src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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   JMenuItem htmlMenuItem = new JMenuItem();
 126
 127   JMenuItem overviewMenuItem = new JMenuItem();
 128
 129   protected JMenuItem undoMenuItem = new JMenuItem();
 130
 131   protected JMenuItem redoMenuItem = new JMenuItem();
 132
 133   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 134
 135   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 136
 137   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 138
 139   JMenuItem printMenuItem = new JMenuItem();
 140
 141   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 142
 143   JMenuItem findMenuItem = new JMenuItem();
 144
 145   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 146
 147   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 148   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 149
 150   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 151
 152   JMenuItem deleteGroups = new JMenuItem();
 153
 154   JMenuItem delete = new JMenuItem();
 155
 156   JMenuItem copy = new JMenuItem();
 157
 158   JMenuItem cut = new JMenuItem();
 159
 160   JMenu pasteMenu = new JMenu();
 161
 162   JMenuItem pasteNew = new JMenuItem();
 163
 164   JMenuItem pasteThis = new JMenuItem();
 165
 166   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 167
 168   JMenuItem createPNG = new JMenuItem();
 169
 170   protected JMenuItem font = new JMenuItem();
 171
 172   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 173
 174   JMenuItem epsFile = new JMenuItem();
 175
 176   JMenuItem LoadtreeMenuItem = new JMenuItem();
 177
 178   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 179
 180   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 183
 184   protected JMenuItem modifyPID = new JMenuItem();
 185
 186   protected JMenuItem modifyConservation = new JMenuItem();
 187
 188   protected JMenu sortByTreeMenu = new JMenu();
 189
 190   protected JMenu sort = new JMenu();
 191
 192   protected JMenu calculateTree = new JMenu();
 193
 194   JMenu jMenu2 = new JMenu();
 195
 196   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 197   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 198   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 199
 200   protected ButtonGroup colours = new ButtonGroup();
 201
 202   JMenuItem vamsasStore = new JMenuItem();
 203
 204   protected JMenuItem showTranslation = new JMenuItem();
 205
 206   protected JMenuItem extractScores = new JMenuItem();
 207
 208   protected JMenu showProducts = new JMenu();
 209
 210   public JMenuItem featureSettings = new JMenuItem();
 211
 212   JMenuItem fetchSequence = new JMenuItem();
 213
 214   JMenuItem annotationColour = new JMenuItem();
 215
 216   JMenuItem associatedData = new JMenuItem();
 217
 218   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 219
 220   JMenu addSequenceMenu = new JMenu();
 221
 222   JMenuItem addFromFile = new JMenuItem();
 223
 224   JMenuItem addFromText = new JMenuItem();
 225
 226   JMenuItem addFromURL = new JMenuItem();
 227
 228   JMenuItem exportAnnotations = new JMenuItem();
 229
 230   JMenuItem exportFeatures = new JMenuItem();
 231
 232   protected JPanel statusPanel = new JPanel();
 233
 234   GridLayout gridLayout1 = new GridLayout();
 235
 236   JMenu jMenu3 = new JMenu();
 237
 238   JMenuItem showAllSeqs = new JMenuItem();
 239
 240   JMenuItem showAllColumns = new JMenuItem();
 241
 242   JMenu hideMenu = new JMenu();
 243
 244   JMenuItem hideSelSequences = new JMenuItem();
 245
 246   JMenuItem hideSelColumns = new JMenuItem();
 247
 248   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 249
 250   JMenuItem invertColSel = new JMenuItem();
 251
 252   protected JTabbedPane tabbedPane = new JTabbedPane();
 253
 254   JMenuItem save = new JMenuItem();
 255
 256   protected JMenuItem reload = new JMenuItem();
 257
 258   JMenuItem newView = new JMenuItem();
 259
 260   JMenuItem textColour = new JMenuItem();
 261
 262   JMenu formatMenu = new JMenu();
 263
 264   JMenu selectMenu = new JMenu();
 265
 266   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 267
 268   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 269
 270   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 271
 272   protected JMenuItem gatherViews = new JMenuItem();
 273
 274   protected JMenuItem expandViews = new JMenuItem();
 275
 276   JMenuItem pageSetup = new JMenuItem();
 277
 278   JMenuItem alignmentProperties = new JMenuItem();
 279
 280   JMenu tooltipSettingsMenu = new JMenu();
 281
 282   private JMenuItem justifyLeftMenuItem=new JMenuItem();
 283
 284   private JMenuItem justifyRightMenuItem=new JMenuItem();
 285
 286   public GAlignFrame()
 287   {
 288     try
 289     {
 290       jbInit();
 291       setJMenuBar(alignFrameMenuBar);
 292
 293       // dynamically fill save as menu with available formats
 294       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 295       {
 296         JMenuItem item = new JMenuItem(
 297                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 298
 299         item.addActionListener(new java.awt.event.ActionListener()
 300         {
 301           public void actionPerformed(ActionEvent e)
 302           {
 303             outputText_actionPerformed(e);
 304           }
 305         });
 306
 307         outputTextboxMenu.add(item);
 308       }
 309     } catch (Exception e)
 310     {
 311     }
 312
 313     if (!new jalview.util.Platform().isAMac())
 314     {
 315       closeMenuItem.setMnemonic('C');
 316       outputTextboxMenu.setMnemonic('T');
 317       undoMenuItem.setMnemonic('Z');
 318       redoMenuItem.setMnemonic('0');
 319       copy.setMnemonic('C');
 320       cut.setMnemonic('U');
 321       pasteMenu.setMnemonic('P');
 322       reload.setMnemonic('R');
 323     }
 324
 325     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 326     {
 327       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 328               .getUserColourSchemes().keys();
 329
 330       while (userColours.hasMoreElements())
 331       {
 332         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 333                 userColours.nextElement().toString());
 334         radioItem.setName("USER_DEFINED");
 335         radioItem.addMouseListener(new MouseAdapter()
 336         {
 337           public void mousePressed(MouseEvent evt)
 338           {
 339             if (evt.isControlDown()
 340                     || SwingUtilities.isRightMouseButton(evt))
 341             {
 342               radioItem
 343                       .removeActionListener(radioItem.getActionListeners()[0]);
 344
 345               int option = JOptionPane.showInternalConfirmDialog(
 346                       jalview.gui.Desktop.desktop,
 347                       "Remove from default list?",
 348                       "Remove user defined colour",
 349                       JOptionPane.YES_NO_OPTION);
 350               if (option == JOptionPane.YES_OPTION)
 351               {
 352                 jalview.gui.UserDefinedColours
 353                         .removeColourFromDefaults(radioItem.getText());
 354                 colourMenu.remove(radioItem);
 355               }
 356               else
 357               {
 358                 radioItem.addActionListener(new ActionListener()
 359                 {
 360                   public void actionPerformed(ActionEvent evt)
 361                   {
 362                     userDefinedColour_actionPerformed(evt);
 363                   }
 364                 });
 365               }
 366             }
 367           }
 368         });
 369         radioItem.addActionListener(new ActionListener()
 370         {
 371           public void actionPerformed(ActionEvent evt)
 372           {
 373             userDefinedColour_actionPerformed(evt);
 374           }
 375         });
 376         colourMenu.insert(radioItem, 15);
 377         colours.add(radioItem);
 378       }
 379     }
 380     colours.add(noColourmenuItem);
 381     colours.add(clustalColour);
 382     colours.add(zappoColour);
 383     colours.add(taylorColour);
 384     colours.add(hydrophobicityColour);
 385     colours.add(helixColour);
 386     colours.add(strandColour);
