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     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 979     showSeqFeaturesHeight.addActionListener(new ActionListener()
 980     {
 981       public void actionPerformed(ActionEvent actionEvent)
 982       {
 983         showSeqFeaturesHeight_actionPerformed(actionEvent);
 984       }
 985     });
 986     showDbRefsMenuitem.setText("Show Database Refs");
 987     showDbRefsMenuitem.addActionListener(new ActionListener()
 988     {
 989
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         showDbRefs_actionPerformed(e);
 993       }
 994
 995     });
 996     showNpFeatsMenuitem.setText("Show Non-Positional Features");
 997     showNpFeatsMenuitem.addActionListener(new ActionListener()
 998     {
 999
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         showNpFeats_actionPerformed(e);
1003       }
1004
1005     });
1006     showGroupConservation.setText("Group Conservation");
1007     showGroupConservation.addActionListener(new ActionListener()
1008     {
1009
1010       public void actionPerformed(ActionEvent e)
1011       {
1012         showGroupConservation_actionPerformed(e);
1013       }
1014
1015     });
1016
1017     showGroupConsensus.setText("Group Consensus");
1018     showGroupConsensus.addActionListener(new ActionListener()
1019     {
1020
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         showGroupConsensus_actionPerformed(e);
1024       }
1025
1026     });
1027
1028     nucleotideColour.setText("Nucleotide");
1029     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1030     {
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         nucleotideColour_actionPerformed(e);
1034       }
1035     });
1036     deleteGroups.setText("Undefine groups");
1037     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1038             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1039                     .getMenuShortcutKeyMask(), false));
1040     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         deleteGroups_actionPerformed(e);
1045       }
1046     });
1047     copy.setText("Copy");
1048     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1049             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1050                     .getMenuShortcutKeyMask(), false));
1051
1052     copy.addActionListener(new java.awt.event.ActionListener()
1053     {
1054       public void actionPerformed(ActionEvent e)
1055       {
1056         copy_actionPerformed(e);
1057       }
1058     });
1059     cut.setText("Cut");
1060     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1061             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1062                     .getMenuShortcutKeyMask(), false));
1063     cut.addActionListener(new java.awt.event.ActionListener()
1064     {
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         cut_actionPerformed(e);
1068       }
1069     });
1070     delete.setText("Delete");
1071     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1072             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1073     delete.addActionListener(new java.awt.event.ActionListener()
1074     {
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         delete_actionPerformed(e);
1078       }
1079     });
1080     pasteMenu.setText("Paste");
1081     pasteNew.setText("To New Alignment");
1082     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1083             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1084                     .getMenuShortcutKeyMask()
1085                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1086     pasteNew.addActionListener(new java.awt.event.ActionListener()
1087     {
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         pasteNew_actionPerformed(e);
1091       }
1092     });
1093     pasteThis.setText("Add To This Alignment");
1094     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1095             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1096                     .getMenuShortcutKeyMask(), false));
1097     pasteThis.addActionListener(new java.awt.event.ActionListener()
1098     {
1099       public void actionPerformed(ActionEvent e)
1100       {
1101         pasteThis_actionPerformed(e);
1102       }
1103     });
1104     applyToAllGroups.setText("Apply Colour To All Groups");
1105     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1106     {
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         applyToAllGroups_actionPerformed(e);
