             .addActionListener(new java.awt.event.ActionListener()
 661             {
 662               public void actionPerformed(ActionEvent e)
 663               {
 664                 sortPairwiseMenuItem_actionPerformed(e);
 665               }
 666             });
 667     sortIDMenuItem.setText("by ID");
 668     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         sortIDMenuItem_actionPerformed(e);
 673       }
 674     });
 675     sortLengthMenuItem.setText("By Length");
 676     sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
 677     {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         sortLengthMenuItem_actionPerformed(e);
 681       }
 682     });
 683     sortGroupMenuItem.setText("by Group");
 684     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 685     {
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         sortGroupMenuItem_actionPerformed(e);
 689       }
 690     });
 691     removeRedundancyMenuItem.setText("Remove Redundancy...");
 692     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 693             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 694                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 695     removeRedundancyMenuItem
 696             .addActionListener(new java.awt.event.ActionListener()
 697             {
 698               public void actionPerformed(ActionEvent e)
 699               {
 700                 removeRedundancyMenuItem_actionPerformed(e);
 701               }
 702             });
 703     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 704     pairwiseAlignmentMenuItem
 705             .addActionListener(new java.awt.event.ActionListener()
 706             {
 707               public void actionPerformed(ActionEvent e)
 708               {
 709                 pairwiseAlignmentMenuItem_actionPerformed(e);
 710               }
 711             });
 712     PCAMenuItem.setText("Principal Component Analysis");
 713     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 714     {
 715       public void actionPerformed(ActionEvent e)
 716       {
 717         PCAMenuItem_actionPerformed(e);
 718       }
 719     });
 720     averageDistanceTreeMenuItem
 721             .setText("Average Distance Using % Identity");
 722     averageDistanceTreeMenuItem
 723             .addActionListener(new java.awt.event.ActionListener()
 724             {
 725               public void actionPerformed(ActionEvent e)
 726               {
 727                 averageDistanceTreeMenuItem_actionPerformed(e);
 728               }
 729             });
 730     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 731     neighbourTreeMenuItem
 732             .addActionListener(new java.awt.event.ActionListener()
 733             {
 734               public void actionPerformed(ActionEvent e)
 735               {
 736                 neighbourTreeMenuItem_actionPerformed(e);
 737               }
 738             });
 739     this.getContentPane().setLayout(borderLayout1);
 740     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 741     statusBar.setBackground(Color.white);
 742     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 743     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 744     statusBar.setText("Status bar");
 745     outputTextboxMenu.setText("Output to Textbox");
 746     clustalColour.setText("Clustalx");
 747
 748     clustalColour.addActionListener(new java.awt.event.ActionListener()
 749     {
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         clustalColour_actionPerformed(e);
 753       }
 754     });
 755     zappoColour.setText("Zappo");
 756     zappoColour.addActionListener(new java.awt.event.ActionListener()
 757     {
 758       public void actionPerformed(ActionEvent e)
 759       {
 760         zappoColour_actionPerformed(e);
 761       }
 762     });
 763     taylorColour.setText("Taylor");
 764     taylorColour.addActionListener(new java.awt.event.ActionListener()
 765     {
 766       public void actionPerformed(ActionEvent e)
 767       {
 768         taylorColour_actionPerformed(e);
 769       }
 770     });
 771     hydrophobicityColour.setText("Hydrophobicity");
 772     hydrophobicityColour
 773             .addActionListener(new java.awt.event.ActionListener()
 774             {
 775               public void actionPerformed(ActionEvent e)
 776               {
 777                 hydrophobicityColour_actionPerformed(e);
 778               }
 779             });
 780     helixColour.setText("Helix Propensity");
 781     helixColour.addActionListener(new java.awt.event.ActionListener()
 782     {
 783       public void actionPerformed(ActionEvent e)
 784       {
 785         helixColour_actionPerformed(e);
 786       }
 787     });
 788     strandColour.setText("Strand Propensity");
 789     strandColour.addActionListener(new java.awt.event.ActionListener()
 790     {
 791       public void actionPerformed(ActionEvent e)
 792       {
 793         strandColour_actionPerformed(e);
 794       }
 795     });
 796     turnColour.setText("Turn Propensity");
 797     turnColour.addActionListener(new java.awt.event.ActionListener()
 798     {
 799       public void actionPerformed(ActionEvent e)
 800       {
 801         turnColour_actionPerformed(e);
 802       }
 803     });
 804     buriedColour.setText("Buried Index");
 805     buriedColour.addActionListener(new java.awt.event.ActionListener()
 806     {
 807       public void actionPerformed(ActionEvent e)
 808       {
 809         buriedColour_actionPerformed(e);
 810       }
 811     });
 812     userDefinedColour.setText("User Defined...");
 813     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 814     {
 815       public void actionPerformed(ActionEvent e)
 816       {
 817         userDefinedColour_actionPerformed(e);
 818       }
 819     });
 820     PIDColour.setText("Percentage Identity");
 821     PIDColour.addActionListener(new java.awt.event.ActionListener()
 822     {
 823       public void actionPerformed(ActionEvent e)
 824       {
 825         PIDColour_actionPerformed(e);
 826       }
 827     });
 828     BLOSUM62Colour.setText("BLOSUM62 Score");
 829     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 830     {
 831       public void actionPerformed(ActionEvent e)
 832       {
 833         BLOSUM62Colour_actionPerformed(e);
 834       }
 835     });
 836     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 837     avDistanceTreeBlosumMenuItem
 838             .addActionListener(new java.awt.event.ActionListener()
 839             {
 840               public void actionPerformed(ActionEvent e)
 841               {
 842                 avTreeBlosumMenuItem_actionPerformed(e);
 843               }
 844             });
 845     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 846     njTreeBlosumMenuItem
 847             .addActionListener(new java.awt.event.ActionListener()
 848             {
 849               public void actionPerformed(ActionEvent e)
 850               {
 851                 njTreeBlosumMenuItem_actionPerformed(e);
 852               }
