src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.schemes.*;
  28
  29 public class GAlignFrame extends JInternalFrame
  30 {
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  32
  33   protected JMenu fileMenu = new JMenu();
  34
  35   protected JMenuItem closeMenuItem = new JMenuItem();
  36
  37   protected JMenu editMenu = new JMenu();
  38
  39   protected JMenu viewMenu = new JMenu();
  40
  41   protected JMenu colourMenu = new JMenu();
  42
  43   protected JMenu calculateMenu = new JMenu();
  44
  45   protected JMenu webService = new JMenu();
  46
  47   protected JMenuItem webServiceNoServices;
  48
  49   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  50
  51   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  52
  53   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  54
  55   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  56
  57   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  58
  59   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  60
  61   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  62
  63   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  64
  65   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  66
  67   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  68
  69   protected JMenuItem sortIDMenuItem = new JMenuItem();
  70
  71   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  72
  73   protected JMenu sortByAnnotScore = new JMenu();
  74
  75   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  76
  77   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  78
  79   protected JMenuItem PCAMenuItem = new JMenuItem();
  80
  81   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  82
  83   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  84
  85   BorderLayout borderLayout1 = new BorderLayout();
  86
  87   public JLabel statusBar = new JLabel();
  88
  89   protected JMenuItem saveAs = new JMenuItem();
  90
  91   protected JMenu outputTextboxMenu = new JMenu();
  92
  93   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  94
  95   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  96
  97   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  98
  99   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 112
 113   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 114
 115   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 116
 117   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 118
 119   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 120
 121   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 122
 123   JMenuItem htmlMenuItem = new JMenuItem();
 124
 125   JMenuItem overviewMenuItem = new JMenuItem();
 126
 127   protected JMenuItem undoMenuItem = new JMenuItem();
 128
 129   protected JMenuItem redoMenuItem = new JMenuItem();
 130
 131   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 132
 133   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 134
 135   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 136
 137   JMenuItem printMenuItem = new JMenuItem();
 138
 139   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 140
 141   JMenuItem findMenuItem = new JMenuItem();
 142
 143   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 144
 145   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 146
 147   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 148
 149   JMenuItem deleteGroups = new JMenuItem();
 150
 151   JMenuItem delete = new JMenuItem();
 152
 153   JMenuItem copy = new JMenuItem();
 154
 155   JMenuItem cut = new JMenuItem();
 156
 157   JMenu pasteMenu = new JMenu();
 158
 159   JMenuItem pasteNew = new JMenuItem();
 160
 161   JMenuItem pasteThis = new JMenuItem();
 162
 163   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 164
 165   JMenuItem createPNG = new JMenuItem();
 166
 167   protected JMenuItem font = new JMenuItem();
 168
 169   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 170
 171   JMenuItem epsFile = new JMenuItem();
 172
 173   JMenuItem LoadtreeMenuItem = new JMenuItem();
 174
 175   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 176
 177   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 178
 179   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 180
 181   protected JMenuItem modifyPID = new JMenuItem();
 182
 183   protected JMenuItem modifyConservation = new JMenuItem();
 184
 185   protected JMenu sortByTreeMenu = new JMenu();
 186
 187   protected JMenu sort = new JMenu();
 188
 189   protected JMenu calculateTree = new JMenu();
 190
 191   JMenu jMenu2 = new JMenu();
 192
 193   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 194   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 195   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 196
 197   protected ButtonGroup colours = new ButtonGroup();
 198
 199   JMenuItem vamsasStore = new JMenuItem();
 200
 201   protected JMenuItem showTranslation = new JMenuItem();
 202
 203   protected JMenuItem extractScores = new JMenuItem();
 204
 205   protected JMenu showProducts = new JMenu();
 206
 207   public JMenuItem featureSettings = new JMenuItem();
 208
 209   JMenuItem fetchSequence = new JMenuItem();
 210
 211   JMenuItem annotationColour = new JMenuItem();
 212
 213   JMenuItem associatedData = new JMenuItem();
 214
 215   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 216
 217   JMenu addSequenceMenu = new JMenu();
 218
 219   JMenuItem addFromFile = new JMenuItem();
 220
 221   JMenuItem addFromText = new JMenuItem();
 222
 223   JMenuItem addFromURL = new JMenuItem();
 224
 225   JMenuItem exportAnnotations = new JMenuItem();
 226
 227   JMenuItem exportFeatures = new JMenuItem();
 228
 229   protected JPanel statusPanel = new JPanel();
 230
 231   GridLayout gridLayout1 = new GridLayout();
 232
 233   JMenu jMenu3 = new JMenu();
 234
 235   JMenuItem showAllSeqs = new JMenuItem();
 236
 237   JMenuItem showAllColumns = new JMenuItem();
 238
 239   JMenu hideMenu = new JMenu();
 240
 241   JMenuItem hideSelSequences = new JMenuItem();
 242
 243   JMenuItem hideSelColumns = new JMenuItem();
 244
 245   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 246
 247   JMenuItem invertColSel = new JMenuItem();
 248
 249   protected JTabbedPane tabbedPane = new JTabbedPane();
 250
 251   JMenuItem save = new JMenuItem();
 252
 253   protected JMenuItem reload = new JMenuItem();
 254
 255   JMenuItem newView = new JMenuItem();
 256
 257   JMenuItem textColour = new JMenuItem();
 258
 259   JMenu formatMenu = new JMenu();
 260
 261   JMenu selectMenu = new JMenu();
 262
 263   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 264
 265   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 266
 267   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 268
 269   protected JMenuItem gatherViews = new JMenuItem();
 270
 271   protected JMenuItem expandViews = new JMenuItem();
 272
 273   JMenuItem pageSetup = new JMenuItem();
 274
 275   JMenuItem alignmentProperties = new JMenuItem();
 276
 277   JMenu tooltipSettingsMenu = new JMenu();
 278
 279   public GAlignFrame()
 280   {
 281     try
 282     {
 283       jbInit();
 284       setJMenuBar(alignFrameMenuBar);
 285
 286       // dynamically fill save as menu with available formats
 287       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 288       {
 289         JMenuItem item = new JMenuItem(
 290                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 291
 292         item.addActionListener(new java.awt.event.ActionListener()
 293         {
 294           public void actionPerformed(ActionEvent e)
 295           {
 296             outputText_actionPerformed(e);
 297           }
 298         });
 299
 300         outputTextboxMenu.add(item);
 301       }
 302     } catch (Exception e)
 303     {
 304     }
 305
 306     if (!new jalview.util.Platform().isAMac())
 307     {
 308       closeMenuItem.setMnemonic('C');
 309       outputTextboxMenu.setMnemonic('T');
 310       undoMenuItem.setMnemonic('Z');
 311       redoMenuItem.setMnemonic('0');
 312       copy.setMnemonic('C');