1110       }
1111     });
1112     createPNG.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         createPNG(null);
1117       }
1118     });
1119     createPNG.setActionCommand("Save As PNG Image");
1120     createPNG.setText("PNG");
1121     font.setText("Font...");
1122     font.addActionListener(new java.awt.event.ActionListener()
1123     {
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         font_actionPerformed(e);
1127       }
1128     });
1129
1130     seqLimits.setText("Show Sequence Limits");
1131     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1132     seqLimits.addActionListener(new java.awt.event.ActionListener()
1133     {
1134       public void actionPerformed(ActionEvent e)
1135       {
1136         seqLimit_actionPerformed(e);
1137       }
1138     });
1139     epsFile.setText("EPS");
1140     epsFile.addActionListener(new java.awt.event.ActionListener()
1141     {
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         createEPS(null);
1145       }
1146     });
1147     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1148     LoadtreeMenuItem.setText("Load Associated Tree");
1149     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1150     {
1151       public void actionPerformed(ActionEvent e)
1152       {
1153         LoadtreeMenuItem_actionPerformed(e);
1154       }
1155     });
1156     scaleAbove.setVisible(false);
1157     scaleAbove.setText("Scale Above");
1158     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1159     {
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         scaleAbove_actionPerformed(e);
1163       }
1164     });
1165     scaleLeft.setVisible(false);
1166     scaleLeft.setSelected(true);
1167     scaleLeft.setText("Scale Left");
1168     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1169     {
1170       public void actionPerformed(ActionEvent e)
1171       {
1172         scaleLeft_actionPerformed(e);
1173       }
1174     });
1175     scaleRight.setVisible(false);
1176     scaleRight.setSelected(true);
1177     scaleRight.setText("Scale Right");
1178     scaleRight.addActionListener(new java.awt.event.ActionListener()
1179     {
1180       public void actionPerformed(ActionEvent e)
1181       {
1182         scaleRight_actionPerformed(e);
1183       }
1184     });
1185     centreColumnLabelsMenuItem.setVisible(true);
1186     centreColumnLabelsMenuItem.setState(false);
1187     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1188     centreColumnLabelsMenuItem
1189             .addActionListener(new java.awt.event.ActionListener()
1190             {
1191               public void actionPerformed(ActionEvent e)
1192               {
1193                 centreColumnLabels_actionPerformed(e);
1194               }
1195             });
1196     followHighlightMenuItem.setVisible(true);
1197     followHighlightMenuItem.setState(true);
1198     followHighlightMenuItem.setText("Automatic Scrolling");
1199     followHighlightMenuItem.addActionListener(new ActionListener()
1200     {
1201
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         followHighlight_actionPerformed();
1205       }
1206
1207     });
1208
1209     modifyPID.setText("Modify Identity Threshold...");
1210     modifyPID.addActionListener(new java.awt.event.ActionListener()
1211     {
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         modifyPID_actionPerformed(e);
1215       }
1216     });
1217     modifyConservation.setText("Modify Conservation Threshold...");
1218     modifyConservation
1219             .addActionListener(new java.awt.event.ActionListener()
1220             {
1221               public void actionPerformed(ActionEvent e)
1222               {
1223                 modifyConservation_actionPerformed(e);
1224               }
1225             });
1226     sortByTreeMenu.setText("By Tree Order");
1227     sort.setText("Sort");
1228     sort.addMenuListener(new MenuListener()
1229     {
1230       public void menuSelected(MenuEvent e)
1231       {
1232         buildTreeMenu();
1233       }
1234
1235       public void menuDeselected(MenuEvent e)
1236       {
1237       }
1238
1239       public void menuCanceled(MenuEvent e)
1240       {
1241       }
1242     });
1243     sortByAnnotScore.setText("by Score");
1244     sort.add(sortByAnnotScore);
1245     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1246     {
1247
1248       public void menuCanceled(MenuEvent e)
1249       {
1250       }
1251
1252       public void menuDeselected(MenuEvent e)