 853             });
 854     annotationPanelMenuItem.setActionCommand("");
 855     annotationPanelMenuItem.setText("Show Annotations");
 856     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 857             "SHOW_ANNOTATIONS", true));
 858     annotationPanelMenuItem
 859             .addActionListener(new java.awt.event.ActionListener()
 860             {
 861               public void actionPerformed(ActionEvent e)
 862               {
 863                 annotationPanelMenuItem_actionPerformed(e);
 864               }
 865             });
 866     colourTextMenuItem.setText("Colour Text");
 867     colourTextMenuItem
 868             .addActionListener(new java.awt.event.ActionListener()
 869             {
 870               public void actionPerformed(ActionEvent e)
 871               {
 872                 colourTextMenuItem_actionPerformed(e);
 873               }
 874             });
 875     htmlMenuItem.setText("HTML");
 876     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 877     {
 878       public void actionPerformed(ActionEvent e)
 879       {
 880         htmlMenuItem_actionPerformed(e);
 881       }
 882     });
 883     overviewMenuItem.setText("Overview Window");
 884     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 885     {
 886       public void actionPerformed(ActionEvent e)
 887       {
 888         overviewMenuItem_actionPerformed(e);
 889       }
 890     });
 891     undoMenuItem.setEnabled(false);
 892     undoMenuItem.setText("Undo");
 893     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 894             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 895                     .getMenuShortcutKeyMask(), false));
 896     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 897     {
 898       public void actionPerformed(ActionEvent e)
 899       {
 900         undoMenuItem_actionPerformed(e);
 901       }
 902     });
 903     redoMenuItem.setEnabled(false);
 904     redoMenuItem.setText("Redo");
 905     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 906             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 907                     .getMenuShortcutKeyMask(), false));
 908     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 909     {
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         redoMenuItem_actionPerformed(e);
 913       }
 914     });
 915     conservationMenuItem.setText("By Conservation");
 916     conservationMenuItem
 917             .addActionListener(new java.awt.event.ActionListener()
 918             {
 919               public void actionPerformed(ActionEvent e)
 920               {
 921                 conservationMenuItem_actionPerformed(e);
 922               }
 923             });
 924     noColourmenuItem.setText("None");
 925     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 926     {
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         noColourmenuItem_actionPerformed(e);
 930       }
 931     });
 932     wrapMenuItem.setText("Wrap");
 933     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         wrapMenuItem_actionPerformed(e);
 938       }
 939     });
 940     printMenuItem.setText("Print ...");
 941     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 942             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 943                     .getMenuShortcutKeyMask(), false));
 944     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 945     {
 946       public void actionPerformed(ActionEvent e)
 947       {
 948         printMenuItem_actionPerformed(e);
 949       }
 950     });
 951     renderGapsMenuItem.setText("Show Gaps");
 952     renderGapsMenuItem.setState(true);
 953     renderGapsMenuItem
 954             .addActionListener(new java.awt.event.ActionListener()
 955             {
 956               public void actionPerformed(ActionEvent e)
 957               {
 958                 renderGapsMenuItem_actionPerformed(e);
 959               }
 960             });
 961     findMenuItem.setText("Find...");
 962     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 963             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 964                     .getMenuShortcutKeyMask(), false));
 965     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 966     {
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         findMenuItem_actionPerformed(e);
 970       }
 971     });
 972     abovePIDThreshold.setText("Above Identity Threshold");
 973     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 974     {
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         abovePIDThreshold_actionPerformed(e);
 978       }
 979     });
 980     showSeqFeatures.setText("Show Sequence Features");
 981     showSeqFeatures.addActionListener(new ActionListener()
 982     {
 983       public void actionPerformed(ActionEvent actionEvent)
 984       {
 985         showSeqFeatures_actionPerformed(actionEvent);
 986       }
 987     });
 988 /*
 989  *     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 990     showSeqFeaturesHeight.addActionListener(new ActionListener()
 991     {
 992       public void actionPerformed(ActionEvent actionEvent)
 993       {
 994         showSeqFeaturesHeight_actionPerformed(actionEvent);
 995       }
 996     }); */
 997     showDbRefsMenuitem.setText("Show Database Refs");
 998     showDbRefsMenuitem.addActionListener(new ActionListener()
 999     {
1000
1001       public void actionPerformed(ActionEvent e)
1002       {
1003         showDbRefs_actionPerformed(e);
1004       }
1005
1006     });
1007     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1008     showNpFeatsMenuitem.addActionListener(new ActionListener()
1009     {
1010
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         showNpFeats_actionPerformed(e);
1014       }
1015
1016     });
1017     showGroupConservation.setText("Group Conservation");
1018     showGroupConservation.addActionListener(new ActionListener()
1019     {
1020
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         showGroupConservation_actionPerformed(e);
1024       }
1025
1026     });
1027
1028     showGroupConsensus.setText("Group Consensus");
1029     showGroupConsensus.addActionListener(new ActionListener()
1030     {
1031
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         showGroupConsensus_actionPerformed(e);
1035       }
1036
1037     });
1038     showConsensusHistogram.setText("Show Consensus Histogram");
1039     showConsensusHistogram.addActionListener(new ActionListener()
1040     {
1041
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         showConsensusHistogram_actionPerformed(e);
1045       }
1046
1047     });
1048     showSequenceLogo.setText("Show Consensus Logo");
1049     showSequenceLogo.addActionListener(new ActionListener()
1050     {
1051
1052       public void actionPerformed(ActionEvent e)
1053       {
1054         showSequenceLogo_actionPerformed(e);
1055       }
1056
1057     });
1058     applyAutoAnnotationSettings.setText("Apply to all groups");
1059     applyAutoAnnotationSettings.setState(false);
1060     applyAutoAnnotationSettings.setVisible(true);