 387     colours.add(turnColour);
 388     colours.add(buriedColour);
 389     colours.add(userDefinedColour);
 390     colours.add(PIDColour);
 391     colours.add(BLOSUM62Colour);
 392     colours.add(nucleotideColour);
 393
 394     setColourSelected(jalview.bin.Cache
 395             .getDefault("DEFAULT_COLOUR", "None"));
 396
 397   }
 398
 399   public void setColourSelected(String defaultColour)
 400   {
 401
 402     if (defaultColour != null)
 403     {
 404       int index = ColourSchemeProperty
 405               .getColourIndexFromName(defaultColour);
 406
 407       switch (index)
 408       {
 409       case ColourSchemeProperty.NONE:
 410         noColourmenuItem.setSelected(true);
 411         break;
 412       case ColourSchemeProperty.CLUSTAL:
 413         clustalColour.setSelected(true);
 414
 415         break;
 416
 417       case ColourSchemeProperty.BLOSUM:
 418         BLOSUM62Colour.setSelected(true);
 419
 420         break;
 421
 422       case ColourSchemeProperty.PID:
 423         PIDColour.setSelected(true);
 424
 425         break;
 426
 427       case ColourSchemeProperty.ZAPPO:
 428         zappoColour.setSelected(true);
 429
 430         break;
 431
 432       case ColourSchemeProperty.TAYLOR:
 433         taylorColour.setSelected(true);
 434         break;
 435
 436       case ColourSchemeProperty.HYDROPHOBIC:
 437         hydrophobicityColour.setSelected(true);
 438
 439         break;
 440
 441       case ColourSchemeProperty.HELIX:
 442         helixColour.setSelected(true);
 443
 444         break;
 445
 446       case ColourSchemeProperty.STRAND:
 447         strandColour.setSelected(true);
 448
 449         break;
 450
 451       case ColourSchemeProperty.TURN:
 452         turnColour.setSelected(true);
 453
 454         break;
 455
 456       case ColourSchemeProperty.BURIED:
 457         buriedColour.setSelected(true);
 458
 459         break;
 460
 461       case ColourSchemeProperty.NUCLEOTIDE:
 462         nucleotideColour.setSelected(true);
 463
 464         break;
 465
 466       case ColourSchemeProperty.USER_DEFINED:
 467         userDefinedColour.setSelected(true);
 468
 469         break;
 470       }
 471     }
 472
 473   }
 474
 475   private void jbInit() throws Exception
 476   {
 477     fileMenu.setText("File");
 478     saveAs.setText("Save As...");
 479     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 480             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 481                     .getMenuShortcutKeyMask()
 482                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 483     saveAs.addActionListener(new ActionListener()
 484     {
 485       public void actionPerformed(ActionEvent e)
 486       {
 487         saveAs_actionPerformed(e);
 488       }
 489     });
 490     closeMenuItem.setText("Close");
 491     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 492             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 493                     .getMenuShortcutKeyMask(), false));
 494     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 495     {
 496       public void actionPerformed(ActionEvent e)
 497       {
 498         closeMenuItem_actionPerformed(false);
 499       }
 500     });
 501     editMenu.setText("Edit");
 502     viewMenu.setText("View");
 503     colourMenu.setText("Colour");
 504     calculateMenu.setText("Calculate");
 505     webService.setText("Web Service");
 506     selectAllSequenceMenuItem.setText("Select All");
 507     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 508             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 509                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 510     selectAllSequenceMenuItem
 511             .addActionListener(new java.awt.event.ActionListener()
 512             {
 513               public void actionPerformed(ActionEvent e)
 514               {
 515                 selectAllSequenceMenuItem_actionPerformed(e);
 516               }
 517             });
 518     deselectAllSequenceMenuItem.setText("Deselect All");
 519     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 520             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 521     deselectAllSequenceMenuItem
 522             .addActionListener(new java.awt.event.ActionListener()
 523             {
 524               public void actionPerformed(ActionEvent e)
 525               {
 526                 deselectAllSequenceMenuItem_actionPerformed(e);
 527               }
 528             });
 529     invertSequenceMenuItem.setText("Invert Sequence Selection");
 530     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 531             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 532                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 533     invertSequenceMenuItem
 534             .addActionListener(new java.awt.event.ActionListener()
 535             {
 536               public void actionPerformed(ActionEvent e)
 537               {
 538                 invertSequenceMenuItem_actionPerformed(e);
 539               }
 540             });
 541     remove2LeftMenuItem.setText("Remove Left");
 542     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 543             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 544                     .getMenuShortcutKeyMask(), false));
 545     remove2LeftMenuItem
 546             .addActionListener(new java.awt.event.ActionListener()
 547             {
 548               public void actionPerformed(ActionEvent e)
 549               {
 550                 remove2LeftMenuItem_actionPerformed(e);
 551               }
 552             });
 553     remove2RightMenuItem.setText("Remove Right");
 554     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 555             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 556                     .getMenuShortcutKeyMask(), false));
 557     remove2RightMenuItem
 558             .addActionListener(new java.awt.event.ActionListener()
 559             {
 560               public void actionPerformed(ActionEvent e)
 561               {
 562                 remove2RightMenuItem_actionPerformed(e);
 563               }
 564             });
 565     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 566     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 567             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 568                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 569     removeGappedColumnMenuItem
 570             .addActionListener(new java.awt.event.ActionListener()
 571             {
 572               public void actionPerformed(ActionEvent e)
 573               {
 574                 removeGappedColumnMenuItem_actionPerformed(e);
 575               }
 576             });
 577     removeAllGapsMenuItem.setText("Remove All Gaps");
 578     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 579             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 580                     .getDefaultToolkit().getMenuShortcutKeyMask()
 581                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 582     removeAllGapsMenuItem
 583             .addActionListener(new java.awt.event.ActionListener()
 584             {
 585               public void actionPerformed(ActionEvent e)
 586               {
 587                 removeAllGapsMenuItem_actionPerformed(e);
 588               }
 589             });
 590     justifyLeftMenuItem.setText("Left Justify Alignment");
 591     justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 592     {
 593         public void actionPerformed(ActionEvent e)
 594         {
 595           justifyLeftMenuItem_actionPerformed(e);
 596         }
 597     });
 598     justifyRightMenuItem.setText("Right Justify Alignment");
 599     justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
 600     {
 601         public void actionPerformed(ActionEvent e)
 602         {
 603           justifyRightMenuItem_actionPerformed(e);
 604         }
 605     });
 606     viewBoxesMenuItem.setText("Boxes");
 607     viewBoxesMenuItem.setState(true);
 608     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 609     {
 610       public void actionPerformed(ActionEvent e)
 611       {
 612         viewBoxesMenuItem_actionPerformed(e);