 313       cut.setMnemonic('U');
 314       pasteMenu.setMnemonic('P');
 315       reload.setMnemonic('R');
 316     }
 317
 318     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 319     {
 320       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 321               .getUserColourSchemes().keys();
 322
 323       while (userColours.hasMoreElements())
 324       {
 325         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 326                 userColours.nextElement().toString());
 327         radioItem.setName("USER_DEFINED");
 328         radioItem.addMouseListener(new MouseAdapter()
 329         {
 330           public void mousePressed(MouseEvent evt)
 331           {
 332             if (evt.isControlDown()
 333                     || SwingUtilities.isRightMouseButton(evt))
 334             {
 335               radioItem
 336                       .removeActionListener(radioItem.getActionListeners()[0]);
 337
 338               int option = JOptionPane.showInternalConfirmDialog(
 339                       jalview.gui.Desktop.desktop,
 340                       "Remove from default list?",
 341                       "Remove user defined colour",
 342                       JOptionPane.YES_NO_OPTION);
 343               if (option == JOptionPane.YES_OPTION)
 344               {
 345                 jalview.gui.UserDefinedColours
 346                         .removeColourFromDefaults(radioItem.getText());
 347                 colourMenu.remove(radioItem);
 348               }
 349               else
 350               {
 351                 radioItem.addActionListener(new ActionListener()
 352                 {
 353                   public void actionPerformed(ActionEvent evt)
 354                   {
 355                     userDefinedColour_actionPerformed(evt);
 356                   }
 357                 });
 358               }
 359             }
 360           }
 361         });
 362         radioItem.addActionListener(new ActionListener()
 363         {
 364           public void actionPerformed(ActionEvent evt)
 365           {
 366             userDefinedColour_actionPerformed(evt);
 367           }
 368         });
 369         colourMenu.insert(radioItem, 15);
 370         colours.add(radioItem);
 371       }
 372     }
 373     colours.add(noColourmenuItem);
 374     colours.add(clustalColour);
 375     colours.add(zappoColour);
 376     colours.add(taylorColour);
 377     colours.add(hydrophobicityColour);
 378     colours.add(helixColour);
 379     colours.add(strandColour);
 380     colours.add(turnColour);
 381     colours.add(buriedColour);
 382     colours.add(userDefinedColour);
 383     colours.add(PIDColour);
 384     colours.add(BLOSUM62Colour);
 385     colours.add(nucleotideColour);
 386
 387     setColourSelected(jalview.bin.Cache
 388             .getDefault("DEFAULT_COLOUR", "None"));
 389
 390   }
 391
 392   public void setColourSelected(String defaultColour)
 393   {
 394
 395     if (defaultColour != null)
 396     {
 397       int index = ColourSchemeProperty
 398               .getColourIndexFromName(defaultColour);
 399
 400       switch (index)
 401       {
 402       case ColourSchemeProperty.NONE:
 403         noColourmenuItem.setSelected(true);
 404         break;
 405       case ColourSchemeProperty.CLUSTAL:
 406         clustalColour.setSelected(true);
 407
 408         break;
 409
 410       case ColourSchemeProperty.BLOSUM:
 411         BLOSUM62Colour.setSelected(true);
 412
 413         break;
 414
 415       case ColourSchemeProperty.PID:
 416         PIDColour.setSelected(true);
 417
 418         break;
 419
 420       case ColourSchemeProperty.ZAPPO:
 421         zappoColour.setSelected(true);
 422
 423         break;
 424
 425       case ColourSchemeProperty.TAYLOR:
 426         taylorColour.setSelected(true);
 427         break;
 428
 429       case ColourSchemeProperty.HYDROPHOBIC:
 430         hydrophobicityColour.setSelected(true);
 431
 432         break;
 433
 434       case ColourSchemeProperty.HELIX:
 435         helixColour.setSelected(true);
 436
 437         break;
 438
 439       case ColourSchemeProperty.STRAND:
 440         strandColour.setSelected(true);
 441
 442         break;
 443
 444       case ColourSchemeProperty.TURN:
 445         turnColour.setSelected(true);
 446
 447         break;
 448
 449       case ColourSchemeProperty.BURIED:
 450         buriedColour.setSelected(true);
 451
 452         break;
 453
 454       case ColourSchemeProperty.NUCLEOTIDE:
 455         nucleotideColour.setSelected(true);
 456
 457         break;
 458
 459       case ColourSchemeProperty.USER_DEFINED:
 460         userDefinedColour.setSelected(true);
 461
 462         break;
 463       }
 464     }
 465
 466   }
 467
 468   private void jbInit() throws Exception
 469   {
 470     fileMenu.setText("File");
 471     saveAs.setText("Save As...");
 472     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 473             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 474                     .getMenuShortcutKeyMask()
 475                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 476     saveAs.addActionListener(new ActionListener()
 477     {
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         saveAs_actionPerformed(e);
 481       }
 482     });
 483     closeMenuItem.setText("Close");
 484     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 485             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 486                     .getMenuShortcutKeyMask(), false));
 487     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 488     {
 489       public void actionPerformed(ActionEvent e)
 490       {
 491         closeMenuItem_actionPerformed(false);
 492       }
 493     });
 494     editMenu.setText("Edit");
 495     viewMenu.setText("View");
 496     colourMenu.setText("Colour");
 497     calculateMenu.setText("Calculate");
 498     webService.setText("Web Service");
 499     selectAllSequenceMenuItem.setText("Select All");
 500     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 501             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 502                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 503     selectAllSequenceMenuItem
 504             .addActionListener(new java.awt.event.ActionListener()
 505             {
 506               public void actionPerformed(ActionEvent e)
 507               {
 508                 selectAllSequenceMenuItem_actionPerformed(e);
 509               }
 510             });
 511     deselectAllSequenceMenuItem.setText("Deselect All");
 512     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 513             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 514     deselectAllSequenceMenuItem
 515             .addActionListener(new java.awt.event.ActionListener()
 516             {
 517               public void actionPerformed(ActionEvent e)
 518               {
 519                 deselectAllSequenceMenuItem_actionPerformed(e);
 520               }
 521             });
 522     invertSequenceMenuItem.setText("Invert Sequence Selection");
 523     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 524             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 525                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 526     invertSequenceMenuItem
 527             .addActionListener(new java.awt.event.ActionListener()
 528             {
 529               public void actionPerformed(ActionEvent e)
 530               {
 531                 invertSequenceMenuItem_actionPerformed(e);
 532               }
 533             });
 534     remove2LeftMenuItem.setText("Remove Left");
 535     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 536             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 537                     .getMenuShortcutKeyMask(), false));
 538     remove2LeftMenuItem
 539             .addActionListener(new java.awt.event.ActionListener()
 540             {
 541               public void actionPerformed(ActionEvent e)
 542               {