1253       {
1254       }
1255
1256       public void menuSelected(MenuEvent e)
1257       {
1258         buildSortByAnnotationScoresMenu();
1259       }
1260     });
1261     sortByAnnotScore.setVisible(false);
1262
1263     calculateTree.setText("Calculate Tree");
1264
1265     jMenu2.setText("Export Image");
1266     padGapsMenuitem.setText("Pad Gaps");
1267     padGapsMenuitem.setState(jalview.bin.Cache
1268             .getDefault("PAD_GAPS", false));
1269     padGapsMenuitem.addActionListener(new ActionListener()
1270     {
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         padGapsMenuitem_actionPerformed(e);
1274       }
1275     });
1276     vamsasStore.setVisible(false);
1277     vamsasStore.setText("VAMSAS store");
1278     vamsasStore.addActionListener(new ActionListener()
1279     {
1280       public void actionPerformed(ActionEvent e)
1281       {
1282         vamsasStore_actionPerformed(e);
1283       }
1284     });
1285     showTranslation.setText("Translate cDNA");
1286     showTranslation.addActionListener(new ActionListener()
1287     {
1288       public void actionPerformed(ActionEvent e)
1289       {
1290         showTranslation_actionPerformed(e);
1291       }
1292     });
1293     extractScores.setText("Extract Scores...");
1294     extractScores.addActionListener(new ActionListener()
1295     {
1296       public void actionPerformed(ActionEvent e)
1297       {
1298         extractScores_actionPerformed(e);
1299       }
1300     });
1301     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1302                                     // score extraction
1303     showProducts.setText("Get Cross References");
1304     /*
1305      * showProducts.addActionListener(new ActionListener() {
1306      *
1307      * public void actionPerformed(ActionEvent e) {
1308      * showProducts_actionPerformed(e); } });
1309      */
1310     featureSettings.setText("Feature Settings...");
1311     featureSettings.addActionListener(new ActionListener()
1312     {
1313       public void actionPerformed(ActionEvent e)
1314       {
1315         featureSettings_actionPerformed(e);
1316       }
1317     });
1318     fetchSequence.setText("Fetch Sequence(s)...");
1319     fetchSequence.addActionListener(new ActionListener()
1320     {
1321       public void actionPerformed(ActionEvent e)
1322       {
1323         fetchSequence_actionPerformed(e);
1324       }
1325     });
1326
1327     annotationColour.setText("By Annotation...");
1328     annotationColour.addActionListener(new ActionListener()
1329     {
1330       public void actionPerformed(ActionEvent e)
1331       {
1332         annotationColour_actionPerformed(e);
1333       }
1334     });
1335     associatedData.setText("Load Features / Annotations");
1336     associatedData.addActionListener(new ActionListener()
1337     {
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         associatedData_actionPerformed(e);
1341       }
1342     });
1343     autoCalculate.setText("Autocalculate Consensus");
1344     autoCalculate.setState(jalview.bin.Cache.getDefault(
1345             "AUTO_CALC_CONSENSUS", true));
1346     autoCalculate.addActionListener(new ActionListener()
1347     {
1348       public void actionPerformed(ActionEvent e)
1349       {
1350         autoCalculate_actionPerformed(e);
1351       }
1352     });
1353     addSequenceMenu.setText("Add Sequences");
1354     addFromFile.setText("From File");
1355     addFromFile.addActionListener(new ActionListener()
1356     {
1357       public void actionPerformed(ActionEvent e)
1358       {
1359         addFromFile_actionPerformed(e);
1360       }
1361     });
1362     addFromText.setText("From Textbox");
1363     addFromText.addActionListener(new ActionListener()
1364     {
1365       public void actionPerformed(ActionEvent e)
1366       {
1367         addFromText_actionPerformed(e);
1368       }
1369     });
1370     addFromURL.setText("From URL");
1371     addFromURL.addActionListener(new ActionListener()
1372     {
1373       public void actionPerformed(ActionEvent e)
1374       {
1375         addFromURL_actionPerformed(e);
1376       }
1377     });
1378     exportFeatures.setText("Export Features...");
1379     exportFeatures.addActionListener(new ActionListener()
1380     {
1381       public void actionPerformed(ActionEvent e)
1382       {
1383         exportFeatures_actionPerformed(e);
1384       }
1385     });
1386     exportAnnotations.setText("Export Annotations...");
1387     exportAnnotations.addActionListener(new ActionListener()
