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