 543                 remove2LeftMenuItem_actionPerformed(e);
 544               }
 545             });
 546     remove2RightMenuItem.setText("Remove Right");
 547     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 548             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 549                     .getMenuShortcutKeyMask(), false));
 550     remove2RightMenuItem
 551             .addActionListener(new java.awt.event.ActionListener()
 552             {
 553               public void actionPerformed(ActionEvent e)
 554               {
 555                 remove2RightMenuItem_actionPerformed(e);
 556               }
 557             });
 558     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 559     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 560             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 561                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 562     removeGappedColumnMenuItem
 563             .addActionListener(new java.awt.event.ActionListener()
 564             {
 565               public void actionPerformed(ActionEvent e)
 566               {
 567                 removeGappedColumnMenuItem_actionPerformed(e);
 568               }
 569             });
 570     removeAllGapsMenuItem.setText("Remove All Gaps");
 571     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 572             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 573                     .getDefaultToolkit().getMenuShortcutKeyMask()
 574                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 575     removeAllGapsMenuItem
 576             .addActionListener(new java.awt.event.ActionListener()
 577             {
 578               public void actionPerformed(ActionEvent e)
 579               {
 580                 removeAllGapsMenuItem_actionPerformed(e);
 581               }
 582             });
 583     viewBoxesMenuItem.setText("Boxes");
 584     viewBoxesMenuItem.setState(true);
 585     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 586     {
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         viewBoxesMenuItem_actionPerformed(e);
 590       }
 591     });
 592     viewTextMenuItem.setText("Text");
 593     viewTextMenuItem.setState(true);
 594     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 595     {
 596       public void actionPerformed(ActionEvent e)
 597       {
 598         viewTextMenuItem_actionPerformed(e);
 599       }
 600     });
 601     sortPairwiseMenuItem.setText("by Pairwise Identity");
 602     sortPairwiseMenuItem
 603             .addActionListener(new java.awt.event.ActionListener()
 604             {
 605               public void actionPerformed(ActionEvent e)
 606               {
 607                 sortPairwiseMenuItem_actionPerformed(e);
 608               }
 609             });
 610     sortIDMenuItem.setText("by ID");
 611     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 612     {
 613       public void actionPerformed(ActionEvent e)
 614       {
 615         sortIDMenuItem_actionPerformed(e);
 616       }
 617     });
 618     sortGroupMenuItem.setText("by Group");
 619     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 620     {
 621       public void actionPerformed(ActionEvent e)
 622       {
 623         sortGroupMenuItem_actionPerformed(e);
 624       }
 625     });
 626     removeRedundancyMenuItem.setText("Remove Redundancy...");
 627     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 628             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 629                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 630     removeRedundancyMenuItem
 631             .addActionListener(new java.awt.event.ActionListener()
 632             {
 633               public void actionPerformed(ActionEvent e)
 634               {
 635                 removeRedundancyMenuItem_actionPerformed(e);
 636               }
 637             });
 638     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 639     pairwiseAlignmentMenuItem
 640             .addActionListener(new java.awt.event.ActionListener()
 641             {
 642               public void actionPerformed(ActionEvent e)
 643               {
 644                 pairwiseAlignmentMenuItem_actionPerformed(e);
 645               }
 646             });
 647     PCAMenuItem.setText("Principal Component Analysis");
 648     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 649     {
 650       public void actionPerformed(ActionEvent e)
 651       {
 652         PCAMenuItem_actionPerformed(e);
 653       }
 654     });
 655     averageDistanceTreeMenuItem
 656             .setText("Average Distance Using % Identity");
 657     averageDistanceTreeMenuItem
 658             .addActionListener(new java.awt.event.ActionListener()
 659             {
 660               public void actionPerformed(ActionEvent e)
 661               {
 662                 averageDistanceTreeMenuItem_actionPerformed(e);
 663               }
 664             });
 665     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 666     neighbourTreeMenuItem
 667             .addActionListener(new java.awt.event.ActionListener()
 668             {
 669               public void actionPerformed(ActionEvent e)
 670               {
 671                 neighbourTreeMenuItem_actionPerformed(e);
 672               }
 673             });
 674     this.getContentPane().setLayout(borderLayout1);
 675     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 676     statusBar.setBackground(Color.white);
 677     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 678     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 679     statusBar.setText("Status bar");
 680     outputTextboxMenu.setText("Output to Textbox");
 681     clustalColour.setText("Clustalx");
 682
 683     clustalColour.addActionListener(new java.awt.event.ActionListener()
 684     {
 685       public void actionPerformed(ActionEvent e)
 686       {
 687         clustalColour_actionPerformed(e);
 688       }
 689     });
 690     zappoColour.setText("Zappo");
 691     zappoColour.addActionListener(new java.awt.event.ActionListener()
 692     {
 693       public void actionPerformed(ActionEvent e)
 694       {
 695         zappoColour_actionPerformed(e);
 696       }
 697     });
 698     taylorColour.setText("Taylor");
 699     taylorColour.addActionListener(new java.awt.event.ActionListener()
 700     {
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         taylorColour_actionPerformed(e);
 704       }
 705     });
 706     hydrophobicityColour.setText("Hydrophobicity");
 707     hydrophobicityColour
 708             .addActionListener(new java.awt.event.ActionListener()
 709             {
 710               public void actionPerformed(ActionEvent e)
 711               {
 712                 hydrophobicityColour_actionPerformed(e);
 713               }
 714             });
 715     helixColour.setText("Helix Propensity");
 716     helixColour.addActionListener(new java.awt.event.ActionListener()
 717     {
 718       public void actionPerformed(ActionEvent e)
 719       {
 720         helixColour_actionPerformed(e);
 721       }
 722     });
 723     strandColour.setText("Strand Propensity");
 724     strandColour.addActionListener(new java.awt.event.ActionListener()
 725     {
 726       public void actionPerformed(ActionEvent e)
 727       {
 728         strandColour_actionPerformed(e);
 729       }
 730     });
 731     turnColour.setText("Turn Propensity");
 732     turnColour.addActionListener(new java.awt.event.ActionListener()
 733     {
 734       public void actionPerformed(ActionEvent e)
 735       {
 736         turnColour_actionPerformed(e);
 737       }
 738     });
 739     buriedColour.setText("Buried Index");
 740     buriedColour.addActionListener(new java.awt.event.ActionListener()
 741     {
 742       public void actionPerformed(ActionEvent e)
 743       {
 744         buriedColour_actionPerformed(e);
 745       }
 746     });
 747     userDefinedColour.setText("User Defined...");
 748     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 749     {