1061     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1062     {
1063
1064       public void actionPerformed(ActionEvent e)
1065       {
1066         applyAutoAnnotationSettings_actionPerformed(e);
1067       }
1068
1069     });
1070
1071     nucleotideColour.setText("Nucleotide");
1072     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1073     {
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         nucleotideColour_actionPerformed(e);
1077       }
1078     });
1079     deleteGroups.setText("Undefine groups");
1080     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1081             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1082                     .getMenuShortcutKeyMask(), false));
1083     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1084     {
1085       public void actionPerformed(ActionEvent e)
1086       {
1087         deleteGroups_actionPerformed(e);
1088       }
1089     });
1090     copy.setText("Copy");
1091     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1092             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1093                     .getMenuShortcutKeyMask(), false));
1094
1095     copy.addActionListener(new java.awt.event.ActionListener()
1096     {
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         copy_actionPerformed(e);
1100       }
1101     });
1102     cut.setText("Cut");
1103     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1104             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1105                     .getMenuShortcutKeyMask(), false));
1106     cut.addActionListener(new java.awt.event.ActionListener()
1107     {
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         cut_actionPerformed(e);
1111       }
1112     });
1113     delete.setText("Delete");
1114     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1115             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1116     delete.addActionListener(new java.awt.event.ActionListener()
1117     {
1118       public void actionPerformed(ActionEvent e)
1119       {
1120         delete_actionPerformed(e);
1121       }
1122     });
1123     pasteMenu.setText("Paste");
1124     pasteNew.setText("To New Alignment");
1125     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1126             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1127                     .getMenuShortcutKeyMask()
1128                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1129     pasteNew.addActionListener(new java.awt.event.ActionListener()
1130     {
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         pasteNew_actionPerformed(e);
1134       }
1135     });
1136     pasteThis.setText("Add To This Alignment");
1137     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1138             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1139                     .getMenuShortcutKeyMask(), false));
1140     pasteThis.addActionListener(new java.awt.event.ActionListener()
1141     {
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         pasteThis_actionPerformed(e);
1145       }
1146     });
1147     applyToAllGroups.setText("Apply Colour To All Groups");
1148     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1149     {
1150       public void actionPerformed(ActionEvent e)
1151       {
1152         applyToAllGroups_actionPerformed(e);
1153       }
1154     });
1155     createPNG.addActionListener(new java.awt.event.ActionListener()
1156     {
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         createPNG(null);
1160       }
1161     });
1162     createPNG.setActionCommand("Save As PNG Image");
1163     createPNG.setText("PNG");
1164     font.setText("Font...");
1165     font.addActionListener(new java.awt.event.ActionListener()
1166     {
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         font_actionPerformed(e);
1170       }
1171     });
1172
1173     seqLimits.setText("Show Sequence Limits");
1174     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1175     seqLimits.addActionListener(new java.awt.event.ActionListener()
1176     {
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         seqLimit_actionPerformed(e);
1180       }
1181     });
1182     epsFile.setText("EPS");
1183     epsFile.addActionListener(new java.awt.event.ActionListener()
1184     {
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         createEPS(null);
1188       }
1189     });
1190     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1191     LoadtreeMenuItem.setText("Load Associated Tree");
1192     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1193     {
1194       public void actionPerformed(ActionEvent e)
1195       {
1196         LoadtreeMenuItem_actionPerformed(e);
1197       }
1198     });
1199     scaleAbove.setVisible(false);
1200     scaleAbove.setText("Scale Above");
1201     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1202     {
1203       public void actionPerformed(ActionEvent e)
1204       {
1205         scaleAbove_actionPerformed(e);
1206       }
1207     });
1208     scaleLeft.setVisible(false);
1209     scaleLeft.setSelected(true);
1210     scaleLeft.setText("Scale Left");
1211     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1212     {
1213       public void actionPerformed(ActionEvent e)
1214       {
1215         scaleLeft_actionPerformed(e);
1216       }
1217     });
1218     scaleRight.setVisible(false);
1219     scaleRight.setSelected(true);
1220     scaleRight.setText("Scale Right");
1221     scaleRight.addActionListener(new java.awt.event.ActionListener()
1222     {
1223       public void actionPerformed(ActionEvent e)
1224       {
1225         scaleRight_actionPerformed(e);
1226       }
1227     });
1228     centreColumnLabelsMenuItem.setVisible(true);
1229     centreColumnLabelsMenuItem.setState(false);
1230     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1231     centreColumnLabelsMenuItem
1232             .addActionListener(new java.awt.event.ActionListener()
1233             {
1234               public void actionPerformed(ActionEvent e)
1235               {
1236                 centreColumnLabels_actionPerformed(e);
1237               }
1238             });
1239     followHighlightMenuItem.setVisible(true);
1240     followHighlightMenuItem.setState(true);
1241     followHighlightMenuItem.setText("Automatic Scrolling");
1242     followHighlightMenuItem.addActionListener(new ActionListener()
1243     {
1244
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         followHighlight_actionPerformed();
1248       }
1249
1250     });
1251
1252     modifyPID.setText("Modify Identity Threshold...");
1253     modifyPID.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         modifyPID_actionPerformed(e);
1258       }
1259     });
1260     modifyConservation.setText("Modify Conservation Threshold...");
1261     modifyConservation
1262             .addActionListener(new java.awt.event.ActionListener()
1263             {
1264               public void actionPerformed(ActionEvent e)
1265               {