1388     {
1389       public void actionPerformed(ActionEvent e)
1390       {
1391         exportAnnotations_actionPerformed(e);
1392       }
1393     });
1394     statusPanel.setLayout(gridLayout1);
1395     jMenu3.setText("Show");
1396     showAllSeqs.setText("All Sequences");
1397     showAllSeqs.addActionListener(new ActionListener()
1398     {
1399       public void actionPerformed(ActionEvent e)
1400       {
1401         showAllSeqs_actionPerformed(e);
1402       }
1403     });
1404     showAllColumns.setText("All Columns");
1405     showAllColumns.addActionListener(new ActionListener()
1406     {
1407       public void actionPerformed(ActionEvent e)
1408       {
1409         showAllColumns_actionPerformed(e);
1410       }
1411     });
1412     hideMenu.setText("Hide");
1413     hideSelSequences.setText("Selected Sequences");
1414     hideSelSequences.addActionListener(new ActionListener()
1415     {
1416       public void actionPerformed(ActionEvent e)
1417       {
1418         hideSelSequences_actionPerformed(e);
1419       }
1420     });
1421     hideSelColumns.setText("Selected Columns");
1422     hideSelColumns.addActionListener(new ActionListener()
1423     {
1424       public void actionPerformed(ActionEvent e)
1425       {
1426         hideSelColumns_actionPerformed(e);
1427       }
1428     });
1429     hiddenMarkers.setText("Show Hidden Markers");
1430     hiddenMarkers.addActionListener(new ActionListener()
1431     {
1432       public void actionPerformed(ActionEvent e)
1433       {
1434         hiddenMarkers_actionPerformed(e);
1435       }
1436     });
1437     invertColSel.setText("Invert Column Selection");
1438     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1439             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1440                     .getMenuShortcutKeyMask()
1441                     | java.awt.event.KeyEvent.ALT_MASK, false));
1442     invertColSel.addActionListener(new ActionListener()
1443     {
1444       public void actionPerformed(ActionEvent e)
1445       {
1446         invertColSel_actionPerformed(e);
1447       }
1448     });
1449     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1450     {
1451       public void stateChanged(ChangeEvent evt)
1452       {
1453         JTabbedPane pane = (JTabbedPane) evt.getSource();
1454         int sel = pane.getSelectedIndex();
1455         tabSelectionChanged(sel);
1456       }
1457     });
1458     tabbedPane.addMouseListener(new MouseAdapter()
1459     {
1460       public void mousePressed(MouseEvent e)
1461       {
1462         tabbedPane_mousePressed(e);
1463       }
1464     });
1465     tabbedPane.addFocusListener(new FocusAdapter()
1466     {
1467       public void focusGained(FocusEvent e)
1468       {
1469         tabbedPane_focusGained(e);
1470       }
1471     });
1472     save.setText("Save");
1473     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1474             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1475                     .getMenuShortcutKeyMask(), false));
1476     save.addActionListener(new ActionListener()
1477     {
1478       public void actionPerformed(ActionEvent e)
1479       {
1480         save_actionPerformed(e);
1481       }
1482     });
1483     reload.setEnabled(false);
1484     reload.setText("Reload");
1485     reload.addActionListener(new ActionListener()
1486     {
1487       public void actionPerformed(ActionEvent e)
1488       {
1489         reload_actionPerformed(e);
1490       }
1491     });
1492     newView.setText("New View");
1493     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1494             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1495                     .getMenuShortcutKeyMask(), false));
1496     newView.addActionListener(new ActionListener()
1497     {
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         newView_actionPerformed(e);
1501       }
1502     });
1503     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1504             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1505     textColour.setText("Colour Text ...");
1506     textColour.addActionListener(new ActionListener()
1507     {
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         textColour_actionPerformed(e);
1511       }
1512     });
1513     formatMenu.setText("Format");
1514     selectMenu.setText("Select");
1515     idRightAlign.setText("Right Align Sequence Id");
1516     idRightAlign.addActionListener(new ActionListener()
1517     {