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         userDefinedColour_actionPerformed(e);
 753       }
 754     });
 755     PIDColour.setText("Percentage Identity");
 756     PIDColour.addActionListener(new java.awt.event.ActionListener()
 757     {
 758       public void actionPerformed(ActionEvent e)
 759       {
 760         PIDColour_actionPerformed(e);
 761       }
 762     });
 763     BLOSUM62Colour.setText("BLOSUM62 Score");
 764     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 765     {
 766       public void actionPerformed(ActionEvent e)
 767       {
 768         BLOSUM62Colour_actionPerformed(e);
 769       }
 770     });
 771     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 772     avDistanceTreeBlosumMenuItem
 773             .addActionListener(new java.awt.event.ActionListener()
 774             {
 775               public void actionPerformed(ActionEvent e)
 776               {
 777                 avTreeBlosumMenuItem_actionPerformed(e);
 778               }
 779             });
 780     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 781     njTreeBlosumMenuItem
 782             .addActionListener(new java.awt.event.ActionListener()
 783             {
 784               public void actionPerformed(ActionEvent e)
 785               {
 786                 njTreeBlosumMenuItem_actionPerformed(e);
 787               }
 788             });
 789     annotationPanelMenuItem.setActionCommand("");
 790     annotationPanelMenuItem.setText("Show Annotations");
 791     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 792             "SHOW_ANNOTATIONS", true));
 793     annotationPanelMenuItem
 794             .addActionListener(new java.awt.event.ActionListener()
 795             {
 796               public void actionPerformed(ActionEvent e)
 797               {
 798                 annotationPanelMenuItem_actionPerformed(e);
 799               }
 800             });
 801     colourTextMenuItem.setText("Colour Text");
 802     colourTextMenuItem
 803             .addActionListener(new java.awt.event.ActionListener()
 804             {
 805               public void actionPerformed(ActionEvent e)
 806               {
 807                 colourTextMenuItem_actionPerformed(e);
 808               }
 809             });
 810     htmlMenuItem.setText("HTML");
 811     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 812     {
 813       public void actionPerformed(ActionEvent e)
 814       {
 815         htmlMenuItem_actionPerformed(e);
 816       }
 817     });
 818     overviewMenuItem.setText("Overview Window");
 819     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 820     {
 821       public void actionPerformed(ActionEvent e)
 822       {
 823         overviewMenuItem_actionPerformed(e);
 824       }
 825     });
 826     undoMenuItem.setEnabled(false);
 827     undoMenuItem.setText("Undo");
 828     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 829             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 830                     .getMenuShortcutKeyMask(), false));
 831     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 832     {
 833       public void actionPerformed(ActionEvent e)
 834       {
 835         undoMenuItem_actionPerformed(e);
 836       }
 837     });
 838     redoMenuItem.setEnabled(false);
 839     redoMenuItem.setText("Redo");
 840     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 841             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 842                     .getMenuShortcutKeyMask(), false));
 843     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 844     {
 845       public void actionPerformed(ActionEvent e)
 846       {
 847         redoMenuItem_actionPerformed(e);
 848       }
 849     });
 850     conservationMenuItem.setText("By Conservation");
 851     conservationMenuItem
 852             .addActionListener(new java.awt.event.ActionListener()
 853             {
 854               public void actionPerformed(ActionEvent e)
 855               {
 856                 conservationMenuItem_actionPerformed(e);
 857               }
 858             });
 859     noColourmenuItem.setText("None");
 860     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 861     {
 862       public void actionPerformed(ActionEvent e)
 863       {
 864         noColourmenuItem_actionPerformed(e);
 865       }
 866     });
 867     wrapMenuItem.setText("Wrap");
 868     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 869     {
 870       public void actionPerformed(ActionEvent e)
 871       {
 872         wrapMenuItem_actionPerformed(e);
 873       }
 874     });
 875     printMenuItem.setText("Print ...");
 876     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 877             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 878                     .getMenuShortcutKeyMask(), false));
 879     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 880     {
 881       public void actionPerformed(ActionEvent e)
 882       {
 883         printMenuItem_actionPerformed(e);
 884       }
 885     });
 886     renderGapsMenuItem.setText("Show Gaps");
 887     renderGapsMenuItem.setState(true);
 888     renderGapsMenuItem
 889             .addActionListener(new java.awt.event.ActionListener()
 890             {
 891               public void actionPerformed(ActionEvent e)
 892               {
 893                 renderGapsMenuItem_actionPerformed(e);
 894               }
 895             });
 896     findMenuItem.setText("Find...");
 897     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 898             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 899                     .getMenuShortcutKeyMask(), false));
 900     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 901     {
 902       public void actionPerformed(ActionEvent e)
 903       {
 904         findMenuItem_actionPerformed(e);
 905       }
 906     });
 907     abovePIDThreshold.setText("Above Identity Threshold");
 908     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 909     {
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         abovePIDThreshold_actionPerformed(e);
 913       }
 914     });
 915     showSeqFeatures.setText("Show Sequence Features");
 916     showSeqFeatures.addActionListener(new ActionListener()
 917     {
 918       public void actionPerformed(ActionEvent actionEvent)
 919       {
 920         showSeqFeatures_actionPerformed(actionEvent);
 921       }
 922     });
 923     showDbRefsMenuitem.setText("Show Database Refs");
 924     showDbRefsMenuitem.addActionListener(new ActionListener()
 925     {
 926
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         showDbRefs_actionPerformed(e);
 930       }
 931
 932     });
 933     showNpFeatsMenuitem.setText("Show Non-Positional Features");
 934     showNpFeatsMenuitem.addActionListener(new ActionListener()
 935     {
 936
 937       public void actionPerformed(ActionEvent e)
 938       {
 939         showNpFeats_actionPerformed(e);
 940       }
 941
 942     });
 943     nucleotideColour.setText("Nucleotide");
 944     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 945     {
 946       public void actionPerformed(ActionEvent e)
 947       {
 948         nucleotideColour_actionPerformed(e);
 949       }
 950     });
 951     deleteGroups.setText("Undefine groups");
 952     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 953             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
 954                     .getMenuShortcutKeyMask(), false));
 955     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 956     {
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         deleteGroups_actionPerformed(e);
 960       }
 961     });
 962     copy.setText("Copy");
 963     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 964             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
 965                     .getMenuShortcutKeyMask(), false));
 966
 967     copy.addActionListener(new java.awt.event.ActionListener()
 968     {
 969       public void actionPerformed(ActionEvent e)