 613       }
 614     });
 615     viewTextMenuItem.setText("Text");
 616     viewTextMenuItem.setState(true);
 617     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 618     {
 619       public void actionPerformed(ActionEvent e)
 620       {
 621         viewTextMenuItem_actionPerformed(e);
 622       }
 623     });
 624     sortPairwiseMenuItem.setText("by Pairwise Identity");
 625     sortPairwiseMenuItem
 626             .addActionListener(new java.awt.event.ActionListener()
 627             {
 628               public void actionPerformed(ActionEvent e)
 629               {
 630                 sortPairwiseMenuItem_actionPerformed(e);
 631               }
 632             });
 633     sortIDMenuItem.setText("by ID");
 634     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 635     {
 636       public void actionPerformed(ActionEvent e)
 637       {
 638         sortIDMenuItem_actionPerformed(e);
 639       }
 640     });
 641     sortLengthMenuItem.setText("By Length");
 642     sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
 643     {
 644       public void actionPerformed(ActionEvent e)
 645       {
 646         sortLengthMenuItem_actionPerformed(e);
 647       }
 648     });
 649     sortGroupMenuItem.setText("by Group");
 650     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 651     {
 652       public void actionPerformed(ActionEvent e)
 653       {
 654         sortGroupMenuItem_actionPerformed(e);
 655       }
 656     });
 657     removeRedundancyMenuItem.setText("Remove Redundancy...");
 658     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 659             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 660                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 661     removeRedundancyMenuItem
 662             .addActionListener(new java.awt.event.ActionListener()
 663             {
 664               public void actionPerformed(ActionEvent e)
 665               {
 666                 removeRedundancyMenuItem_actionPerformed(e);
 667               }
 668             });
 669     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 670     pairwiseAlignmentMenuItem
 671             .addActionListener(new java.awt.event.ActionListener()
 672             {
 673               public void actionPerformed(ActionEvent e)
 674               {
 675                 pairwiseAlignmentMenuItem_actionPerformed(e);
 676               }
 677             });
 678     PCAMenuItem.setText("Principal Component Analysis");
 679     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 680     {
 681       public void actionPerformed(ActionEvent e)
 682       {
 683         PCAMenuItem_actionPerformed(e);
 684       }
 685     });
 686     averageDistanceTreeMenuItem
 687             .setText("Average Distance Using % Identity");
 688     averageDistanceTreeMenuItem
 689             .addActionListener(new java.awt.event.ActionListener()
 690             {
 691               public void actionPerformed(ActionEvent e)
 692               {
 693                 averageDistanceTreeMenuItem_actionPerformed(e);
 694               }
 695             });
 696     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 697     neighbourTreeMenuItem
 698             .addActionListener(new java.awt.event.ActionListener()
 699             {
 700               public void actionPerformed(ActionEvent e)
 701               {
 702                 neighbourTreeMenuItem_actionPerformed(e);
 703               }
 704             });
 705     this.getContentPane().setLayout(borderLayout1);
 706     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 707     statusBar.setBackground(Color.white);
 708     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 709     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 710     statusBar.setText("Status bar");
 711     outputTextboxMenu.setText("Output to Textbox");
 712     clustalColour.setText("Clustalx");
 713
 714     clustalColour.addActionListener(new java.awt.event.ActionListener()
 715     {
 716       public void actionPerformed(ActionEvent e)
 717       {
 718         clustalColour_actionPerformed(e);
 719       }
 720     });
 721     zappoColour.setText("Zappo");
 722     zappoColour.addActionListener(new java.awt.event.ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         zappoColour_actionPerformed(e);
 727       }
 728     });
 729     taylorColour.setText("Taylor");
 730     taylorColour.addActionListener(new java.awt.event.ActionListener()
 731     {
 732       public void actionPerformed(ActionEvent e)
 733       {
 734         taylorColour_actionPerformed(e);
 735       }
 736     });
 737     hydrophobicityColour.setText("Hydrophobicity");
 738     hydrophobicityColour
 739             .addActionListener(new java.awt.event.ActionListener()
 740             {
 741               public void actionPerformed(ActionEvent e)
 742               {
 743                 hydrophobicityColour_actionPerformed(e);
 744               }
 745             });
 746     helixColour.setText("Helix Propensity");
 747     helixColour.addActionListener(new java.awt.event.ActionListener()
 748     {
 749       public void actionPerformed(ActionEvent e)
 750       {
 751         helixColour_actionPerformed(e);
 752       }
 753     });
 754     strandColour.setText("Strand Propensity");
 755     strandColour.addActionListener(new java.awt.event.ActionListener()
 756     {
 757       public void actionPerformed(ActionEvent e)
 758       {
 759         strandColour_actionPerformed(e);
 760       }
 761     });
 762     turnColour.setText("Turn Propensity");
 763     turnColour.addActionListener(new java.awt.event.ActionListener()
 764     {
 765       public void actionPerformed(ActionEvent e)
 766       {
 767         turnColour_actionPerformed(e);
 768       }
 769     });
 770     buriedColour.setText("Buried Index");
 771     buriedColour.addActionListener(new java.awt.event.ActionListener()
 772     {
 773       public void actionPerformed(ActionEvent e)
 774       {
 775         buriedColour_actionPerformed(e);
 776       }
 777     });
 778     userDefinedColour.setText("User Defined...");
 779     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 780     {
 781       public void actionPerformed(ActionEvent e)
 782       {
 783         userDefinedColour_actionPerformed(e);
 784       }
 785     });
 786     PIDColour.setText("Percentage Identity");
 787     PIDColour.addActionListener(new java.awt.event.ActionListener()
 788     {
 789       public void actionPerformed(ActionEvent e)
 790       {
 791         PIDColour_actionPerformed(e);
 792       }
 793     });
 794     BLOSUM62Colour.setText("BLOSUM62 Score");
 795     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 796     {
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         BLOSUM62Colour_actionPerformed(e);
 800       }
 801     });
 802     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 803     avDistanceTreeBlosumMenuItem
 804             .addActionListener(new java.awt.event.ActionListener()
 805             {
 806               public void actionPerformed(ActionEvent e)
 807               {
 808                 avTreeBlosumMenuItem_actionPerformed(e);
 809               }
 810             });
 811     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 812     njTreeBlosumMenuItem
 813             .addActionListener(new java.awt.event.ActionListener()
 814             {
 815               public void actionPerformed(ActionEvent e)
 816               {
 817                 njTreeBlosumMenuItem_actionPerformed(e);
 818               }
 819             });
 820     annotationPanelMenuItem.setActionCommand("");
 821     annotationPanelMenuItem.setText("Show Annotations");
 822     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 823             "SHOW_ANNOTATIONS", true));
 824     annotationPanelMenuItem
 825             .addActionListener(new java.awt.event.ActionListener()
 826             {
 827               public void actionPerformed(ActionEvent e)
 828               {
 829                 annotationPanelMenuItem_actionPerformed(e);
 830               }
 831             });
 832     colourTextMenuItem.setText("Colour Text");
 833     colourTextMenuItem
