src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.jbgui;
  19
  20 import java.awt.*;
  21 import java.awt.event.*;
  22
  23 import javax.swing.*;
  24 import javax.swing.event.*;
  25
  26 import jalview.schemes.*;
  27
  28 public class GAlignFrame extends JInternalFrame
  29 {
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  31
  32   protected JMenu fileMenu = new JMenu();
  33
  34   protected JMenuItem closeMenuItem = new JMenuItem();
  35
  36   protected JMenu editMenu = new JMenu();
  37
  38   protected JMenu viewMenu = new JMenu();
  39
  40   protected JMenu colourMenu = new JMenu();
  41
  42   protected JMenu calculateMenu = new JMenu();
  43
  44   protected JMenu webService = new JMenu();
  45
  46   protected JMenuItem webServiceNoServices;
  47
  48   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  49
  50   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  51
  52   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  53
  54   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  55
  56   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  57
  58   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  59
  60   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  61
  62   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  63
  64   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  65
  66   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  67
  68   protected JMenuItem sortIDMenuItem = new JMenuItem();
  69
  70   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  71
  72   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  73
  74   protected JMenu sortByAnnotScore = new JMenu();
  75
  76   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  77
  78   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  79
  80   protected JMenuItem PCAMenuItem = new JMenuItem();
  81
  82   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  83
  84   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  85
  86   BorderLayout borderLayout1 = new BorderLayout();
  87
  88   public JLabel statusBar = new JLabel();
  89
  90   protected JMenuItem saveAs = new JMenuItem();
  91
  92   protected JMenu outputTextboxMenu = new JMenu();
  93
  94   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  95
  96   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  97
  98   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  99
 100   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 115
 116   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 117
 118   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 119
 120   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 121
 122   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 123
 124   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 125
 126   JMenuItem htmlMenuItem = new JMenuItem();
 127
 128   JMenuItem overviewMenuItem = new JMenuItem();
 129
 130   protected JMenuItem undoMenuItem = new JMenuItem();
 131
 132   protected JMenuItem redoMenuItem = new JMenuItem();
 133
 134   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 135
 136   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 137
 138   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 139
 140   JMenuItem printMenuItem = new JMenuItem();
 141
 142   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 143
 144   JMenuItem findMenuItem = new JMenuItem();
 145
 146   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 147
 148   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 149
 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
 200   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 203
 204   protected ButtonGroup colours = new ButtonGroup();
 205
 206   JMenuItem vamsasStore = new JMenuItem();
 207
 208   protected JMenuItem showTranslation = new JMenuItem();
 209
 210   protected JMenuItem extractScores = new JMenuItem();
 211
 212   protected JMenu showProducts = new JMenu();
 213
 214   public JMenuItem featureSettings = new JMenuItem();
 215
 216   JMenuItem fetchSequence = new JMenuItem();
 217
 218   JMenuItem annotationColour = new JMenuItem();
 219
 220   JMenuItem associatedData = new JMenuItem();
 221
 222   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 223
 224   JMenu addSequenceMenu = new JMenu();
 225
 226   JMenuItem addFromFile = new JMenuItem();
 227
 228   JMenuItem addFromText = new JMenuItem();
 229
 230   JMenuItem addFromURL = new JMenuItem();
 231
 232   JMenuItem exportAnnotations = new JMenuItem();
 233
 234   JMenuItem exportFeatures = new JMenuItem();
 235
 236   protected JPanel statusPanel = new JPanel();
 237
 238   GridLayout gridLayout1 = new GridLayout();
 239
 240   JMenu jMenu3 = new JMenu();
 241
 242   JMenuItem showAllSeqs = new JMenuItem();
 243
 244   JMenuItem showAllColumns = new JMenuItem();
 245
 246   JMenu hideMenu = new JMenu();
 247
 248   JMenuItem hideSelSequences = new JMenuItem();
 249
 250   JMenuItem hideSelColumns = new JMenuItem();
 251
 252   JMenuItem hideAllButSelection = new JMenuItem();
 253
 254   JMenuItem hideAllSelection = new JMenuItem();
 255
 256   JMenuItem showAllhidden = new JMenuItem();
 257
 258   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 259
 260   JMenuItem invertColSel = new JMenuItem();
 261
 262   protected JTabbedPane tabbedPane = new JTabbedPane();
 263