 970       {
 971         copy_actionPerformed(e);
 972       }
 973     });
 974     cut.setText("Cut");
 975     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 976             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
 977                     .getMenuShortcutKeyMask(), false));
 978     cut.addActionListener(new java.awt.event.ActionListener()
 979     {
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         cut_actionPerformed(e);
 983       }
 984     });
 985     delete.setText("Delete");
 986     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 987             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
 988     delete.addActionListener(new java.awt.event.ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         delete_actionPerformed(e);
 993       }
 994     });
 995     pasteMenu.setText("Paste");
 996     pasteNew.setText("To New Alignment");
 997     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 998             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
 999                     .getMenuShortcutKeyMask()
1000                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1001     pasteNew.addActionListener(new java.awt.event.ActionListener()
1002     {
1003       public void actionPerformed(ActionEvent e)
1004       {
1005         pasteNew_actionPerformed(e);
1006       }
1007     });
1008     pasteThis.setText("Add To This Alignment");
1009     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1010             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1011                     .getMenuShortcutKeyMask(), false));
1012     pasteThis.addActionListener(new java.awt.event.ActionListener()
1013     {
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         pasteThis_actionPerformed(e);
1017       }
1018     });
1019     applyToAllGroups.setText("Apply Colour To All Groups");
1020     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1021     {
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         applyToAllGroups_actionPerformed(e);
1025       }
1026     });
1027     createPNG.addActionListener(new java.awt.event.ActionListener()
1028     {
1029       public void actionPerformed(ActionEvent e)
1030       {
1031         createPNG(null);
1032       }
1033     });
1034     createPNG.setActionCommand("Save As PNG Image");
1035     createPNG.setText("PNG");
1036     font.setText("Font...");
1037     font.addActionListener(new java.awt.event.ActionListener()
1038     {
1039       public void actionPerformed(ActionEvent e)
1040       {
1041         font_actionPerformed(e);
1042       }
1043     });
1044
1045     seqLimits.setText("Show Sequence Limits");
1046     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1047     seqLimits.addActionListener(new java.awt.event.ActionListener()
1048     {
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         seqLimit_actionPerformed(e);
1052       }
1053     });
1054     epsFile.setText("EPS");
1055     epsFile.addActionListener(new java.awt.event.ActionListener()
1056     {
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         createEPS(null);
1060       }
1061     });
1062     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1063     LoadtreeMenuItem.setText("Load Associated Tree");
1064     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1065     {
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         LoadtreeMenuItem_actionPerformed(e);
1069       }
1070     });
1071     scaleAbove.setVisible(false);
1072     scaleAbove.setText("Scale Above");
1073     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1074     {
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         scaleAbove_actionPerformed(e);
1078       }
1079     });
1080     scaleLeft.setVisible(false);
1081     scaleLeft.setSelected(true);
1082     scaleLeft.setText("Scale Left");
1083     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1084     {
1085       public void actionPerformed(ActionEvent e)
1086       {
1087         scaleLeft_actionPerformed(e);
1088       }
1089     });
1090     scaleRight.setVisible(false);
1091     scaleRight.setSelected(true);
1092     scaleRight.setText("Scale Right");
1093     scaleRight.addActionListener(new java.awt.event.ActionListener()
1094     {
1095       public void actionPerformed(ActionEvent e)
1096       {
1097         scaleRight_actionPerformed(e);
1098       }
1099     });
1100     centreColumnLabelsMenuItem.setVisible(true);
1101     centreColumnLabelsMenuItem.setState(false);
1102     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1103     centreColumnLabelsMenuItem
1104             .addActionListener(new java.awt.event.ActionListener()
1105             {
1106               public void actionPerformed(ActionEvent e)
1107               {
1108                 centreColumnLabels_actionPerformed(e);
1109               }
1110             });
1111     followHighlightMenuItem.setVisible(true);
1112     followHighlightMenuItem.setState(true);
1113     followHighlightMenuItem.setText("Automatic Scrolling");
1114     followHighlightMenuItem.addActionListener(new ActionListener()
1115     {
1116
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         followHighlight_actionPerformed();
1120       }
1121
1122     });
1123
1124     modifyPID.setText("Modify Identity Threshold...");
1125     modifyPID.addActionListener(new java.awt.event.ActionListener()
1126     {
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         modifyPID_actionPerformed(e);
1130       }
1131     });
1132     modifyConservation.setText("Modify Conservation Threshold...");
1133     modifyConservation
1134             .addActionListener(new java.awt.event.ActionListener()
1135             {
1136               public void actionPerformed(ActionEvent e)
1137               {
1138                 modifyConservation_actionPerformed(e);
1139               }
1140             });
1141     sortByTreeMenu.setText("By Tree Order");
1142     sort.setText("Sort");
1143     sort.addMenuListener(new MenuListener()
1144     {
1145       public void menuSelected(MenuEvent e)
1146       {
1147         buildTreeMenu();
1148       }
1149
1150       public void menuDeselected(MenuEvent e)
1151       {
1152       }
1153
1154       public void menuCanceled(MenuEvent e)
1155       {
1156       }
1157     });
1158     sortByAnnotScore.setText("by Score");
1159     sort.add(sortByAnnotScore);
1160     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1161     {
1162
1163       public void menuCanceled(MenuEvent e)
1164       {
1165       }
1166
1167       public void menuDeselected(MenuEvent e)
1168       {
1169       }
1170
1171       public void menuSelected(MenuEvent e)
1172       {
1173         buildSortByAnnotationScoresMenu();
1174       }
1175     });
1176     sortByAnnotScore.setVisible(false);
1177
1178     calculateTree.setText("Calculate Tree");
1179
1180     jMenu2.setText("Export Image");
1181     padGapsMenuitem.setText("Pad Gaps");
1182     padGapsMenuitem.setState(jalview.bin.Cache
1183             .getDefault("PAD_GAPS", false));
1184     padGapsMenuitem.addActionListener(new ActionListener()
1185     {
1186       public void actionPerformed(ActionEvent e)
1187       {
1188         padGapsMenuitem_actionPerformed(e);
1189       }
1190     });
1191     vamsasStore.setVisible(false);
1192     vamsasStore.setText("VAMSAS store");
1193     vamsasStore.addActionListener(new ActionListener()
1194     {
1195       public void actionPerformed(ActionEvent e)
1196       {
1197         vamsasStore_actionPerformed(e);
1198       }
1199     });
1200     showTranslation.setText("Translate cDNA");
1201     showTranslation.addActionListener(new ActionListener()
1202     {
1203       public void actionPerformed(ActionEvent e)
1204       {
1205         showTranslation_actionPerformed(e);
1206       }
1207     });
1208     extractScores.setText("Extract Scores...");
1209     extractScores.addActionListener(new ActionListener()
1210     {
1211       public void actionPerformed(ActionEvent e)
1212       {
1213         extractScores_actionPerformed(e);