 834             .addActionListener(new java.awt.event.ActionListener()
 835             {
 836               public void actionPerformed(ActionEvent e)
 837               {
 838                 colourTextMenuItem_actionPerformed(e);
 839               }
 840             });
 841     htmlMenuItem.setText("HTML");
 842     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 843     {
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         htmlMenuItem_actionPerformed(e);
 847       }
 848     });
 849     overviewMenuItem.setText("Overview Window");
 850     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 851     {
 852       public void actionPerformed(ActionEvent e)
 853       {
 854         overviewMenuItem_actionPerformed(e);
 855       }
 856     });
 857     undoMenuItem.setEnabled(false);
 858     undoMenuItem.setText("Undo");
 859     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 860             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 861                     .getMenuShortcutKeyMask(), false));
 862     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 863     {
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         undoMenuItem_actionPerformed(e);
 867       }
 868     });
 869     redoMenuItem.setEnabled(false);
 870     redoMenuItem.setText("Redo");
 871     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 872             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 873                     .getMenuShortcutKeyMask(), false));
 874     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 875     {
 876       public void actionPerformed(ActionEvent e)
 877       {
 878         redoMenuItem_actionPerformed(e);
 879       }
 880     });
 881     conservationMenuItem.setText("By Conservation");
 882     conservationMenuItem
 883             .addActionListener(new java.awt.event.ActionListener()
 884             {
 885               public void actionPerformed(ActionEvent e)
 886               {
 887                 conservationMenuItem_actionPerformed(e);
 888               }
 889             });
 890     noColourmenuItem.setText("None");
 891     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 892     {
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         noColourmenuItem_actionPerformed(e);
 896       }
 897     });
 898     wrapMenuItem.setText("Wrap");
 899     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 900     {
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         wrapMenuItem_actionPerformed(e);
 904       }
 905     });
 906     printMenuItem.setText("Print ...");
 907     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 908             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 909                     .getMenuShortcutKeyMask(), false));
 910     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 911     {
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         printMenuItem_actionPerformed(e);
 915       }
 916     });
 917     renderGapsMenuItem.setText("Show Gaps");
 918     renderGapsMenuItem.setState(true);
 919     renderGapsMenuItem
 920             .addActionListener(new java.awt.event.ActionListener()
 921             {
 922               public void actionPerformed(ActionEvent e)
 923               {
 924                 renderGapsMenuItem_actionPerformed(e);
 925               }
 926             });
 927     findMenuItem.setText("Find...");
 928     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 929             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 930                     .getMenuShortcutKeyMask(), false));
 931     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 932     {
 933       public void actionPerformed(ActionEvent e)
 934       {
 935         findMenuItem_actionPerformed(e);
 936       }
 937     });
 938     abovePIDThreshold.setText("Above Identity Threshold");
 939     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 940     {
 941       public void actionPerformed(ActionEvent e)
 942       {
 943         abovePIDThreshold_actionPerformed(e);
 944       }
 945     });
 946     showSeqFeatures.setText("Show Sequence Features");
 947     showSeqFeatures.addActionListener(new ActionListener()
 948     {
 949       public void actionPerformed(ActionEvent actionEvent)
 950       {
 951         showSeqFeatures_actionPerformed(actionEvent);
 952       }
 953     });
 954     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 955     showSeqFeaturesHeight.addActionListener(new ActionListener()
 956     {
 957       public void actionPerformed(ActionEvent actionEvent)
 958       {
 959         showSeqFeaturesHeight_actionPerformed(actionEvent);
 960       }
 961     });
 962     showDbRefsMenuitem.setText("Show Database Refs");
 963     showDbRefsMenuitem.addActionListener(new ActionListener()
 964     {
 965
 966       public void actionPerformed(ActionEvent e)
 967       {
 968         showDbRefs_actionPerformed(e);
 969       }
 970
 971     });
 972     showNpFeatsMenuitem.setText("Show Non-Positional Features");
 973     showNpFeatsMenuitem.addActionListener(new ActionListener()
 974     {
 975
 976       public void actionPerformed(ActionEvent e)
 977       {
 978         showNpFeats_actionPerformed(e);
 979       }
 980
 981     });
 982     nucleotideColour.setText("Nucleotide");
 983     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 984     {
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         nucleotideColour_actionPerformed(e);
 988       }
 989     });
 990     deleteGroups.setText("Undefine groups");
 991     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 992             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
 993                     .getMenuShortcutKeyMask(), false));
 994     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 995     {
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         deleteGroups_actionPerformed(e);
 999       }
1000     });
1001     copy.setText("Copy");
1002     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1003             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1004                     .getMenuShortcutKeyMask(), false));
1005
1006     copy.addActionListener(new java.awt.event.ActionListener()
1007     {
1008       public void actionPerformed(ActionEvent e)
1009       {
1010         copy_actionPerformed(e);
1011       }
1012     });
1013     cut.setText("Cut");
1014     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1015             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1016                     .getMenuShortcutKeyMask(), false));
1017     cut.addActionListener(new java.awt.event.ActionListener()
1018     {
1019       public void actionPerformed(ActionEvent e)
1020       {
1021         cut_actionPerformed(e);
1022       }
1023     });
1024     delete.setText("Delete");
1025     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1026             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1027     delete.addActionListener(new java.awt.event.ActionListener()
1028     {
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         delete_actionPerformed(e);
1032       }
1033     });
1034     pasteMenu.setText("Paste");
1035     pasteNew.setText("To New Alignment");
1036     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1037             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1038                     .getMenuShortcutKeyMask()
1039                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1040     pasteNew.addActionListener(new java.awt.event.ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         pasteNew_actionPerformed(e);
1045       }
1046     });
1047     pasteThis.setText("Add To This Alignment");
1048     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1050                     .getMenuShortcutKeyMask(), false));
1051     pasteThis.addActionListener(new java.awt.event.ActionListener()
1052     {
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         pasteThis_actionPerformed(e);
1056       }
1057     });
1058     applyToAllGroups.setText("Apply Colour To All Groups");
1059     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1060     {
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         applyToAllGroups_actionPerformed(e);