 264   JMenuItem save = new JMenuItem();
 265
 266   protected JMenuItem reload = new JMenuItem();
 267
 268   JMenuItem newView = new JMenuItem();
 269
 270   JMenuItem textColour = new JMenuItem();
 271
 272   JMenu formatMenu = new JMenu();
 273
 274   JMenu selectMenu = new JMenu();
 275
 276   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 277
 278   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 279
 280   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 281
 282   protected JMenuItem gatherViews = new JMenuItem();
 283
 284   protected JMenuItem expandViews = new JMenuItem();
 285
 286   JMenuItem pageSetup = new JMenuItem();
 287
 288   JMenuItem alignmentProperties = new JMenuItem();
 289
 290   JMenu tooltipSettingsMenu = new JMenu();
 291
 292   private JMenuItem justifyLeftMenuItem = new JMenuItem();
 293
 294   private JMenuItem justifyRightMenuItem = new JMenuItem();
 295
 296   JMenu autoAnnMenu = new JMenu();
 297
 298   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 299
 300   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
 301
 302   protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
 303
 304   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 305
 306   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 307
 308   private JMenuItem grpsFromSelection = new JMenuItem();
 309
 310   public GAlignFrame()
 311   {
 312     try
 313     {
 314       jbInit();
 315       setJMenuBar(alignFrameMenuBar);
 316
 317       // dynamically fill save as menu with available formats
 318       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 319       {
 320         JMenuItem item = new JMenuItem(
 321                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 322
 323         item.addActionListener(new java.awt.event.ActionListener()
 324         {
 325           public void actionPerformed(ActionEvent e)
 326           {
 327             outputText_actionPerformed(e);
 328           }
 329         });
 330
 331         outputTextboxMenu.add(item);
 332       }
 333     } catch (Exception e)
 334     {
 335     }
 336
 337     if (!new jalview.util.Platform().isAMac())
 338     {
 339       closeMenuItem.setMnemonic('C');
 340       outputTextboxMenu.setMnemonic('T');
 341       undoMenuItem.setMnemonic('Z');
 342       redoMenuItem.setMnemonic('0');
 343       copy.setMnemonic('C');
 344       cut.setMnemonic('U');
 345       pasteMenu.setMnemonic('P');
 346       reload.setMnemonic('R');
 347     }
 348
 349     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 350     {
 351       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 352               .getUserColourSchemes().keys();
 353
 354       while (userColours.hasMoreElements())
 355       {
 356         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 357                 userColours.nextElement().toString());
 358         radioItem.setName("USER_DEFINED");
 359         radioItem.addMouseListener(new MouseAdapter()
 360         {
 361           public void mousePressed(MouseEvent evt)
 362           {
 363             if (evt.isControlDown()
 364                     || SwingUtilities.isRightMouseButton(evt))
 365             {
 366               radioItem
 367                       .removeActionListener(radioItem.getActionListeners()[0]);
 368
 369               int option = JOptionPane.showInternalConfirmDialog(
 370                       jalview.gui.Desktop.desktop,
 371                       "Remove from default list?",
 372                       "Remove user defined colour",
 373                       JOptionPane.YES_NO_OPTION);
 374               if (option == JOptionPane.YES_OPTION)
 375               {
 376                 jalview.gui.UserDefinedColours
 377                         .removeColourFromDefaults(radioItem.getText());
 378                 colourMenu.remove(radioItem);
 379               }
 380               else
 381               {
 382                 radioItem.addActionListener(new ActionListener()
 383                 {
 384                   public void actionPerformed(ActionEvent evt)
 385                   {
 386                     userDefinedColour_actionPerformed(evt);
 387                   }
 388                 });
 389               }
 390             }
 391           }
 392         });
 393         radioItem.addActionListener(new ActionListener()
 394         {
 395           public void actionPerformed(ActionEvent evt)
 396           {
 397             userDefinedColour_actionPerformed(evt);
 398           }
 399         });
 400         colourMenu.insert(radioItem, 15);
 401         colours.add(radioItem);
 402       }
 403     }
 404     colours.add(noColourmenuItem);
 405     colours.add(clustalColour);
 406     colours.add(zappoColour);
 407     colours.add(taylorColour);
 408     colours.add(hydrophobicityColour);
 409     colours.add(helixColour);
 410     colours.add(strandColour);
 411     colours.add(turnColour);
 412     colours.add(buriedColour);
 413     colours.add(userDefinedColour);
 414     colours.add(PIDColour);
 415     colours.add(BLOSUM62Colour);
 416     colours.add(nucleotideColour);
 417
 418     setColourSelected(jalview.bin.Cache
 419             .getDefault("DEFAULT_COLOUR", "None"));
 420
 421   }
 422
 423   public void setColourSelected(String defaultColour)
 424   {
 425
 426     if (defaultColour != null)