1266                 modifyConservation_actionPerformed(e);
1267               }
1268             });
1269     sortByTreeMenu.setText("By Tree Order");
1270     sort.setText("Sort");
1271     sort.addMenuListener(new MenuListener()
1272     {
1273       public void menuSelected(MenuEvent e)
1274       {
1275         buildTreeMenu();
1276       }
1277
1278       public void menuDeselected(MenuEvent e)
1279       {
1280       }
1281
1282       public void menuCanceled(MenuEvent e)
1283       {
1284       }
1285     });
1286     sortByAnnotScore.setText("by Score");
1287     sort.add(sortByAnnotScore);
1288     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1289     {
1290
1291       public void menuCanceled(MenuEvent e)
1292       {
1293       }
1294
1295       public void menuDeselected(MenuEvent e)
1296       {
1297       }
1298
1299       public void menuSelected(MenuEvent e)
1300       {
1301         buildSortByAnnotationScoresMenu();
1302       }
1303     });
1304     sortByAnnotScore.setVisible(false);
1305
1306     calculateTree.setText("Calculate Tree");
1307
1308     jMenu2.setText("Export Image");
1309     padGapsMenuitem.setText("Pad Gaps");
1310     padGapsMenuitem.setState(jalview.bin.Cache
1311             .getDefault("PAD_GAPS", false));
1312     padGapsMenuitem.addActionListener(new ActionListener()
1313     {
1314       public void actionPerformed(ActionEvent e)
1315       {
1316         padGapsMenuitem_actionPerformed(e);
1317       }
1318     });
1319     vamsasStore.setVisible(false);
1320     vamsasStore.setText("VAMSAS store");
1321     vamsasStore.addActionListener(new ActionListener()
1322     {
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         vamsasStore_actionPerformed(e);
1326       }
1327     });
1328     showTranslation.setText("Translate cDNA");
1329     showTranslation.addActionListener(new ActionListener()
1330     {
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         showTranslation_actionPerformed(e);
1334       }
1335     });
1336     extractScores.setText("Extract Scores...");
1337     extractScores.addActionListener(new ActionListener()
1338     {
1339       public void actionPerformed(ActionEvent e)
1340       {
1341         extractScores_actionPerformed(e);
1342       }
1343     });
1344     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1345                                     // score extraction
1346     showProducts.setText("Get Cross References");
1347     /*
1348      * showProducts.addActionListener(new ActionListener() {
1349      *
1350      * public void actionPerformed(ActionEvent e) {
1351      * showProducts_actionPerformed(e); } });
1352      */
1353     featureSettings.setText("Feature Settings...");
1354     featureSettings.addActionListener(new ActionListener()
1355     {
1356       public void actionPerformed(ActionEvent e)
1357       {
1358         featureSettings_actionPerformed(e);
1359       }
1360     });
1361     fetchSequence.setText("Fetch Sequence(s)...");
1362     fetchSequence.addActionListener(new ActionListener()
1363     {
1364       public void actionPerformed(ActionEvent e)
1365       {
1366         fetchSequence_actionPerformed(e);
1367       }
1368     });
1369
1370     annotationColour.setText("By Annotation...");
1371     annotationColour.addActionListener(new ActionListener()
1372     {
1373       public void actionPerformed(ActionEvent e)
1374       {
1375         annotationColour_actionPerformed(e);
1376       }
1377     });
1378     associatedData.setText("Load Features / Annotations");
1379     associatedData.addActionListener(new ActionListener()
1380     {
1381       public void actionPerformed(ActionEvent e)
1382       {
1383         associatedData_actionPerformed(e);
1384       }
1385     });
1386     autoCalculate.setText("Autocalculate Consensus");
1387     autoCalculate.setState(jalview.bin.Cache.getDefault(
1388             "AUTO_CALC_CONSENSUS", true));
1389     autoCalculate.addActionListener(new ActionListener()
1390     {
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         autoCalculate_actionPerformed(e);
1394       }
1395     });
1396     addSequenceMenu.setText("Add Sequences");
1397     addFromFile.setText("From File");
1398     addFromFile.addActionListener(new ActionListener()
1399     {
1400       public void actionPerformed(ActionEvent e)
1401       {
1402         addFromFile_actionPerformed(e);
1403       }
1404     });
1405     addFromText.setText("From Textbox");
1406     addFromText.addActionListener(new ActionListener()
1407     {
1408       public void actionPerformed(ActionEvent e)
1409       {
1410         addFromText_actionPerformed(e);
1411       }
1412     });
1413     addFromURL.setText("From URL");
1414     addFromURL.addActionListener(new ActionListener()
1415     {
1416       public void actionPerformed(ActionEvent e)
1417       {
1418         addFromURL_actionPerformed(e);
1419       }
1420     });
1421     exportFeatures.setText("Export Features...");
1422     exportFeatures.addActionListener(new ActionListener()
1423     {
1424       public void actionPerformed(ActionEvent e)
1425       {
1426         exportFeatures_actionPerformed(e);
1427       }
1428     });
1429     exportAnnotations.setText("Export Annotations...");
1430     exportAnnotations.addActionListener(new ActionListener()
1431     {
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         exportAnnotations_actionPerformed(e);
1435       }
1436     });
1437     statusPanel.setLayout(gridLayout1);
1438     jMenu3.setText("Show");
1439     showAllSeqs.setText("All Sequences");
1440     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1441     showAllSeqs.addActionListener(new ActionListener()
1442     {
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         showAllSeqs_actionPerformed(e);
1446       }
1447     });
1448     showAllColumns.setText("All Columns");
1449     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1450     showAllColumns.addActionListener(new ActionListener()
1451     {
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         showAllColumns_actionPerformed(e);
1455       }
1456     });
1457     hideMenu.setText("Hide");
1458     hideSelSequences.setText("Selected Sequences");
1459     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1460     hideSelSequences.addActionListener(new ActionListener()
1461     {
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         hideSelSequences_actionPerformed(e);
1465       }
1466     });
1467     hideSelColumns.setText("Selected Columns");
1468     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1469     hideSelColumns.addActionListener(new ActionListener()
1470     {
1471       public void actionPerformed(ActionEvent e)
1472       {
1473         hideSelColumns_actionPerformed(e);
1474       }
1475     });
1476     hideAllSelection.setText("Selected Region");
1477     hideAllSelection.addActionListener(new ActionListener()
1478     {
1479       public void actionPerformed(ActionEvent e)
1480       {
1481         hideAllSelection_actionPerformed(e);
1482       }
1483     });
1484     // TODO: should be hidden if no selection exists.