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         idRightAlign_actionPerformed(e);
1521       }
1522     });
1523     gatherViews.setEnabled(false);
1524     gatherViews.setText("Gather Views");
1525     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1526             java.awt.event.KeyEvent.VK_G, 0, false));
1527     gatherViews.addActionListener(new ActionListener()
1528     {
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         gatherViews_actionPerformed(e);
1532       }
1533     });
1534     expandViews.setEnabled(false);
1535     expandViews.setText("Expand Views");
1536     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1537             java.awt.event.KeyEvent.VK_X, 0, false));
1538     expandViews.addActionListener(new ActionListener()
1539     {
1540       public void actionPerformed(ActionEvent e)
1541       {
1542         expandViews_actionPerformed(e);
1543       }
1544     });
1545     pageSetup.setText("Page Setup ...");
1546     pageSetup.addActionListener(new ActionListener()
1547     {
1548       public void actionPerformed(ActionEvent e)
1549       {
1550         pageSetup_actionPerformed(e);
1551       }
1552     });
1553     alignmentProperties.setText("Alignment Properties...");
1554     alignmentProperties.addActionListener(new ActionListener()
1555     {
1556       public void actionPerformed(ActionEvent actionEvent)
1557       {
1558         alignmentProperties();
1559       }
1560     });
1561     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1562     alignFrameMenuBar.add(fileMenu);
1563     alignFrameMenuBar.add(editMenu);
1564     alignFrameMenuBar.add(selectMenu);
1565     alignFrameMenuBar.add(viewMenu);
1566     alignFrameMenuBar.add(formatMenu);
1567     alignFrameMenuBar.add(colourMenu);
1568     alignFrameMenuBar.add(calculateMenu);
1569     alignFrameMenuBar.add(webService);
1570     fileMenu.add(fetchSequence);
1571     fileMenu.add(addSequenceMenu);
1572     fileMenu.add(reload);
1573     fileMenu.addSeparator();
1574     fileMenu.add(vamsasStore);
1575     fileMenu.add(save);
1576     fileMenu.add(saveAs);
1577     fileMenu.add(outputTextboxMenu);
1578     fileMenu.add(pageSetup);
1579     fileMenu.add(printMenuItem);
1580     fileMenu.addSeparator();
1581     fileMenu.add(jMenu2);
1582     fileMenu.add(exportFeatures);
1583     fileMenu.add(exportAnnotations);
1584     fileMenu.add(LoadtreeMenuItem);
1585     fileMenu.add(associatedData);
1586     fileMenu.addSeparator();
1587     fileMenu.add(closeMenuItem);
1588     editMenu.add(undoMenuItem);
1589     editMenu.add(redoMenuItem);
1590     editMenu.add(cut);
1591     editMenu.add(copy);
1592     editMenu.add(pasteMenu);
1593     editMenu.add(delete);
1594     editMenu.addSeparator();
1595     editMenu.add(remove2LeftMenuItem);
1596     editMenu.add(remove2RightMenuItem);
1597     editMenu.add(removeGappedColumnMenuItem);
1598     editMenu.add(removeAllGapsMenuItem);
1599     editMenu.add(removeRedundancyMenuItem);
1600     editMenu.addSeparator();
1601     // dont add these yet in the CVS build - they cannot be undone!
1602     editMenu.add(justifyLeftMenuItem);
1603     editMenu.add(justifyRightMenuItem);
1604     editMenu.addSeparator();
1605     editMenu.add(padGapsMenuitem);
1606     viewMenu.add(newView);
1607     viewMenu.add(expandViews);
1608     viewMenu.add(gatherViews);
1609     viewMenu.addSeparator();
1610     viewMenu.add(jMenu3);
1611     viewMenu.add(hideMenu);
1612     viewMenu.addSeparator();
1613     viewMenu.add(followHighlightMenuItem);
1614     viewMenu.add(annotationPanelMenuItem);
1615     viewMenu.add(showGroupConservation);
1616     viewMenu.add(showGroupConsensus);
1617     viewMenu.addSeparator();
1618     viewMenu.add(showSeqFeatures);
1619     viewMenu.add(showSeqFeaturesHeight);
1620
1621     viewMenu.add(featureSettings);
1622     tooltipSettingsMenu.add(showDbRefsMenuitem);
1623     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1624     viewMenu.add(tooltipSettingsMenu);
1625     viewMenu.addSeparator();
1626     viewMenu.add(alignmentProperties);
1627     viewMenu.addSeparator();
1628     viewMenu.add(overviewMenuItem);
1629     colourMenu.add(applyToAllGroups);
1630     colourMenu.add(textColour);
1631     colourMenu.addSeparator();
1632     colourMenu.add(noColourmenuItem);
1633     colourMenu.add(clustalColour);
1634     colourMenu.add(BLOSUM62Colour);
1635     colourMenu.add(PIDColour);
1636     colourMenu.add(zappoColour);
1637     colourMenu.add(taylorColour);
1638     colourMenu.add(hydrophobicityColour);