 427     {
 428       int index = ColourSchemeProperty
 429               .getColourIndexFromName(defaultColour);
 430
 431       switch (index)
 432       {
 433       case ColourSchemeProperty.CLUSTAL:
 434         clustalColour.setSelected(true);
 435
 436         break;
 437
 438       case ColourSchemeProperty.BLOSUM:
 439         BLOSUM62Colour.setSelected(true);
 440
 441         break;
 442
 443       case ColourSchemeProperty.PID:
 444         PIDColour.setSelected(true);
 445
 446         break;
 447
 448       case ColourSchemeProperty.ZAPPO:
 449         zappoColour.setSelected(true);
 450
 451         break;
 452
 453       case ColourSchemeProperty.TAYLOR:
 454         taylorColour.setSelected(true);
 455         break;
 456
 457       case ColourSchemeProperty.HYDROPHOBIC:
 458         hydrophobicityColour.setSelected(true);
 459
 460         break;
 461
 462       case ColourSchemeProperty.HELIX:
 463         helixColour.setSelected(true);
 464
 465         break;
 466
 467       case ColourSchemeProperty.STRAND:
 468         strandColour.setSelected(true);
 469
 470         break;
 471
 472       case ColourSchemeProperty.TURN:
 473         turnColour.setSelected(true);
 474
 475         break;
 476
 477       case ColourSchemeProperty.BURIED:
 478         buriedColour.setSelected(true);
 479
 480         break;
 481
 482       case ColourSchemeProperty.NUCLEOTIDE:
 483         nucleotideColour.setSelected(true);
 484
 485         break;
 486
 487       case ColourSchemeProperty.USER_DEFINED:
 488         userDefinedColour.setSelected(true);
 489
 490         break;
 491       case ColourSchemeProperty.NONE:
 492       default:
 493         noColourmenuItem.setSelected(true);
 494         break;
 495
 496       }
 497     }
 498
 499   }
 500
 501   private void jbInit() throws Exception
 502   {
 503     fileMenu.setText("File");
 504     saveAs.setText("Save As...");
 505     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 506             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 507                     .getMenuShortcutKeyMask()
 508                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 509     saveAs.addActionListener(new ActionListener()
 510     {
 511       public void actionPerformed(ActionEvent e)
 512       {
 513         saveAs_actionPerformed(e);
 514       }
 515     });
 516     closeMenuItem.setText("Close");
 517     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 518             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 519                     .getMenuShortcutKeyMask(), false));
 520     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 521     {
 522       public void actionPerformed(ActionEvent e)
 523       {
 524         closeMenuItem_actionPerformed(false);
 525       }
 526     });
 527     editMenu.setText("Edit");
 528     viewMenu.setText("View");
 529     colourMenu.setText("Colour");
 530     calculateMenu.setText("Calculate");
 531     webService.setText("Web Service");
 532     selectAllSequenceMenuItem.setText("Select All");
 533     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 534             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 535                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 536     selectAllSequenceMenuItem
 537             .addActionListener(new java.awt.event.ActionListener()
 538             {
 539               public void actionPerformed(ActionEvent e)
 540               {
 541                 selectAllSequenceMenuItem_actionPerformed(e);
 542               }
 543             });
 544     deselectAllSequenceMenuItem.setText("Deselect All");
 545     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 546             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 547     deselectAllSequenceMenuItem
 548             .addActionListener(new java.awt.event.ActionListener()
 549             {
 550               public void actionPerformed(ActionEvent e)
 551               {
 552                 deselectAllSequenceMenuItem_actionPerformed(e);
 553               }
 554             });
 555     invertSequenceMenuItem.setText("Invert Sequence Selection");
 556     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 557             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 558                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 559     invertSequenceMenuItem
 560             .addActionListener(new java.awt.event.ActionListener()
 561             {
 562               public void actionPerformed(ActionEvent e)
 563               {
 564                 invertSequenceMenuItem_actionPerformed(e);
 565               }
 566             });
 567     grpsFromSelection.setText("Make Groups for selection");
 568     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
 569     {
 570       public void actionPerformed(ActionEvent e)
 571       {
 572         makeGrpsFromSelection_actionPerformed(e);
 573       }
 574     });
 575
 576     remove2LeftMenuItem.setText("Remove Left");
 577     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 578             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 579                     .getMenuShortcutKeyMask(), false));
 580     remove2LeftMenuItem
 581             .addActionListener(new java.awt.event.ActionListener()
 582             {