1485     hideAllButSelection.setText("All but Selected Rregion (Shift+Ctrl+H)");
1486     hideAllButSelection.addActionListener(new ActionListener()
1487     {
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         hideAllButSelection_actionPerformed(e);
1491       }
1492     });
1493     showAllhidden.setText("All Sequences and Columns");
1494     showAllhidden.setToolTipText("H toggles visibility of hidden or selected regions.");
1495     showAllhidden.addActionListener(new ActionListener()
1496     {
1497       public void actionPerformed(ActionEvent e)
1498       {
1499         showAllhidden_actionPerformed(e);
1500       }
1501     });
1502
1503     hiddenMarkers.setText("Show Hidden Markers");
1504     hiddenMarkers.addActionListener(new ActionListener()
1505     {
1506       public void actionPerformed(ActionEvent e)
1507       {
1508         hiddenMarkers_actionPerformed(e);
1509       }
1510     });
1511     invertColSel.setText("Invert Column Selection");
1512     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1513             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1514                     .getMenuShortcutKeyMask()
1515                     | java.awt.event.KeyEvent.ALT_MASK, false));
1516     invertColSel.addActionListener(new ActionListener()
1517     {
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         invertColSel_actionPerformed(e);
1521       }
1522     });
1523     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1524     {
1525       public void stateChanged(ChangeEvent evt)
1526       {
1527         JTabbedPane pane = (JTabbedPane) evt.getSource();
1528         int sel = pane.getSelectedIndex();
1529         tabSelectionChanged(sel);
1530       }
1531     });
1532     tabbedPane.addMouseListener(new MouseAdapter()
1533     {
1534       public void mousePressed(MouseEvent e)
1535       {
1536         tabbedPane_mousePressed(e);
1537       }
1538     });
1539     tabbedPane.addFocusListener(new FocusAdapter()
1540     {
1541       public void focusGained(FocusEvent e)
1542       {
1543         tabbedPane_focusGained(e);
1544       }
1545     });
1546     save.setText("Save");
1547     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1548             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1549                     .getMenuShortcutKeyMask(), false));
1550     save.addActionListener(new ActionListener()
1551     {
1552       public void actionPerformed(ActionEvent e)
1553       {
1554         save_actionPerformed(e);
1555       }
1556     });
1557     reload.setEnabled(false);
1558     reload.setText("Reload");
1559     reload.addActionListener(new ActionListener()
1560     {
1561       public void actionPerformed(ActionEvent e)
1562       {
1563         reload_actionPerformed(e);
1564       }
1565     });
1566     newView.setText("New View");
1567     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1568             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1569                     .getMenuShortcutKeyMask(), false));
1570     newView.addActionListener(new ActionListener()
1571     {
1572       public void actionPerformed(ActionEvent e)
1573       {
1574         newView_actionPerformed(e);
1575       }
1576     });
1577     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1578             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1579     textColour.setText("Colour Text ...");
1580     textColour.addActionListener(new ActionListener()
1581     {
1582       public void actionPerformed(ActionEvent e)
1583       {
1584         textColour_actionPerformed(e);
1585       }
1586     });
1587     formatMenu.setText("Format");
1588     selectMenu.setText("Select");
1589     idRightAlign.setText("Right Align Sequence Id");
1590     idRightAlign.addActionListener(new ActionListener()
1591     {
1592       public void actionPerformed(ActionEvent e)
1593       {
1594         idRightAlign_actionPerformed(e);
1595       }
1596     });
1597     gatherViews.setEnabled(false);
1598     gatherViews.setText("Gather Views");
1599     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1600             java.awt.event.KeyEvent.VK_G, 0, false));
1601     gatherViews.addActionListener(new ActionListener()
1602     {
1603       public void actionPerformed(ActionEvent e)
1604       {
1605         gatherViews_actionPerformed(e);
1606       }
1607     });
1608     expandViews.setEnabled(false);
1609     expandViews.setText("Expand Views");
1610     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1611             java.awt.event.KeyEvent.VK_X, 0, false));
1612     expandViews.addActionListener(new ActionListener()
1613     {
1614       public void actionPerformed(ActionEvent e)
1615       {
1616         expandViews_actionPerformed(e);
1617       }
1618     });
1619     pageSetup.setText("Page Setup ...");
1620     pageSetup.addActionListener(new ActionListener()
1621     {
1622       public void actionPerformed(ActionEvent e)
1623       {
1624         pageSetup_actionPerformed(e);
1625       }
1626     });
1627     alignmentProperties.setText("Alignment Properties...");
1628     alignmentProperties.addActionListener(new ActionListener()
1629     {
1630       public void actionPerformed(ActionEvent actionEvent)
1631       {
1632         alignmentProperties();
1633       }
1634     });
1635     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1636     autoAnnMenu.setText("Autocalculated Annotation");
1637     alignFrameMenuBar.add(fileMenu);
1638     alignFrameMenuBar.add(editMenu);
1639     alignFrameMenuBar.add(selectMenu);
1640     alignFrameMenuBar.add(viewMenu);
1641     alignFrameMenuBar.add(formatMenu);
1642     alignFrameMenuBar.add(colourMenu);
1643     alignFrameMenuBar.add(calculateMenu);
1644     alignFrameMenuBar.add(webService);
1645     fileMenu.add(fetchSequence);
1646     fileMenu.add(addSequenceMenu);
1647     fileMenu.add(reload);
1648     fileMenu.addSeparator();
1649     fileMenu.add(vamsasStore);
1650     fileMenu.add(save);
1651     fileMenu.add(saveAs);
1652     fileMenu.add(outputTextboxMenu);
1653     fileMenu.add(pageSetup);
1654     fileMenu.add(printMenuItem);
1655     fileMenu.addSeparator();
1656     fileMenu.add(jMenu2);
1657     fileMenu.add(exportFeatures);
1658     fileMenu.add(exportAnnotations);
1659     fileMenu.add(LoadtreeMenuItem);
1660     fileMenu.add(associatedData);
1661     fileMenu.addSeparator();
1662     fileMenu.add(closeMenuItem);
1663     editMenu.add(undoMenuItem);
1664     editMenu.add(redoMenuItem);
1665     editMenu.add(cut);
1666     editMenu.add(copy);
1667     editMenu.add(pasteMenu);
1668     editMenu.add(delete);
1669     editMenu.addSeparator();
1670     editMenu.add(remove2LeftMenuItem);
1671     editMenu.add(remove2RightMenuItem);
1672     editMenu.add(removeGappedColumnMenuItem);
1673     editMenu.add(removeAllGapsMenuItem);
1674     editMenu.add(removeRedundancyMenuItem);
1675     editMenu.addSeparator();
1676     // dont add these yet in the CVS build - they cannot be undone!