1639     colourMenu.add(helixColour);
1640     colourMenu.add(strandColour);
1641     colourMenu.add(turnColour);
1642     colourMenu.add(buriedColour);
1643     colourMenu.add(nucleotideColour);
1644     colourMenu.add(userDefinedColour);
1645     colourMenu.addSeparator();
1646     colourMenu.add(conservationMenuItem);
1647     colourMenu.add(modifyConservation);
1648     colourMenu.add(abovePIDThreshold);
1649     colourMenu.add(modifyPID);
1650     colourMenu.add(annotationColour);
1651     calculateMenu.add(sort);
1652     calculateMenu.add(calculateTree);
1653     calculateMenu.addSeparator();
1654     calculateMenu.add(pairwiseAlignmentMenuItem);
1655     calculateMenu.add(PCAMenuItem);
1656     calculateMenu.addSeparator();
1657     calculateMenu.add(showTranslation);
1658     calculateMenu.add(showProducts);
1659     calculateMenu.add(autoCalculate);
1660     calculateMenu.addSeparator();
1661     calculateMenu.add(extractScores);
1662     webServiceNoServices = new JMenuItem("<No Services>");
1663     webService.add(webServiceNoServices);
1664     pasteMenu.add(pasteNew);
1665     pasteMenu.add(pasteThis);
1666     sort.add(sortIDMenuItem);
1667     sort.add(sortLengthMenuItem);
1668     sort.add(sortGroupMenuItem);
1669     sort.add(sortPairwiseMenuItem);
1670     sort.add(sortByTreeMenu);
1671     calculateTree.add(averageDistanceTreeMenuItem);
1672     calculateTree.add(neighbourTreeMenuItem);
1673     calculateTree.add(avDistanceTreeBlosumMenuItem);
1674     calculateTree.add(njTreeBlosumMenuItem);
1675     jMenu2.add(htmlMenuItem);
1676     jMenu2.add(epsFile);
1677     jMenu2.add(createPNG);
1678     addSequenceMenu.add(addFromFile);
1679     addSequenceMenu.add(addFromText);
1680     addSequenceMenu.add(addFromURL);
1681     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1682     statusPanel.add(statusBar, null);
1683     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1684     jMenu3.add(showAllColumns);
1685     jMenu3.add(showAllSeqs);
1686     hideMenu.add(hideSelColumns);
1687     hideMenu.add(hideSelSequences);
1688     formatMenu.add(font);
1689     formatMenu.addSeparator();
1690     formatMenu.add(wrapMenuItem);
1691     formatMenu.add(scaleAbove);
1692     formatMenu.add(scaleLeft);
1693     formatMenu.add(scaleRight);
1694     formatMenu.add(seqLimits);
1695     formatMenu.add(idRightAlign);
1696     formatMenu.add(hiddenMarkers);
1697     formatMenu.add(viewBoxesMenuItem);
1698     formatMenu.add(viewTextMenuItem);
1699     formatMenu.add(colourTextMenuItem);
1700     formatMenu.add(renderGapsMenuItem);
1701     formatMenu.add(centreColumnLabelsMenuItem);
1702     formatMenu.add(showUnconservedMenuItem);
1703     selectMenu.add(findMenuItem);
1704     selectMenu.addSeparator();
1705     selectMenu.add(selectAllSequenceMenuItem);
1706     selectMenu.add(deselectAllSequenceMenuItem);
1707     selectMenu.add(invertSequenceMenuItem);
1708     selectMenu.add(invertColSel);
1709     selectMenu.add(deleteGroups);
1710     selectMenu.add(grpsFromSelection);
1711   }
1712
1713   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1714   {
1715     // TODO Auto-generated method stub
1716
1717   }
1718
1719   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1720   {
1721     // TODO Auto-generated method stub
1722
1723   }
1724
1725   protected void showGroupConservation_actionPerformed(ActionEvent e)
1726   {
1727     // TODO Auto-generated method stub
1728
1729   }
1730
1731   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1732   {
1733     // TODO Auto-generated method stub
1734
1735   }
1736
1737   protected void showSeqFeaturesHeight_actionPerformed(
1738           ActionEvent actionEvent)
1739   {
1740     // TODO Auto-generated method stub
1741
1742   }
1743
1744   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1745   {
1746     // TODO Auto-generated method stub
1747
1748   }
1749
1750   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1751   {
1752     // TODO Auto-generated method stub
1753
1754   }
1755
1756   protected void followHighlight_actionPerformed()
1757   {
1758     // TODO Auto-generated method stub
1759
1760   }
1761
1762   protected void showNpFeats_actionPerformed(ActionEvent e)
1763   {
1764     // TODO Auto-generated method stub
1765
1766   }
1767
1768   protected void showDbRefs_actionPerformed(ActionEvent e)
1769   {
1770     // TODO Auto-generated method stub
1771
1772   }
1773
1774   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1775   {
1776   }
1777
1778   protected void showProducts_actionPerformed(ActionEvent e)