1064       }
1065     });
1066     createPNG.addActionListener(new java.awt.event.ActionListener()
1067     {
1068       public void actionPerformed(ActionEvent e)
1069       {
1070         createPNG(null);
1071       }
1072     });
1073     createPNG.setActionCommand("Save As PNG Image");
1074     createPNG.setText("PNG");
1075     font.setText("Font...");
1076     font.addActionListener(new java.awt.event.ActionListener()
1077     {
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         font_actionPerformed(e);
1081       }
1082     });
1083
1084     seqLimits.setText("Show Sequence Limits");
1085     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1086     seqLimits.addActionListener(new java.awt.event.ActionListener()
1087     {
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         seqLimit_actionPerformed(e);
1091       }
1092     });
1093     epsFile.setText("EPS");
1094     epsFile.addActionListener(new java.awt.event.ActionListener()
1095     {
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         createEPS(null);
1099       }
1100     });
1101     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1102     LoadtreeMenuItem.setText("Load Associated Tree");
1103     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1104     {
1105       public void actionPerformed(ActionEvent e)
1106       {
1107         LoadtreeMenuItem_actionPerformed(e);
1108       }
1109     });
1110     scaleAbove.setVisible(false);
1111     scaleAbove.setText("Scale Above");
1112     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         scaleAbove_actionPerformed(e);
1117       }
1118     });
1119     scaleLeft.setVisible(false);
1120     scaleLeft.setSelected(true);
1121     scaleLeft.setText("Scale Left");
1122     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1123     {
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         scaleLeft_actionPerformed(e);
1127       }
1128     });
1129     scaleRight.setVisible(false);
1130     scaleRight.setSelected(true);
1131     scaleRight.setText("Scale Right");
1132     scaleRight.addActionListener(new java.awt.event.ActionListener()
1133     {
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         scaleRight_actionPerformed(e);
1137       }
1138     });
1139     centreColumnLabelsMenuItem.setVisible(true);
1140     centreColumnLabelsMenuItem.setState(false);
1141     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1142     centreColumnLabelsMenuItem
1143             .addActionListener(new java.awt.event.ActionListener()
1144             {
1145               public void actionPerformed(ActionEvent e)
1146               {
1147                 centreColumnLabels_actionPerformed(e);
1148               }
1149             });
1150     followHighlightMenuItem.setVisible(true);
1151     followHighlightMenuItem.setState(true);
1152     followHighlightMenuItem.setText("Automatic Scrolling");
1153     followHighlightMenuItem.addActionListener(new ActionListener()
1154     {
1155
1156       public void actionPerformed(ActionEvent e)
1157       {
1158         followHighlight_actionPerformed();
1159       }
1160
1161     });
1162
1163     modifyPID.setText("Modify Identity Threshold...");
1164     modifyPID.addActionListener(new java.awt.event.ActionListener()
1165     {
1166       public void actionPerformed(ActionEvent e)
1167       {
1168         modifyPID_actionPerformed(e);
1169       }
1170     });
1171     modifyConservation.setText("Modify Conservation Threshold...");
1172     modifyConservation
1173             .addActionListener(new java.awt.event.ActionListener()
1174             {
1175               public void actionPerformed(ActionEvent e)
1176               {
1177                 modifyConservation_actionPerformed(e);
1178               }
1179             });
1180     sortByTreeMenu.setText("By Tree Order");
1181     sort.setText("Sort");
1182     sort.addMenuListener(new MenuListener()
1183     {
1184       public void menuSelected(MenuEvent e)
1185       {
1186         buildTreeMenu();
1187       }
1188
1189       public void menuDeselected(MenuEvent e)
1190       {
1191       }
1192
1193       public void menuCanceled(MenuEvent e)
1194       {
1195       }
1196     });
1197     sortByAnnotScore.setText("by Score");
1198     sort.add(sortByAnnotScore);
1199     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1200     {
1201
1202       public void menuCanceled(MenuEvent e)
1203       {
1204       }
1205
1206       public void menuDeselected(MenuEvent e)
1207       {
1208       }
1209
1210       public void menuSelected(MenuEvent e)
1211       {
1212         buildSortByAnnotationScoresMenu();
1213       }
1214     });
1215     sortByAnnotScore.setVisible(false);
1216
1217     calculateTree.setText("Calculate Tree");
1218
1219     jMenu2.setText("Export Image");
1220     padGapsMenuitem.setText("Pad Gaps");
1221     padGapsMenuitem.setState(jalview.bin.Cache
1222             .getDefault("PAD_GAPS", false));
1223     padGapsMenuitem.addActionListener(new ActionListener()
1224     {
1225       public void actionPerformed(ActionEvent e)
1226       {
1227         padGapsMenuitem_actionPerformed(e);
1228       }
1229     });
1230     vamsasStore.setVisible(false);
1231     vamsasStore.setText("VAMSAS store");
1232     vamsasStore.addActionListener(new ActionListener()
1233     {
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         vamsasStore_actionPerformed(e);
1237       }
1238     });
1239     showTranslation.setText("Translate cDNA");
1240     showTranslation.addActionListener(new ActionListener()
1241     {
1242       public void actionPerformed(ActionEvent e)
1243       {
1244         showTranslation_actionPerformed(e);
1245       }
1246     });
1247     extractScores.setText("Extract Scores...");
1248     extractScores.addActionListener(new ActionListener()
1249     {
1250       public void actionPerformed(ActionEvent e)
1251       {
1252         extractScores_actionPerformed(e);
1253       }
1254     });
1255     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1256                                     // score extraction
1257     showProducts.setText("Get Cross References");
1258     /*
1259      * showProducts.addActionListener(new ActionListener() {
1260      *
1261      * public void actionPerformed(ActionEvent e) {
1262      * showProducts_actionPerformed(e); } });
1263      */
1264     featureSettings.setText("Feature Settings...");
1265     featureSettings.addActionListener(new ActionListener()
1266     {
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         featureSettings_actionPerformed(e);
1270       }
1271     });
1272     fetchSequence.setText("Fetch Sequence(s)...");
1273     fetchSequence.addActionListener(new ActionListener()
1274     {
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         fetchSequence_actionPerformed(e);
1278       }
1279     });
1280
1281     annotationColour.setText("By Annotation...");
1282     annotationColour.addActionListener(new ActionListener()
1283     {
1284       public void actionPerformed(ActionEvent e)
1285       {
1286         annotationColour_actionPerformed(e);
1287       }
1288     });
1289     associatedData.setText("Load Features / Annotations");
1290     associatedData.addActionListener(new ActionListener()
1291     {
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         associatedData_actionPerformed(e);
1295       }
1296     });
1297     autoCalculate.setText("Autocalculate Consensus");
1298     autoCalculate.setState(jalview.bin.Cache.getDefault(
1299             "AUTO_CALC_CONSENSUS", true));
1300     autoCalculate.addActionListener(new ActionListener()
1301     {
1302       public void actionPerformed(ActionEvent e)
1303       {
1304         autoCalculate_actionPerformed(e);
1305       }
1306     });
1307     addSequenceMenu.setText("Add Sequences");
1308     addFromFile.setText("From File");
1309     addFromFile.addActionListener(new ActionListener()
1310     {
1311       public void actionPerformed(ActionEvent e)
1312       {
1313         addFromFile_actionPerformed(e);
1314       }
1315     });
1316     addFromText.setText("From Textbox");
1317     addFromText.addActionListener(new ActionListener()
1318     {
1319       public void actionPerformed(ActionEvent e)
1320       {