1677     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1678     // editMenu.add(justifyLeftMenuItem);
1679     // editMenu.add(justifyRightMenuItem);
1680     // editMenu.addSeparator();
1681     editMenu.add(padGapsMenuitem);
1682     viewMenu.add(newView);
1683     viewMenu.add(expandViews);
1684     viewMenu.add(gatherViews);
1685     viewMenu.addSeparator();
1686     viewMenu.add(jMenu3);
1687     viewMenu.add(hideMenu);
1688     viewMenu.addSeparator();
1689     viewMenu.add(followHighlightMenuItem);
1690     viewMenu.add(annotationPanelMenuItem);
1691     autoAnnMenu.add(applyAutoAnnotationSettings);
1692     autoAnnMenu.add(showConsensusHistogram);
1693     autoAnnMenu.add(showSequenceLogo);
1694     autoAnnMenu.addSeparator();
1695     autoAnnMenu.add(showGroupConservation);
1696     autoAnnMenu.add(showGroupConsensus);
1697     viewMenu.add(autoAnnMenu);
1698     viewMenu.addSeparator();
1699     viewMenu.add(showSeqFeatures);
1700     //viewMenu.add(showSeqFeaturesHeight);
1701
1702     viewMenu.add(featureSettings);
1703     tooltipSettingsMenu.add(showDbRefsMenuitem);
1704     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1705     viewMenu.add(tooltipSettingsMenu);
1706     viewMenu.addSeparator();
1707     viewMenu.add(alignmentProperties);
1708     viewMenu.addSeparator();
1709     viewMenu.add(overviewMenuItem);
1710     colourMenu.add(applyToAllGroups);
1711     colourMenu.add(textColour);
1712     colourMenu.addSeparator();
1713     colourMenu.add(noColourmenuItem);
1714     colourMenu.add(clustalColour);
1715     colourMenu.add(BLOSUM62Colour);
1716     colourMenu.add(PIDColour);
1717     colourMenu.add(zappoColour);
1718     colourMenu.add(taylorColour);
1719     colourMenu.add(hydrophobicityColour);
1720     colourMenu.add(helixColour);
1721     colourMenu.add(strandColour);
1722     colourMenu.add(turnColour);
1723     colourMenu.add(buriedColour);
1724     colourMenu.add(nucleotideColour);
1725     colourMenu.add(userDefinedColour);
1726     colourMenu.addSeparator();
1727     colourMenu.add(conservationMenuItem);
1728     colourMenu.add(modifyConservation);
1729     colourMenu.add(abovePIDThreshold);
1730     colourMenu.add(modifyPID);
1731     colourMenu.add(annotationColour);
1732     calculateMenu.add(sort);
1733     calculateMenu.add(calculateTree);
1734     calculateMenu.addSeparator();
1735     calculateMenu.add(pairwiseAlignmentMenuItem);
1736     calculateMenu.add(PCAMenuItem);
1737     calculateMenu.addSeparator();
1738     calculateMenu.add(showTranslation);
1739     calculateMenu.add(showProducts);
1740     calculateMenu.add(autoCalculate);
1741     calculateMenu.addSeparator();
1742     calculateMenu.add(extractScores);
1743     webServiceNoServices = new JMenuItem("<No Services>");
1744     webService.add(webServiceNoServices);
1745     pasteMenu.add(pasteNew);
1746     pasteMenu.add(pasteThis);
1747     sort.add(sortIDMenuItem);
1748     sort.add(sortLengthMenuItem);
1749     sort.add(sortGroupMenuItem);
1750     sort.add(sortPairwiseMenuItem);
1751     sort.add(sortByTreeMenu);
1752     calculateTree.add(averageDistanceTreeMenuItem);
1753     calculateTree.add(neighbourTreeMenuItem);
1754     calculateTree.add(avDistanceTreeBlosumMenuItem);
1755     calculateTree.add(njTreeBlosumMenuItem);
1756     jMenu2.add(htmlMenuItem);
1757     jMenu2.add(epsFile);
1758     jMenu2.add(createPNG);
1759     addSequenceMenu.add(addFromFile);
1760     addSequenceMenu.add(addFromText);
1761     addSequenceMenu.add(addFromURL);
1762     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1763     statusPanel.add(statusBar, null);
1764     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1765     jMenu3.add(showAllColumns);
1766     jMenu3.add(showAllSeqs);
1767     jMenu3.add(showAllhidden);
1768     hideMenu.add(hideSelColumns);
1769     hideMenu.add(hideSelSequences);
1770     hideMenu.add(hideAllSelection);
1771     hideMenu.add(hideAllButSelection);
1772
1773     formatMenu.add(font);
1774     formatMenu.addSeparator();
1775     formatMenu.add(wrapMenuItem);
1776     formatMenu.add(scaleAbove);
1777     formatMenu.add(scaleLeft);
1778     formatMenu.add(scaleRight);
1779     formatMenu.add(seqLimits);
1780     formatMenu.add(idRightAlign);
1781     formatMenu.add(hiddenMarkers);
1782     formatMenu.add(viewBoxesMenuItem);
1783     formatMenu.add(viewTextMenuItem);
1784     formatMenu.add(colourTextMenuItem);
1785     formatMenu.add(renderGapsMenuItem);
1786     formatMenu.add(centreColumnLabelsMenuItem);
1787     formatMenu.add(showUnconservedMenuItem);
1788     selectMenu.add(findMenuItem);
1789     selectMenu.addSeparator();
1790     selectMenu.add(selectAllSequenceMenuItem);
1791     selectMenu.add(deselectAllSequenceMenuItem);
1792     selectMenu.add(invertSequenceMenuItem);
1793     selectMenu.add(invertColSel);
1794     selectMenu.add(deleteGroups);
1795     selectMenu.add(grpsFromSelection);
1796   }
1797
1798   protected void showAllhidden_actionPerformed(ActionEvent e)
1799   {
1800     // TODO Auto-generated method stub
1801
1802   }
1803
1804   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1805   {
1806     // TODO Auto-generated method stub
1807
1808   }
1809
1810   protected void hideAllSelection_actionPerformed(ActionEvent e)
1811   {
1812     // TODO Auto-generated method stub
1813