1779   {
1780   }
1781
1782   protected void buildSortByAnnotationScoresMenu()
1783   {
1784   }
1785
1786   protected void extractScores_actionPerformed(ActionEvent e)
1787   {
1788   }
1789
1790   protected void outputText_actionPerformed(ActionEvent e)
1791   {
1792   }
1793
1794   public void addFromFile_actionPerformed(ActionEvent e)
1795   {
1796
1797   }
1798
1799   public void addFromText_actionPerformed(ActionEvent e)
1800   {
1801
1802   }
1803
1804   public void addFromURL_actionPerformed(ActionEvent e)
1805   {
1806
1807   }
1808
1809   public void exportFeatures_actionPerformed(ActionEvent e)
1810   {
1811
1812   }
1813
1814   public void exportAnnotations_actionPerformed(ActionEvent e)
1815   {
1816
1817   }
1818
1819   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1820   {
1821   }
1822
1823   protected void closeMenuItem_actionPerformed(boolean b)
1824   {
1825   }
1826
1827   protected void redoMenuItem_actionPerformed(ActionEvent e)
1828   {
1829   }
1830
1831   protected void undoMenuItem_actionPerformed(ActionEvent e)
1832   {
1833   }
1834
1835   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1836   {
1837   }
1838
1839   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1840   {
1841   }
1842
1843   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1844   {
1845   }
1846
1847   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1848   {
1849   }
1850
1851   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1852   {
1853   }
1854
1855   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1856   {
1857   }
1858
1859   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1860   {
1861   }
1862
1863   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1864   {
1865   }
1866
1867   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1868   {
1869   }
1870
1871   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1872   {
1873   }
1874
1875   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1876   {
1877   }
1878
1879   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1880   {
1881   }
1882
1883   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1884   {
1885   }
1886
1887   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1888   {
1889   }
1890
1891   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1892   {
1893   }
1894
1895   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1896   {
1897   }
1898
1899   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1900   {
1901   }
1902
1903   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1904   {
1905   }
1906
1907   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1908   {
1909   }
1910
1911   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1912   {
1913   }
1914
1915   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1916   {
1917   }
1918
1919   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1920   {
1921   }
1922
1923   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1924   {
1925   }
1926
1927   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1928   {
1929   }
1930
1931   protected void clustalColour_actionPerformed(ActionEvent e)
1932   {
1933   }
1934
1935   protected void zappoColour_actionPerformed(ActionEvent e)
1936   {
1937   }
1938
1939   protected void taylorColour_actionPerformed(ActionEvent e)
1940   {
1941   }
1942
1943   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1944   {
1945   }
1946
1947   protected void helixColour_actionPerformed(ActionEvent e)
1948   {
1949   }
1950
1951   protected void strandColour_actionPerformed(ActionEvent e)
1952   {
1953   }
1954
1955   protected void turnColour_actionPerformed(ActionEvent e)
1956   {
1957   }
1958
1959   protected void buriedColour_actionPerformed(ActionEvent e)
1960   {
1961   }
1962
1963   protected void userDefinedColour_actionPerformed(ActionEvent e)
1964   {
1965   }
1966
1967   protected void PIDColour_actionPerformed(ActionEvent e)
1968   {
1969   }
1970
1971   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1972   {
1973   }
1974
1975   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1976   {
1977   }
1978
1979   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1980   {
1981   }
1982
1983   protected void printMenuItem_actionPerformed(ActionEvent e)
1984   {
1985   }
1986
1987   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1988   {
1989   }
1990
1991   protected void findMenuItem_actionPerformed(ActionEvent e)
1992   {
1993   }
1994
1995   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1996   {