1321         addFromText_actionPerformed(e);
1322       }
1323     });
1324     addFromURL.setText("From URL");
1325     addFromURL.addActionListener(new ActionListener()
1326     {
1327       public void actionPerformed(ActionEvent e)
1328       {
1329         addFromURL_actionPerformed(e);
1330       }
1331     });
1332     exportFeatures.setText("Export Features...");
1333     exportFeatures.addActionListener(new ActionListener()
1334     {
1335       public void actionPerformed(ActionEvent e)
1336       {
1337         exportFeatures_actionPerformed(e);
1338       }
1339     });
1340     exportAnnotations.setText("Export Annotations...");
1341     exportAnnotations.addActionListener(new ActionListener()
1342     {
1343       public void actionPerformed(ActionEvent e)
1344       {
1345         exportAnnotations_actionPerformed(e);
1346       }
1347     });
1348     statusPanel.setLayout(gridLayout1);
1349     jMenu3.setText("Show");
1350     showAllSeqs.setText("All Sequences");
1351     showAllSeqs.addActionListener(new ActionListener()
1352     {
1353       public void actionPerformed(ActionEvent e)
1354       {
1355         showAllSeqs_actionPerformed(e);
1356       }
1357     });
1358     showAllColumns.setText("All Columns");
1359     showAllColumns.addActionListener(new ActionListener()
1360     {
1361       public void actionPerformed(ActionEvent e)
1362       {
1363         showAllColumns_actionPerformed(e);
1364       }
1365     });
1366     hideMenu.setText("Hide");
1367     hideSelSequences.setText("Selected Sequences");
1368     hideSelSequences.addActionListener(new ActionListener()
1369     {
1370       public void actionPerformed(ActionEvent e)
1371       {
1372         hideSelSequences_actionPerformed(e);
1373       }
1374     });
1375     hideSelColumns.setText("Selected Columns");
1376     hideSelColumns.addActionListener(new ActionListener()
1377     {
1378       public void actionPerformed(ActionEvent e)
1379       {
1380         hideSelColumns_actionPerformed(e);
1381       }
1382     });
1383     hiddenMarkers.setText("Show Hidden Markers");
1384     hiddenMarkers.addActionListener(new ActionListener()
1385     {
1386       public void actionPerformed(ActionEvent e)
1387       {
1388         hiddenMarkers_actionPerformed(e);
1389       }
1390     });
1391     invertColSel.setText("Invert Column Selection");
1392     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1393             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1394                     .getMenuShortcutKeyMask()
1395                     | java.awt.event.KeyEvent.ALT_MASK, false));
1396     invertColSel.addActionListener(new ActionListener()
1397     {
1398       public void actionPerformed(ActionEvent e)
1399       {
1400         invertColSel_actionPerformed(e);
1401       }
1402     });
1403     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1404     {
1405       public void stateChanged(ChangeEvent evt)
1406       {
1407         JTabbedPane pane = (JTabbedPane) evt.getSource();
1408         int sel = pane.getSelectedIndex();
1409         tabSelectionChanged(sel);
1410       }
1411     });
1412     tabbedPane.addMouseListener(new MouseAdapter()
1413     {
1414       public void mousePressed(MouseEvent e)
1415       {
1416         tabbedPane_mousePressed(e);
1417       }
1418     });
1419     tabbedPane.addFocusListener(new FocusAdapter()
1420     {
1421       public void focusGained(FocusEvent e)
1422       {
1423         tabbedPane_focusGained(e);
1424       }
1425     });
1426     save.setText("Save");
1427     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1428             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1429                     .getMenuShortcutKeyMask(), false));
1430     save.addActionListener(new ActionListener()
1431     {
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         save_actionPerformed(e);
1435       }
1436     });
1437     reload.setEnabled(false);
1438     reload.setText("Reload");
1439     reload.addActionListener(new ActionListener()
1440     {
1441       public void actionPerformed(ActionEvent e)
1442       {
1443         reload_actionPerformed(e);
1444       }
1445     });
1446     newView.setText("New View");
1447     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1448             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1449                     .getMenuShortcutKeyMask(), false));
1450     newView.addActionListener(new ActionListener()
1451     {
1452       public void actionPerformed(ActionEvent e)
1453       {
1454         newView_actionPerformed(e);
1455       }
1456     });
1457     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1458             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1459     textColour.setText("Colour Text ...");
1460     textColour.addActionListener(new ActionListener()
1461     {
1462       public void actionPerformed(ActionEvent e)
1463       {
1464         textColour_actionPerformed(e);
1465       }
1466     });
1467     formatMenu.setText("Format");
1468     selectMenu.setText("Select");
1469     idRightAlign.setText("Right Align Sequence Id");
1470     idRightAlign.addActionListener(new ActionListener()
1471     {
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         idRightAlign_actionPerformed(e);
1475       }
1476     });
1477     gatherViews.setEnabled(false);
1478     gatherViews.setText("Gather Views");
1479     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1480             java.awt.event.KeyEvent.VK_G, 0, false));
1481     gatherViews.addActionListener(new ActionListener()
1482     {
1483       public void actionPerformed(ActionEvent e)
1484       {
1485         gatherViews_actionPerformed(e);
1486       }
1487     });
1488     expandViews.setEnabled(false);
1489     expandViews.setText("Expand Views");
1490     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1491             java.awt.event.KeyEvent.VK_X, 0, false));
1492     expandViews.addActionListener(new ActionListener()
1493     {
1494       public void actionPerformed(ActionEvent e)
1495       {
1496         expandViews_actionPerformed(e);
1497       }
1498     });
1499     pageSetup.setText("Page Setup ...");
1500     pageSetup.addActionListener(new ActionListener()
1501     {
1502       public void actionPerformed(ActionEvent e)
1503       {
1504         pageSetup_actionPerformed(e);
1505       }
1506     });
1507     alignmentProperties.setText("Alignment Properties...");
1508     alignmentProperties.addActionListener(new ActionListener()
1509     {
1510       public void actionPerformed(ActionEvent actionEvent)
1511       {
1512         alignmentProperties();
1513       }
1514     });
1515     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1516     alignFrameMenuBar.add(fileMenu);
1517     alignFrameMenuBar.add(editMenu);
1518     alignFrameMenuBar.add(selectMenu);
1519     alignFrameMenuBar.add(viewMenu);
1520     alignFrameMenuBar.add(formatMenu);
1521     alignFrameMenuBar.add(colourMenu);
1522     alignFrameMenuBar.add(calculateMenu);
1523     alignFrameMenuBar.add(webService);
1524     fileMenu.add(fetchSequence);
1525     fileMenu.add(addSequenceMenu);
1526     fileMenu.add(reload);
1527     fileMenu.addSeparator();
1528     fileMenu.add(vamsasStore);
1529     fileMenu.add(save);
1530     fileMenu.add(saveAs);
1531     fileMenu.add(outputTextboxMenu);
1532     fileMenu.add(pageSetup);
1533     fileMenu.add(printMenuItem);
1534     fileMenu.addSeparator();
1535     fileMenu.add(jMenu2);
1536     fileMenu.add(exportFeatures);
1537     fileMenu.add(exportAnnotations);
1538     fileMenu.add(LoadtreeMenuItem);
1539     fileMenu.add(associatedData);
1540     fileMenu.addSeparator();
1541     fileMenu.add(closeMenuItem);
1542     editMenu.add(undoMenuItem);
1543     editMenu.add(redoMenuItem);
1544     editMenu.add(cut);
1545     editMenu.add(copy);
1546     editMenu.add(pasteMenu);
1547     editMenu.add(delete);
1548     editMenu.addSeparator();
1549     editMenu.add(remove2LeftMenuItem);
1550     editMenu.add(remove2RightMenuItem);
1551     editMenu.add(removeGappedColumnMenuItem);
1552     editMenu.add(removeAllGapsMenuItem);
1553     editMenu.add(removeRedundancyMenuItem);
1554     editMenu.addSeparator();
1555     // dont add these yet - they cannot be undone!