1214       }
1215     });
1216     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1217                                     // score extraction
1218     showProducts.setText("Get Cross References");
1219     /*
1220      * showProducts.addActionListener(new ActionListener() {
1221      *
1222      * public void actionPerformed(ActionEvent e) {
1223      * showProducts_actionPerformed(e); } });
1224      */
1225     featureSettings.setText("Feature Settings...");
1226     featureSettings.addActionListener(new ActionListener()
1227     {
1228       public void actionPerformed(ActionEvent e)
1229       {
1230         featureSettings_actionPerformed(e);
1231       }
1232     });
1233     fetchSequence.setText("Fetch Sequence(s)...");
1234     fetchSequence.addActionListener(new ActionListener()
1235     {
1236       public void actionPerformed(ActionEvent e)
1237       {
1238         fetchSequence_actionPerformed(e);
1239       }
1240     });
1241
1242     annotationColour.setText("By Annotation...");
1243     annotationColour.addActionListener(new ActionListener()
1244     {
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         annotationColour_actionPerformed(e);
1248       }
1249     });
1250     associatedData.setText("Load Features / Annotations");
1251     associatedData.addActionListener(new ActionListener()
1252     {
1253       public void actionPerformed(ActionEvent e)
1254       {
1255         associatedData_actionPerformed(e);
1256       }
1257     });
1258     autoCalculate.setText("Autocalculate Consensus");
1259     autoCalculate.setState(jalview.bin.Cache.getDefault(
1260             "AUTO_CALC_CONSENSUS", true));
1261     autoCalculate.addActionListener(new ActionListener()
1262     {
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         autoCalculate_actionPerformed(e);
1266       }
1267     });
1268     addSequenceMenu.setText("Add Sequences");
1269     addFromFile.setText("From File");
1270     addFromFile.addActionListener(new ActionListener()
1271     {
1272       public void actionPerformed(ActionEvent e)
1273       {
1274         addFromFile_actionPerformed(e);
1275       }
1276     });
1277     addFromText.setText("From Textbox");
1278     addFromText.addActionListener(new ActionListener()
1279     {
1280       public void actionPerformed(ActionEvent e)
1281       {
1282         addFromText_actionPerformed(e);
1283       }
1284     });
1285     addFromURL.setText("From URL");
1286     addFromURL.addActionListener(new ActionListener()
1287     {
1288       public void actionPerformed(ActionEvent e)
1289       {
1290         addFromURL_actionPerformed(e);
1291       }
1292     });
1293     exportFeatures.setText("Export Features...");
1294     exportFeatures.addActionListener(new ActionListener()
1295     {
1296       public void actionPerformed(ActionEvent e)
1297       {
1298         exportFeatures_actionPerformed(e);
1299       }
1300     });
1301     exportAnnotations.setText("Export Annotations...");
1302     exportAnnotations.addActionListener(new ActionListener()
1303     {
1304       public void actionPerformed(ActionEvent e)
1305       {
1306         exportAnnotations_actionPerformed(e);
1307       }
1308     });
1309     statusPanel.setLayout(gridLayout1);
1310     jMenu3.setText("Show");
1311     showAllSeqs.setText("All Sequences");
1312     showAllSeqs.addActionListener(new ActionListener()
1313     {
1314       public void actionPerformed(ActionEvent e)
1315       {
1316         showAllSeqs_actionPerformed(e);
1317       }
1318     });
1319     showAllColumns.setText("All Columns");
1320     showAllColumns.addActionListener(new ActionListener()
1321     {
1322       public void actionPerformed(ActionEvent e)
1323       {
1324         showAllColumns_actionPerformed(e);
1325       }
1326     });
1327     hideMenu.setText("Hide");
1328     hideSelSequences.setText("Selected Sequences");
1329     hideSelSequences.addActionListener(new ActionListener()
1330     {
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         hideSelSequences_actionPerformed(e);
1334       }
1335     });
1336     hideSelColumns.setText("Selected Columns");
1337     hideSelColumns.addActionListener(new ActionListener()
1338     {
1339       public void actionPerformed(ActionEvent e)
1340       {
1341         hideSelColumns_actionPerformed(e);
1342       }
1343     });
1344     hiddenMarkers.setText("Show Hidden Markers");
1345     hiddenMarkers.addActionListener(new ActionListener()
1346     {
1347       public void actionPerformed(ActionEvent e)
1348       {
1349         hiddenMarkers_actionPerformed(e);
1350       }
1351     });
1352     invertColSel.setText("Invert Column Selection");
1353     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1354             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1355                     .getMenuShortcutKeyMask()
1356                     | java.awt.event.KeyEvent.ALT_MASK, false));
1357     invertColSel.addActionListener(new ActionListener()
1358     {
1359       public void actionPerformed(ActionEvent e)
1360       {
1361         invertColSel_actionPerformed(e);
1362       }
1363     });
1364     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1365     {
1366       public void stateChanged(ChangeEvent evt)
1367       {
1368         JTabbedPane pane = (JTabbedPane) evt.getSource();
1369         int sel = pane.getSelectedIndex();
1370         tabSelectionChanged(sel);
1371       }
1372     });
1373     tabbedPane.addMouseListener(new MouseAdapter()
1374     {
1375       public void mousePressed(MouseEvent e)
1376       {
1377         tabbedPane_mousePressed(e);
1378       }
1379     });
1380     tabbedPane.addFocusListener(new FocusAdapter()
1381     {
1382       public void focusGained(FocusEvent e)
1383       {
1384         tabbedPane_focusGained(e);
1385       }
1386     });
1387     save.setText("Save");
1388     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1389             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1390                     .getMenuShortcutKeyMask(), false));
1391     save.addActionListener(new ActionListener()
1392     {
1393       public void actionPerformed(ActionEvent e)
1394       {
1395         save_actionPerformed(e);
1396       }
1397     });
1398     reload.setEnabled(false);
1399     reload.setText("Reload");
1400     reload.addActionListener(new ActionListener()
1401     {
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         reload_actionPerformed(e);
1405       }
1406     });
1407     newView.setText("New View");
1408     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1409             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1410                     .getMenuShortcutKeyMask(), false));
1411     newView.addActionListener(new ActionListener()
1412     {
1413       public void actionPerformed(ActionEvent e)
1414       {
1415         newView_actionPerformed(e);
1416       }
1417     });
1418     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1419             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1420     textColour.setText("Colour Text ...");
1421     textColour.addActionListener(new ActionListener()
1422     {
1423       public void actionPerformed(ActionEvent e)
1424       {
1425         textColour_actionPerformed(e);
1426       }
1427     });
1428     formatMenu.setText("Format");
1429     selectMenu.setText("Select");
1430     idRightAlign.setText("Right Align Sequence Id");
1431     idRightAlign.addActionListener(new ActionListener()
1432     {
1433       public void actionPerformed(ActionEvent e)
1434       {
1435         idRightAlign_actionPerformed(e);
1436       }
1437     });
1438     gatherViews.setEnabled(false);
1439     gatherViews.setText("Gather Views");
1440     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1441             java.awt.event.KeyEvent.VK_G, 0, false));
1442     gatherViews.addActionListener(new ActionListener()
1443     {
1444       public void actionPerformed(ActionEvent e)
1445       {
1446         gatherViews_actionPerformed(e);
1447       }
1448     });