1997   }
1998
1999   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2000   {
2001   }
2002
2003   protected void nucleotideColour_actionPerformed(ActionEvent e)
2004   {
2005   }
2006
2007   protected void deleteGroups_actionPerformed(ActionEvent e)
2008   {
2009   }
2010
2011   protected void copy_actionPerformed(ActionEvent e)
2012   {
2013   }
2014
2015   protected void cut_actionPerformed(ActionEvent e)
2016   {
2017   }
2018
2019   protected void delete_actionPerformed(ActionEvent e)
2020   {
2021   }
2022
2023   protected void pasteNew_actionPerformed(ActionEvent e)
2024   {
2025   }
2026
2027   protected void pasteThis_actionPerformed(ActionEvent e)
2028   {
2029   }
2030
2031   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2032   {
2033   }
2034
2035   public void createPNG(java.io.File f)
2036   {
2037   }
2038
2039   protected void font_actionPerformed(ActionEvent e)
2040   {
2041   }
2042
2043   protected void seqLimit_actionPerformed(ActionEvent e)
2044   {
2045   }
2046
2047   public void seqDBRef_actionPerformed(ActionEvent e)
2048   {
2049
2050   }
2051
2052   public void createEPS(java.io.File f)
2053   {
2054   }
2055
2056   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2057   {
2058   }
2059
2060   protected void jpred_actionPerformed(ActionEvent e)
2061   {
2062   }
2063
2064   protected void scaleAbove_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void scaleLeft_actionPerformed(ActionEvent e)
2069   {
2070   }
2071
2072   protected void scaleRight_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void modifyPID_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void modifyConservation_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void saveAs_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   public void vamsasStore_actionPerformed(ActionEvent e)
2093   {
2094
2095   }
2096
2097   public void vamsasLoad_actionPerformed(ActionEvent e)
2098   {
2099
2100   }
2101
2102   public void showTranslation_actionPerformed(ActionEvent e)
2103   {
2104
2105   }
2106
2107   public void featureSettings_actionPerformed(ActionEvent e)
2108   {
2109
2110   }
2111
2112   public void fetchSequence_actionPerformed(ActionEvent e)
2113   {
2114
2115   }
2116
2117   public void smoothFont_actionPerformed(ActionEvent e)
2118   {
2119
2120   }
2121
2122   public void annotationColour_actionPerformed(ActionEvent e)
2123   {
2124
2125   }
2126
2127   public void associatedData_actionPerformed(ActionEvent e)
2128   {
2129
2130   }
2131
2132   public void autoCalculate_actionPerformed(ActionEvent e)
2133   {
2134
2135   }
2136
2137   public void showAllSeqs_actionPerformed(ActionEvent e)
2138   {
2139
2140   }
2141
2142   public void showAllColumns_actionPerformed(ActionEvent e)
2143   {
2144
2145   }
2146
2147   public void hideSelSequences_actionPerformed(ActionEvent e)
2148   {
2149
2150   }
2151
2152   public void hideSelColumns_actionPerformed(ActionEvent e)
2153   {
2154
2155   }
2156
2157   public void hiddenMarkers_actionPerformed(ActionEvent e)
2158   {
2159
2160   }
2161
2162   public void findPdbId_actionPerformed(ActionEvent e)
2163   {
2164
2165   }
2166
2167   public void enterPdbId_actionPerformed(ActionEvent e)
2168   {
2169
2170   }
2171
2172   public void pdbFile_actionPerformed(ActionEvent e)
2173   {
2174
2175   }
2176
2177   public void invertColSel_actionPerformed(ActionEvent e)
2178   {
2179
2180   }
2181
2182   public void tabSelectionChanged(int sel)
2183   {
2184
2185   }
2186
2187   public void tabbedPane_mousePressed(MouseEvent e)
2188   {
2189
2190   }
2191
2192   public void tabbedPane_focusGained(FocusEvent e)
2193   {
2194     requestFocus();
2195   }
2196
2197   public void save_actionPerformed(ActionEvent e)
2198   {
2199
2200   }
2201
2202   public void reload_actionPerformed(ActionEvent e)
2203   {
2204
2205   }
2206
2207   public void newView_actionPerformed(ActionEvent e)
2208   {
2209
2210   }
2211
2212   public void textColour_actionPerformed(ActionEvent e)
2213   {
2214
2215   }
2216
2217   public void idRightAlign_actionPerformed(ActionEvent e)
2218   {
2219
2220   }
2221
2222   public void expandViews_actionPerformed(ActionEvent e)
2223   {
2224
2225   }
2226
2227   public void gatherViews_actionPerformed(ActionEvent e)
2228   {
2229
2230   }
2231
2232   public void buildTreeMenu()
2233   {
2234
2235   }
2236
2237   public void pageSetup_actionPerformed(ActionEvent e)
2238   {
2239
2240   }
2241
2242   public void alignmentProperties()
2243   {
2244
2245   }
2246 }