1814   }
1815
1816   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1817   {
1818     // TODO Auto-generated method stub
1819
1820   }
1821
1822   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1823   {
1824     // TODO Auto-generated method stub
1825
1826   }
1827
1828   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1829   {
1830     // TODO Auto-generated method stub
1831
1832   }
1833
1834   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1835   {
1836     // TODO Auto-generated method stub
1837
1838   }
1839
1840   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1841   {
1842     // TODO Auto-generated method stub
1843
1844   }
1845
1846   protected void showGroupConservation_actionPerformed(ActionEvent e)
1847   {
1848     // TODO Auto-generated method stub
1849
1850   }
1851
1852   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1853   {
1854     // TODO Auto-generated method stub
1855
1856   }
1857
1858   protected void showSeqFeaturesHeight_actionPerformed(
1859           ActionEvent actionEvent)
1860   {
1861     // TODO Auto-generated method stub
1862
1863   }
1864
1865   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1866   {
1867     // TODO Auto-generated method stub
1868
1869   }
1870
1871   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1872   {
1873     // TODO Auto-generated method stub
1874
1875   }
1876
1877   protected void followHighlight_actionPerformed()
1878   {
1879     // TODO Auto-generated method stub
1880
1881   }
1882
1883   protected void showNpFeats_actionPerformed(ActionEvent e)
1884   {
1885     // TODO Auto-generated method stub
1886
1887   }
1888
1889   protected void showDbRefs_actionPerformed(ActionEvent e)
1890   {
1891     // TODO Auto-generated method stub
1892
1893   }
1894
1895   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1896   {
1897   }
1898
1899   protected void showProducts_actionPerformed(ActionEvent e)
1900   {
1901   }
1902
1903   protected void buildSortByAnnotationScoresMenu()
1904   {
1905   }
1906
1907   protected void extractScores_actionPerformed(ActionEvent e)
1908   {
1909   }
1910
1911   protected void outputText_actionPerformed(ActionEvent e)
1912   {
1913   }
1914
1915   public void addFromFile_actionPerformed(ActionEvent e)
1916   {
1917
1918   }
1919
1920   public void addFromText_actionPerformed(ActionEvent e)
1921   {
1922
1923   }
1924
1925   public void addFromURL_actionPerformed(ActionEvent e)
1926   {
1927
1928   }
1929
1930   public void exportFeatures_actionPerformed(ActionEvent e)
1931   {
1932
1933   }
1934
1935   public void exportAnnotations_actionPerformed(ActionEvent e)
1936   {
1937
1938   }
1939
1940   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1941   {
1942   }
1943
1944   protected void closeMenuItem_actionPerformed(boolean b)
1945   {
1946   }
1947
1948   protected void redoMenuItem_actionPerformed(ActionEvent e)
1949   {
1950   }
1951
1952   protected void undoMenuItem_actionPerformed(ActionEvent e)
1953   {
1954   }
1955
1956   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1957   {
1958   }
1959
1960   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1961   {
1962   }
1963
1964   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1965   {
1966   }
1967
1968   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1969   {
1970   }
1971
1972   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1973   {
1974   }
1975
1976   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1977   {
1978   }
1979
1980   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1981   {
1982   }
1983
1984   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1985   {
1986   }
1987
1988   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1989   {
1990   }
1991
1992   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1993   {
1994   }
1995
1996   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1997   {
1998   }
1999
2000   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2001   {
2002   }
2003
2004   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2005   {
2006   }
2007
2008   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2009   {
2010   }
2011
2012   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2013   {
2014   }
2015
2016   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2017   {
2018   }
2019
2020   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2021   {
2022   }
2023
2024   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2025   {
2026   }
2027
2028   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2029   {
2030   }
2031
2032   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2033   {
2034   }
2035
2036   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2037   {
2038   }
2039
2040   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2041   {
2042   }
2043
2044   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2045   {
2046   }
2047
2048   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2049   {
2050   }
2051
2052   protected void clustalColour_actionPerformed(ActionEvent e)
2053   {
2054   }
2055
2056   protected void zappoColour_actionPerformed(ActionEvent e)
2057   {
2058   }
2059
2060   protected void taylorColour_actionPerformed(ActionEvent e)
2061   {
2062   }
2063
2064   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void helixColour_actionPerformed(ActionEvent e)