1449     expandViews.setEnabled(false);
1450     expandViews.setText("Expand Views");
1451     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1452             java.awt.event.KeyEvent.VK_X, 0, false));
1453     expandViews.addActionListener(new ActionListener()
1454     {
1455       public void actionPerformed(ActionEvent e)
1456       {
1457         expandViews_actionPerformed(e);
1458       }
1459     });
1460     pageSetup.setText("Page Setup ...");
1461     pageSetup.addActionListener(new ActionListener()
1462     {
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         pageSetup_actionPerformed(e);
1466       }
1467     });
1468     alignmentProperties.setText("Alignment Properties...");
1469     alignmentProperties.addActionListener(new ActionListener()
1470     {
1471       public void actionPerformed(ActionEvent actionEvent)
1472       {
1473         alignmentProperties();
1474       }
1475     });
1476     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1477     alignFrameMenuBar.add(fileMenu);
1478     alignFrameMenuBar.add(editMenu);
1479     alignFrameMenuBar.add(selectMenu);
1480     alignFrameMenuBar.add(viewMenu);
1481     alignFrameMenuBar.add(formatMenu);
1482     alignFrameMenuBar.add(colourMenu);
1483     alignFrameMenuBar.add(calculateMenu);
1484     alignFrameMenuBar.add(webService);
1485     fileMenu.add(fetchSequence);
1486     fileMenu.add(addSequenceMenu);
1487     fileMenu.add(reload);
1488     fileMenu.addSeparator();
1489     fileMenu.add(vamsasStore);
1490     fileMenu.add(save);
1491     fileMenu.add(saveAs);
1492     fileMenu.add(outputTextboxMenu);
1493     fileMenu.add(pageSetup);
1494     fileMenu.add(printMenuItem);
1495     fileMenu.addSeparator();
1496     fileMenu.add(jMenu2);
1497     fileMenu.add(exportFeatures);
1498     fileMenu.add(exportAnnotations);
1499     fileMenu.add(LoadtreeMenuItem);
1500     fileMenu.add(associatedData);
1501     fileMenu.addSeparator();
1502     fileMenu.add(closeMenuItem);
1503     editMenu.add(undoMenuItem);
1504     editMenu.add(redoMenuItem);
1505     editMenu.add(cut);
1506     editMenu.add(copy);
1507     editMenu.add(pasteMenu);
1508     editMenu.add(delete);
1509     editMenu.addSeparator();
1510     editMenu.add(remove2LeftMenuItem);
1511     editMenu.add(remove2RightMenuItem);
1512     editMenu.add(removeGappedColumnMenuItem);
1513     editMenu.add(removeAllGapsMenuItem);
1514     editMenu.add(removeRedundancyMenuItem);
1515     editMenu.addSeparator();
1516     editMenu.add(padGapsMenuitem);
1517     viewMenu.add(newView);
1518     viewMenu.add(expandViews);
1519     viewMenu.add(gatherViews);
1520     viewMenu.addSeparator();
1521     viewMenu.add(jMenu3);
1522     viewMenu.add(hideMenu);
1523     viewMenu.addSeparator();
1524     viewMenu.add(followHighlightMenuItem);
1525     viewMenu.add(annotationPanelMenuItem);
1526     viewMenu.addSeparator();
1527     viewMenu.add(showSeqFeatures);
1528     viewMenu.add(featureSettings);
1529     tooltipSettingsMenu.add(showDbRefsMenuitem);
1530     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1531     viewMenu.add(tooltipSettingsMenu);
1532     viewMenu.addSeparator();
1533     viewMenu.add(alignmentProperties);
1534     viewMenu.addSeparator();
1535     viewMenu.add(overviewMenuItem);
1536     colourMenu.add(applyToAllGroups);
1537     colourMenu.add(textColour);
1538     colourMenu.addSeparator();
1539     colourMenu.add(noColourmenuItem);
1540     colourMenu.add(clustalColour);
1541     colourMenu.add(BLOSUM62Colour);
1542     colourMenu.add(PIDColour);
1543     colourMenu.add(zappoColour);
1544     colourMenu.add(taylorColour);
1545     colourMenu.add(hydrophobicityColour);
1546     colourMenu.add(helixColour);
1547     colourMenu.add(strandColour);
1548     colourMenu.add(turnColour);
1549     colourMenu.add(buriedColour);
1550     colourMenu.add(nucleotideColour);
1551     colourMenu.add(userDefinedColour);
1552     colourMenu.addSeparator();
1553     colourMenu.add(conservationMenuItem);
1554     colourMenu.add(modifyConservation);
1555     colourMenu.add(abovePIDThreshold);
1556     colourMenu.add(modifyPID);
1557     colourMenu.add(annotationColour);
1558     calculateMenu.add(sort);
1559     calculateMenu.add(calculateTree);
1560     calculateMenu.addSeparator();
1561     calculateMenu.add(pairwiseAlignmentMenuItem);
1562     calculateMenu.add(PCAMenuItem);
1563     calculateMenu.addSeparator();
1564     calculateMenu.add(showTranslation);
1565     calculateMenu.add(showProducts);
1566     calculateMenu.add(autoCalculate);
1567     calculateMenu.addSeparator();
1568     calculateMenu.add(extractScores);
1569     webServiceNoServices = new JMenuItem("<No Services>");
1570     webService.add(webServiceNoServices);
1571     pasteMenu.add(pasteNew);
1572     pasteMenu.add(pasteThis);
1573     sort.add(sortIDMenuItem);
1574     sort.add(sortGroupMenuItem);
1575     sort.add(sortPairwiseMenuItem);
1576     sort.add(sortByTreeMenu);
1577     calculateTree.add(averageDistanceTreeMenuItem);
1578     calculateTree.add(neighbourTreeMenuItem);
1579     calculateTree.add(avDistanceTreeBlosumMenuItem);
1580     calculateTree.add(njTreeBlosumMenuItem);
1581     jMenu2.add(htmlMenuItem);
1582     jMenu2.add(epsFile);
1583     jMenu2.add(createPNG);
1584     addSequenceMenu.add(addFromFile);
1585     addSequenceMenu.add(addFromText);
1586     addSequenceMenu.add(addFromURL);
1587     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1588     statusPanel.add(statusBar, null);
1589     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1590     jMenu3.add(showAllColumns);
1591     jMenu3.add(showAllSeqs);
1592     hideMenu.add(hideSelColumns);
1593     hideMenu.add(hideSelSequences);
1594     formatMenu.add(font);
1595     formatMenu.addSeparator();
1596     formatMenu.add(wrapMenuItem);
1597     formatMenu.add(scaleAbove);
1598     formatMenu.add(scaleLeft);
1599     formatMenu.add(scaleRight);
1600     formatMenu.add(seqLimits);
1601     formatMenu.add(idRightAlign);
1602     formatMenu.add(hiddenMarkers);
1603     formatMenu.add(viewBoxesMenuItem);
1604     formatMenu.add(viewTextMenuItem);
1605     formatMenu.add(colourTextMenuItem);
1606     formatMenu.add(renderGapsMenuItem);
1607     formatMenu.add(centreColumnLabelsMenuItem);
1608     selectMenu.add(findMenuItem);
1609     selectMenu.addSeparator();
1610     selectMenu.add(selectAllSequenceMenuItem);
1611     selectMenu.add(deselectAllSequenceMenuItem);
1612     selectMenu.add(invertSequenceMenuItem);
1613     selectMenu.add(invertColSel);
1614     selectMenu.add(deleteGroups);
1615   }
1616
1617   protected void followHighlight_actionPerformed()
1618   {
1619     // TODO Auto-generated method stub
1620
1621   }
1622
1623   protected void showNpFeats_actionPerformed(ActionEvent e)
1624   {
1625     // TODO Auto-generated method stub
1626
1627   }
1628
1629   protected void showDbRefs_actionPerformed(ActionEvent e)
1630   {
1631     // TODO Auto-generated method stub
1632
1633   }
1634
1635   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1636   {
1637   }
1638
1639   protected void showProducts_actionPerformed(ActionEvent e)
1640   {
1641   }
1642
1643   protected void buildSortByAnnotationScoresMenu()
1644   {
1645   }
1646
1647   protected void extractScores_actionPerformed(ActionEvent e)
1648   {
1649   }
1650
1651   protected void outputText_actionPerformed(ActionEvent e)
1652   {
1653   }
1654
1655   public void addFromFile_actionPerformed(ActionEvent e)
1656   {
1657
1658   }
1659
1660   public void addFromText_actionPerformed(ActionEvent e)
1661   {
1662
1663   }
1664
1665   public void addFromURL_actionPerformed(ActionEvent e)
1666   {
1667
1668   }
1669
1670   public void exportFeatures_actionPerformed(ActionEvent e)
1671   {
1672
1673   }
1674
1675   public void exportAnnotations_actionPerformed(ActionEvent e)
1676   {
1677
1678   }
1679
1680   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1681   {
1682   }
1683
1684   protected void closeMenuItem_actionPerformed(boolean b)
1685   {
1686   }
1687
1688   protected void redoMenuItem_actionPerformed(ActionEvent e)
1689   {
1690   }
1691