1556     //editMenu.add(justifyLeftMenuItem);
1557     //editMenu.add(justifyRightMenuItem);
1558     editMenu.addSeparator();
1559     editMenu.add(padGapsMenuitem);
1560     viewMenu.add(newView);
1561     viewMenu.add(expandViews);
1562     viewMenu.add(gatherViews);
1563     viewMenu.addSeparator();
1564     viewMenu.add(jMenu3);
1565     viewMenu.add(hideMenu);
1566     viewMenu.addSeparator();
1567     viewMenu.add(followHighlightMenuItem);
1568     viewMenu.add(annotationPanelMenuItem);
1569     viewMenu.addSeparator();
1570     viewMenu.add(showSeqFeatures);
1571     viewMenu.add(showSeqFeaturesHeight);
1572
1573     viewMenu.add(featureSettings);
1574     tooltipSettingsMenu.add(showDbRefsMenuitem);
1575     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1576     viewMenu.add(tooltipSettingsMenu);
1577     viewMenu.addSeparator();
1578     viewMenu.add(alignmentProperties);
1579     viewMenu.addSeparator();
1580     viewMenu.add(overviewMenuItem);
1581     colourMenu.add(applyToAllGroups);
1582     colourMenu.add(textColour);
1583     colourMenu.addSeparator();
1584     colourMenu.add(noColourmenuItem);
1585     colourMenu.add(clustalColour);
1586     colourMenu.add(BLOSUM62Colour);
1587     colourMenu.add(PIDColour);
1588     colourMenu.add(zappoColour);
1589     colourMenu.add(taylorColour);
1590     colourMenu.add(hydrophobicityColour);
1591     colourMenu.add(helixColour);
1592     colourMenu.add(strandColour);
1593     colourMenu.add(turnColour);
1594     colourMenu.add(buriedColour);
1595     colourMenu.add(nucleotideColour);
1596     colourMenu.add(userDefinedColour);
1597     colourMenu.addSeparator();
1598     colourMenu.add(conservationMenuItem);
1599     colourMenu.add(modifyConservation);
1600     colourMenu.add(abovePIDThreshold);
1601     colourMenu.add(modifyPID);
1602     colourMenu.add(annotationColour);
1603     calculateMenu.add(sort);
1604     calculateMenu.add(calculateTree);
1605     calculateMenu.addSeparator();
1606     calculateMenu.add(pairwiseAlignmentMenuItem);
1607     calculateMenu.add(PCAMenuItem);
1608     calculateMenu.addSeparator();
1609     calculateMenu.add(showTranslation);
1610     calculateMenu.add(showProducts);
1611     calculateMenu.add(autoCalculate);
1612     calculateMenu.addSeparator();
1613     calculateMenu.add(extractScores);
1614     webServiceNoServices = new JMenuItem("<No Services>");
1615     webService.add(webServiceNoServices);
1616     pasteMenu.add(pasteNew);
1617     pasteMenu.add(pasteThis);
1618     sort.add(sortIDMenuItem);
1619     sort.add(sortLengthMenuItem);
1620     sort.add(sortGroupMenuItem);
1621     sort.add(sortPairwiseMenuItem);
1622     sort.add(sortByTreeMenu);
1623     calculateTree.add(averageDistanceTreeMenuItem);
1624     calculateTree.add(neighbourTreeMenuItem);
1625     calculateTree.add(avDistanceTreeBlosumMenuItem);
1626     calculateTree.add(njTreeBlosumMenuItem);
1627     jMenu2.add(htmlMenuItem);
1628     jMenu2.add(epsFile);
1629     jMenu2.add(createPNG);
1630     addSequenceMenu.add(addFromFile);
1631     addSequenceMenu.add(addFromText);
1632     addSequenceMenu.add(addFromURL);
1633     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1634     statusPanel.add(statusBar, null);
1635     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1636     jMenu3.add(showAllColumns);
1637     jMenu3.add(showAllSeqs);
1638     hideMenu.add(hideSelColumns);
1639     hideMenu.add(hideSelSequences);
1640     formatMenu.add(font);
1641     formatMenu.addSeparator();
1642     formatMenu.add(wrapMenuItem);
1643     formatMenu.add(scaleAbove);
1644     formatMenu.add(scaleLeft);
1645     formatMenu.add(scaleRight);
1646     formatMenu.add(seqLimits);
1647     formatMenu.add(idRightAlign);
1648     formatMenu.add(hiddenMarkers);
1649     formatMenu.add(viewBoxesMenuItem);
1650     formatMenu.add(viewTextMenuItem);
1651     formatMenu.add(colourTextMenuItem);
1652     formatMenu.add(renderGapsMenuItem);
1653     formatMenu.add(centreColumnLabelsMenuItem);
1654     selectMenu.add(findMenuItem);
1655     selectMenu.addSeparator();
1656     selectMenu.add(selectAllSequenceMenuItem);
1657     selectMenu.add(deselectAllSequenceMenuItem);
1658     selectMenu.add(invertSequenceMenuItem);
1659     selectMenu.add(invertColSel);
1660     selectMenu.add(deleteGroups);
1661   }
1662
1663   protected void showSeqFeaturesHeight_actionPerformed(
1664           ActionEvent actionEvent)
1665   {
1666     // TODO Auto-generated method stub
1667
1668   }
1669
1670   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1671   {
1672     // TODO Auto-generated method stub
1673
1674   }
1675
1676   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1677   {
1678     // TODO Auto-generated method stub
1679
1680   }
1681
1682   protected void followHighlight_actionPerformed()
1683   {
1684     // TODO Auto-generated method stub
1685
1686   }
1687
1688   protected void showNpFeats_actionPerformed(ActionEvent e)
1689   {
1690     // TODO Auto-generated method stub
1691
1692   }
1693
1694   protected void showDbRefs_actionPerformed(ActionEvent e)
1695   {
1696     // TODO Auto-generated method stub
1697
1698   }
1699
1700   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1701   {
1702   }
1703
1704   protected void showProducts_actionPerformed(ActionEvent e)
1705   {
1706   }
1707
1708   protected void buildSortByAnnotationScoresMenu()
1709   {
1710   }
1711
1712   protected void extractScores_actionPerformed(ActionEvent e)
1713   {
1714   }
1715
1716   protected void outputText_actionPerformed(ActionEvent e)
1717   {
1718   }
1719
1720   public void addFromFile_actionPerformed(ActionEvent e)
1721   {
1722
1723   }
1724
1725   public void addFromText_actionPerformed(ActionEvent e)
1726   {
1727
1728   }
1729
1730   public void addFromURL_actionPerformed(ActionEvent e)
1731   {
1732
1733   }
1734
1735   public void exportFeatures_actionPerformed(ActionEvent e)
1736   {
1737
1738   }
1739
1740   public void exportAnnotations_actionPerformed(ActionEvent e)
1741   {
1742
1743   }
1744
1745   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1746   {
1747   }
1748
1749   protected void closeMenuItem_actionPerformed(boolean b)
1750   {
1751   }
1752
1753   protected void redoMenuItem_actionPerformed(ActionEvent e)
1754   {
1755   }
1756
1757   protected void undoMenuItem_actionPerformed(ActionEvent e)
1758   {
1759   }
1760
1761   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1762   {
1763   }
1764
1765   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1766   {
1767   }
1768
1769   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1770   {
1771   }
1772
1773   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1774   {
1775   }
1776
1777   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1778   {
1779   }
1780
1781   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1782   {
1783   }
1784
1785   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1786   {
1787   }
1788
1789   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1790   {
1791   }
1792
1793   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1794   {
1795   }
1796
1797   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1798   {
1799   }
1800