2069   {
2070   }
2071
2072   protected void strandColour_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void turnColour_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void buriedColour_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void userDefinedColour_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void PIDColour_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2097   {
2098   }
2099
2100   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void printMenuItem_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2109   {
2110   }
2111
2112   protected void findMenuItem_actionPerformed(ActionEvent e)
2113   {
2114   }
2115
2116   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2117   {
2118   }
2119
2120   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2121   {
2122   }
2123
2124   protected void nucleotideColour_actionPerformed(ActionEvent e)
2125   {
2126   }
2127
2128   protected void deleteGroups_actionPerformed(ActionEvent e)
2129   {
2130   }
2131
2132   protected void copy_actionPerformed(ActionEvent e)
2133   {
2134   }
2135
2136   protected void cut_actionPerformed(ActionEvent e)
2137   {
2138   }
2139
2140   protected void delete_actionPerformed(ActionEvent e)
2141   {
2142   }
2143
2144   protected void pasteNew_actionPerformed(ActionEvent e)
2145   {
2146   }
2147
2148   protected void pasteThis_actionPerformed(ActionEvent e)
2149   {
2150   }
2151
2152   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2153   {
2154   }
2155
2156   public void createPNG(java.io.File f)
2157   {
2158   }
2159
2160   protected void font_actionPerformed(ActionEvent e)
2161   {
2162   }
2163
2164   protected void seqLimit_actionPerformed(ActionEvent e)
2165   {
2166   }
2167
2168   public void seqDBRef_actionPerformed(ActionEvent e)
2169   {
2170
2171   }
2172
2173   public void createEPS(java.io.File f)
2174   {
2175   }
2176
2177   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2178   {
2179   }
2180
2181   protected void jpred_actionPerformed(ActionEvent e)
2182   {
2183   }
2184
2185   protected void scaleAbove_actionPerformed(ActionEvent e)
2186   {
2187   }
2188
2189   protected void scaleLeft_actionPerformed(ActionEvent e)
2190   {
2191   }
2192
2193   protected void scaleRight_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void modifyPID_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void modifyConservation_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void saveAs_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2210   {
2211   }
2212
2213   public void vamsasStore_actionPerformed(ActionEvent e)
2214   {
2215
2216   }
2217
2218   public void vamsasLoad_actionPerformed(ActionEvent e)
2219   {
2220
2221   }
2222
2223   public void showTranslation_actionPerformed(ActionEvent e)
2224   {
2225
2226   }
2227
2228   public void featureSettings_actionPerformed(ActionEvent e)
2229   {
2230
2231   }
2232
2233   public void fetchSequence_actionPerformed(ActionEvent e)
2234   {
2235
2236   }
2237
2238   public void smoothFont_actionPerformed(ActionEvent e)
2239   {
2240
2241   }
2242
2243   public void annotationColour_actionPerformed(ActionEvent e)
2244   {
2245
2246   }
2247
2248   public void associatedData_actionPerformed(ActionEvent e)
2249   {
2250
2251   }
2252
2253   public void autoCalculate_actionPerformed(ActionEvent e)
2254   {
2255
2256   }
2257
2258   public void showAllSeqs_actionPerformed(ActionEvent e)
2259   {
2260
2261   }
2262
2263   public void showAllColumns_actionPerformed(ActionEvent e)
2264   {
2265
2266   }
2267
2268   public void hideSelSequences_actionPerformed(ActionEvent e)
2269   {
2270
2271   }
2272
2273   public void hideSelColumns_actionPerformed(ActionEvent e)
2274   {
2275
2276   }
2277
2278   public void hiddenMarkers_actionPerformed(ActionEvent e)
2279   {
2280
2281   }
2282
2283   public void findPdbId_actionPerformed(ActionEvent e)
2284   {
2285
2286   }
2287
2288   public void enterPdbId_actionPerformed(ActionEvent e)
2289   {
2290
2291   }
2292
2293   public void pdbFile_actionPerformed(ActionEvent e)
2294   {
2295
2296   }
2297
2298   public void invertColSel_actionPerformed(ActionEvent e)
2299   {
2300
2301   }
2302
2303   public void tabSelectionChanged(int sel)
2304   {
2305
2306   }
2307
2308   public void tabbedPane_mousePressed(MouseEvent e)
2309   {
2310
2311   }
2312
2313   public void tabbedPane_focusGained(FocusEvent e)
2314   {
2315     requestFocus();
2316   }
2317
2318   public void save_actionPerformed(ActionEvent e)
2319   {
2320
2321   }
2322
2323   public void reload_actionPerformed(ActionEvent e)
2324   {
2325
2326   }
2327
2328   public void newView_actionPerformed(ActionEvent e)
2329   {
2330
2331   }
2332
2333   public void textColour_actionPerformed(ActionEvent e)
2334   {
2335
2336   }
2337
2338   public void idRightAlign_actionPerformed(ActionEvent e)
2339   {
2340
2341   }
2342
2343   public void expandViews_actionPerformed(ActionEvent e)
2344   {
2345
2346   }
2347
2348   public void gatherViews_actionPerformed(ActionEvent e)
2349   {
2350
2351   }
2352
2353   public void buildTreeMenu()
2354   {
2355
2356   }
2357
2358   public void pageSetup_actionPerformed(ActionEvent e)
2359   {
2360
2361   }
2362
2363   public void alignmentProperties()
2364   {
2365
2366   }
2367 }