1692   protected void undoMenuItem_actionPerformed(ActionEvent e)
1693   {
1694   }
1695
1696   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1697   {
1698   }
1699
1700   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1701   {
1702   }
1703
1704   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1705   {
1706   }
1707
1708   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1709   {
1710   }
1711
1712   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1713   {
1714   }
1715
1716   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1717   {
1718   }
1719
1720   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1721   {
1722   }
1723
1724   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1725   {
1726   }
1727
1728   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1729   {
1730   }
1731
1732   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1733   {
1734   }
1735
1736   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1737   {
1738   }
1739
1740   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1741   {
1742   }
1743
1744   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1745   {
1746   }
1747
1748   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1749   {
1750   }
1751
1752   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1753   {
1754   }
1755
1756   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1757   {
1758   }
1759
1760   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1761   {
1762   }
1763
1764   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1765   {
1766   }
1767
1768   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1769   {
1770   }
1771
1772   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1773   {
1774   }
1775
1776   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1777   {
1778   }
1779
1780   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1781   {
1782   }
1783
1784   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1785   {
1786   }
1787
1788   protected void clustalColour_actionPerformed(ActionEvent e)
1789   {
1790   }
1791
1792   protected void zappoColour_actionPerformed(ActionEvent e)
1793   {
1794   }
1795
1796   protected void taylorColour_actionPerformed(ActionEvent e)
1797   {
1798   }
1799
1800   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1801   {
1802   }
1803
1804   protected void helixColour_actionPerformed(ActionEvent e)
1805   {
1806   }
1807
1808   protected void strandColour_actionPerformed(ActionEvent e)
1809   {
1810   }
1811
1812   protected void turnColour_actionPerformed(ActionEvent e)
1813   {
1814   }
1815
1816   protected void buriedColour_actionPerformed(ActionEvent e)
1817   {
1818   }
1819
1820   protected void userDefinedColour_actionPerformed(ActionEvent e)
1821   {
1822   }
1823
1824   protected void PIDColour_actionPerformed(ActionEvent e)
1825   {
1826   }
1827
1828   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1829   {
1830   }
1831
1832   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1833   {
1834   }
1835
1836   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1837   {
1838   }
1839
1840   protected void printMenuItem_actionPerformed(ActionEvent e)
1841   {
1842   }
1843
1844   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1845   {
1846   }
1847
1848   protected void findMenuItem_actionPerformed(ActionEvent e)
1849   {
1850   }
1851
1852   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1853   {
1854   }
1855
1856   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1857   {
1858   }
1859
1860   protected void nucleotideColour_actionPerformed(ActionEvent e)
1861   {
1862   }
1863
1864   protected void deleteGroups_actionPerformed(ActionEvent e)
1865   {
1866   }
1867
1868   protected void copy_actionPerformed(ActionEvent e)
1869   {
1870   }
1871
1872   protected void cut_actionPerformed(ActionEvent e)
1873   {
1874   }
1875
1876   protected void delete_actionPerformed(ActionEvent e)
1877   {
1878   }
1879
1880   protected void pasteNew_actionPerformed(ActionEvent e)
1881   {
1882   }
1883
1884   protected void pasteThis_actionPerformed(ActionEvent e)
1885   {
1886   }
1887
1888   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1889   {
1890   }
1891
1892   public void createPNG(java.io.File f)
1893   {
1894   }
1895
1896   protected void font_actionPerformed(ActionEvent e)
1897   {
1898   }
1899
1900   protected void seqLimit_actionPerformed(ActionEvent e)
1901   {
1902   }
1903
1904   public void seqDBRef_actionPerformed(ActionEvent e)
1905   {
1906
1907   }
1908
1909   public void createEPS(java.io.File f)
1910   {
1911   }
1912
1913   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
1914   {
1915   }
1916
1917   protected void jpred_actionPerformed(ActionEvent e)
1918   {
1919   }
1920
1921   protected void scaleAbove_actionPerformed(ActionEvent e)
1922   {
1923   }
1924
1925   protected void scaleLeft_actionPerformed(ActionEvent e)
1926   {
1927   }
1928
1929   protected void scaleRight_actionPerformed(ActionEvent e)
1930   {
1931   }
1932
1933   protected void modifyPID_actionPerformed(ActionEvent e)
1934   {
1935   }
1936
1937   protected void modifyConservation_actionPerformed(ActionEvent e)
1938   {
1939   }
1940
1941   protected void saveAs_actionPerformed(ActionEvent e)
1942   {
1943   }
1944
1945   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
1946   {
1947   }
1948
1949   public void vamsasStore_actionPerformed(ActionEvent e)
1950   {
1951
1952   }
1953
1954   public void vamsasLoad_actionPerformed(ActionEvent e)
1955   {
1956
1957   }
1958
1959   public void showTranslation_actionPerformed(ActionEvent e)
1960   {
1961
1962   }
1963
1964   public void featureSettings_actionPerformed(ActionEvent e)
1965   {
1966
1967   }
1968
1969   public void fetchSequence_actionPerformed(ActionEvent e)
1970   {
1971
1972   }
1973
1974   public void smoothFont_actionPerformed(ActionEvent e)
1975   {
1976
1977   }
1978
1979   public void annotationColour_actionPerformed(ActionEvent e)
1980   {
1981
1982   }
1983
1984   public void associatedData_actionPerformed(ActionEvent e)
1985   {
1986
1987   }
1988
1989   public void autoCalculate_actionPerformed(ActionEvent e)
1990   {
1991
1992   }
1993
1994   public void showAllSeqs_actionPerformed(ActionEvent e)
1995   {
1996
1997   }
1998
1999   public void showAllColumns_actionPerformed(ActionEvent e)
2000   {
2001
2002   }
2003
2004   public void hideSelSequences_actionPerformed(ActionEvent e)
2005   {
2006
2007   }
2008
2009   public void hideSelColumns_actionPerformed(ActionEvent e)
2010   {
2011
2012   }
2013
2014   public void hiddenMarkers_actionPerformed(ActionEvent e)
2015   {
2016
2017   }
2018
2019   public void findPdbId_actionPerformed(ActionEvent e)
2020   {
2021
2022   }
2023
2024   public void enterPdbId_actionPerformed(ActionEvent e)
2025   {
2026
2027   }
2028
2029   public void pdbFile_actionPerformed(ActionEvent e)
2030   {
2031
2032   }
2033
2034   public void invertColSel_actionPerformed(ActionEvent e)
2035   {
2036
2037   }
2038
2039   public void tabSelectionChanged(int sel)
2040   {
2041
2042   }
2043
2044   public void tabbedPane_mousePressed(MouseEvent e)
2045   {
2046
2047   }
2048
2049   public void tabbedPane_focusGained(FocusEvent e)
2050   {
2051     requestFocus();
2052   }
2053
2054   public void save_actionPerformed(ActionEvent e)
2055   {
2056
2057   }
2058
2059   public void reload_actionPerformed(ActionEvent e)
2060   {
2061
2062   }
2063
2064   public void newView_actionPerformed(ActionEvent e)
2065   {
2066
2067   }
2068
2069   public void textColour_actionPerformed(ActionEvent e)
2070   {
2071
2072   }
2073
2074   public void idRightAlign_actionPerformed(ActionEvent e)
2075   {
2076
2077   }
2078
2079   public void expandViews_actionPerformed(ActionEvent e)
2080   {
2081
2082   }
2083
2084   public void gatherViews_actionPerformed(ActionEvent e)
2085   {
2086
2087   }
2088
2089   public void buildTreeMenu()
2090   {
2091
2092   }
2093
2094   public void pageSetup_actionPerformed(ActionEvent e)
2095   {
2096
2097   }
2098
2099   public void alignmentProperties()
2100   {
2101
2102   }
2103 }