1801   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1802   {
1803   }
1804
1805   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1806   {
1807   }
1808
1809   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1810   {
1811   }
1812
1813   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1814   {
1815   }
1816
1817   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1818   {
1819   }
1820
1821   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1822   {
1823   }
1824
1825   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1826   {
1827   }
1828
1829   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1830   {
1831   }
1832
1833   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1834   {
1835   }
1836
1837   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1838   {
1839   }
1840
1841   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1842   {
1843   }
1844
1845   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1846   {
1847   }
1848
1849   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1850   {
1851   }
1852
1853   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1854   {
1855   }
1856
1857   protected void clustalColour_actionPerformed(ActionEvent e)
1858   {
1859   }
1860
1861   protected void zappoColour_actionPerformed(ActionEvent e)
1862   {
1863   }
1864
1865   protected void taylorColour_actionPerformed(ActionEvent e)
1866   {
1867   }
1868
1869   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1870   {
1871   }
1872
1873   protected void helixColour_actionPerformed(ActionEvent e)
1874   {
1875   }
1876
1877   protected void strandColour_actionPerformed(ActionEvent e)
1878   {
1879   }
1880
1881   protected void turnColour_actionPerformed(ActionEvent e)
1882   {
1883   }
1884
1885   protected void buriedColour_actionPerformed(ActionEvent e)
1886   {
1887   }
1888
1889   protected void userDefinedColour_actionPerformed(ActionEvent e)
1890   {
1891   }
1892
1893   protected void PIDColour_actionPerformed(ActionEvent e)
1894   {
1895   }
1896
1897   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1898   {
1899   }
1900
1901   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1902   {
1903   }
1904
1905   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1906   {
1907   }
1908
1909   protected void printMenuItem_actionPerformed(ActionEvent e)
1910   {
1911   }
1912
1913   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1914   {
1915   }
1916
1917   protected void findMenuItem_actionPerformed(ActionEvent e)
1918   {
1919   }
1920
1921   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1922   {
1923   }
1924
1925   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1926   {
1927   }
1928
1929   protected void nucleotideColour_actionPerformed(ActionEvent e)
1930   {
1931   }
1932
1933   protected void deleteGroups_actionPerformed(ActionEvent e)
1934   {
1935   }
1936
1937   protected void copy_actionPerformed(ActionEvent e)
1938   {
1939   }
1940
1941   protected void cut_actionPerformed(ActionEvent e)
1942   {
1943   }
1944
1945   protected void delete_actionPerformed(ActionEvent e)
1946   {
1947   }
1948
1949   protected void pasteNew_actionPerformed(ActionEvent e)
1950   {
1951   }
1952
1953   protected void pasteThis_actionPerformed(ActionEvent e)
1954   {
1955   }
1956
1957   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1958   {
1959   }
1960
1961   public void createPNG(java.io.File f)
1962   {
1963   }
1964
1965   protected void font_actionPerformed(ActionEvent e)
1966   {
1967   }
1968
1969   protected void seqLimit_actionPerformed(ActionEvent e)
1970   {
1971   }
1972
1973   public void seqDBRef_actionPerformed(ActionEvent e)
1974   {
1975
1976   }
1977
1978   public void createEPS(java.io.File f)
1979   {
1980   }
1981
1982   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1983   {
1984   }
1985
1986   protected void jpred_actionPerformed(ActionEvent e)
1987   {
1988   }
1989
1990   protected void scaleAbove_actionPerformed(ActionEvent e)
1991   {
1992   }
1993
1994   protected void scaleLeft_actionPerformed(ActionEvent e)
1995   {
1996   }
1997
1998   protected void scaleRight_actionPerformed(ActionEvent e)
1999   {
2000   }
2001
2002   protected void modifyPID_actionPerformed(ActionEvent e)
2003   {
2004   }
2005
2006   protected void modifyConservation_actionPerformed(ActionEvent e)
2007   {
2008   }
2009
2010   protected void saveAs_actionPerformed(ActionEvent e)
2011   {
2012   }
2013
2014   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2015   {
2016   }
2017
2018   public void vamsasStore_actionPerformed(ActionEvent e)
2019   {
2020
2021   }
2022
2023   public void vamsasLoad_actionPerformed(ActionEvent e)
2024   {
2025
2026   }
2027
2028   public void showTranslation_actionPerformed(ActionEvent e)
2029   {
2030
2031   }
2032
2033   public void featureSettings_actionPerformed(ActionEvent e)
2034   {
2035
2036   }
2037
2038   public void fetchSequence_actionPerformed(ActionEvent e)
2039   {
2040
2041   }
2042
2043   public void smoothFont_actionPerformed(ActionEvent e)
2044   {
2045
2046   }
2047
2048   public void annotationColour_actionPerformed(ActionEvent e)
2049   {
2050
2051   }
2052
2053   public void associatedData_actionPerformed(ActionEvent e)
2054   {
2055
2056   }
2057
2058   public void autoCalculate_actionPerformed(ActionEvent e)
2059   {
2060
2061   }
2062
2063   public void showAllSeqs_actionPerformed(ActionEvent e)
2064   {
2065
2066   }
2067
2068   public void showAllColumns_actionPerformed(ActionEvent e)
2069   {
2070
2071   }
2072
2073   public void hideSelSequences_actionPerformed(ActionEvent e)
2074   {
2075
2076   }
2077
2078   public void hideSelColumns_actionPerformed(ActionEvent e)
2079   {
2080
2081   }
2082
2083   public void hiddenMarkers_actionPerformed(ActionEvent e)
2084   {
2085
2086   }
2087
2088   public void findPdbId_actionPerformed(ActionEvent e)
2089   {
2090
2091   }
2092
2093   public void enterPdbId_actionPerformed(ActionEvent e)
2094   {
2095
2096   }
2097
2098   public void pdbFile_actionPerformed(ActionEvent e)
2099   {
2100
2101   }
2102
2103   public void invertColSel_actionPerformed(ActionEvent e)
2104   {
2105
2106   }
2107
2108   public void tabSelectionChanged(int sel)
2109   {
2110
2111   }
2112
2113   public void tabbedPane_mousePressed(MouseEvent e)
2114   {
2115
2116   }
2117
2118   public void tabbedPane_focusGained(FocusEvent e)
2119   {
2120     requestFocus();
2121   }
2122
2123   public void save_actionPerformed(ActionEvent e)
2124   {
2125
2126   }
2127
2128   public void reload_actionPerformed(ActionEvent e)
2129   {
2130
2131   }
2132
2133   public void newView_actionPerformed(ActionEvent e)
2134   {
2135
2136   }
2137
2138   public void textColour_actionPerformed(ActionEvent e)
2139   {
2140
2141   }
2142
2143   public void idRightAlign_actionPerformed(ActionEvent e)
2144   {
2145
2146   }
2147
2148   public void expandViews_actionPerformed(ActionEvent e)
2149   {
2150
2151   }
2152
2153   public void gatherViews_actionPerformed(ActionEvent e)
2154   {
2155
2156   }
2157
2158   public void buildTreeMenu()
2159   {
2160
2161   }
2162
2163   public void pageSetup_actionPerformed(ActionEvent e)
2164   {
2165
2166   }
2167
2168   public void alignmentProperties()
2169   {
2170
2171   }
2172 }