 583               public void actionPerformed(ActionEvent e)
 584               {
 585                 remove2LeftMenuItem_actionPerformed(e);
 586               }
 587             });
 588     remove2RightMenuItem.setText("Remove Right");
 589     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 590             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 591                     .getMenuShortcutKeyMask(), false));
 592     remove2RightMenuItem
 593             .addActionListener(new java.awt.event.ActionListener()
 594             {
 595               public void actionPerformed(ActionEvent e)
 596               {
 597                 remove2RightMenuItem_actionPerformed(e);
 598               }
 599             });
 600     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 601     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 602             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 603                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 604     removeGappedColumnMenuItem
 605             .addActionListener(new java.awt.event.ActionListener()
 606             {
 607               public void actionPerformed(ActionEvent e)
 608               {
 609                 removeGappedColumnMenuItem_actionPerformed(e);
 610               }
 611             });
 612     removeAllGapsMenuItem.setText("Remove All Gaps");
 613     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 614             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 615                     .getDefaultToolkit().getMenuShortcutKeyMask()
 616                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 617     removeAllGapsMenuItem
 618             .addActionListener(new java.awt.event.ActionListener()
 619             {
 620               public void actionPerformed(ActionEvent e)
 621               {
 622                 removeAllGapsMenuItem_actionPerformed(e);
 623               }
 624             });
 625     justifyLeftMenuItem.setText("Left Justify Alignment");
 626     justifyLeftMenuItem
 627             .addActionListener(new java.awt.event.ActionListener()
 628             {
 629               public void actionPerformed(ActionEvent e)
 630               {
 631                 justifyLeftMenuItem_actionPerformed(e);
 632               }
 633             });
 634     justifyRightMenuItem.setText("Right Justify Alignment");
 635     justifyRightMenuItem
 636             .addActionListener(new java.awt.event.ActionListener()
 637             {
 638               public void actionPerformed(ActionEvent e)
 639               {
 640                 justifyRightMenuItem_actionPerformed(e);
 641               }
 642             });
 643     viewBoxesMenuItem.setText("Boxes");
 644     viewBoxesMenuItem.setState(true);
 645     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 646     {
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         viewBoxesMenuItem_actionPerformed(e);
 650       }
 651     });
 652     viewTextMenuItem.setText("Text");
 653     viewTextMenuItem.setState(true);
 654     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 655     {
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         viewTextMenuItem_actionPerformed(e);
 659       }
 660     });
 661     showNonconservedMenuItem.setText("Show nonconserved");
 662     showNonconservedMenuItem.setState(false);
 663     showNonconservedMenuItem
 664             .addActionListener(new java.awt.event.ActionListener()
 665             {
 666               public void actionPerformed(ActionEvent e)
 667               {
 668                 showUnconservedMenuItem_actionPerformed(e);
 669               }
 670             });
 671     sortPairwiseMenuItem.setText("by Pairwise Identity");
 672     sortPairwiseMenuItem
 673             .addActionListener(new java.awt.event.ActionListener()
 674             {
 675               public void actionPerformed(ActionEvent e)
 676               {
 677                 sortPairwiseMenuItem_actionPerformed(e);
 678               }
 679             });
 680     sortIDMenuItem.setText("by ID");
 681     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 682     {
 683       public void actionPerformed(ActionEvent e)
 684       {
 685         sortIDMenuItem_actionPerformed(e);
 686       }
 687     });
 688     sortLengthMenuItem.setText("By Length");
 689     sortLengthMenuItem
 690             .addActionListener(new java.awt.event.ActionListener()
 691             {
 692               public void actionPerformed(ActionEvent e)
 693               {
 694                 sortLengthMenuItem_actionPerformed(e);
 695               }
 696             });
 697     sortGroupMenuItem.setText("by Group");
 698     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 699     {
 700       public void actionPerformed(ActionEvent e)
 701       {
 702         sortGroupMenuItem_actionPerformed(e);
 703       }
 704     });
 705     removeRedundancyMenuItem.setText("Remove Redundancy...");
 706     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 707             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 708                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 709     removeRedundancyMenuItem
 710             .addActionListener(new java.awt.event.ActionListener()
 711             {
 712               public void actionPerformed(ActionEvent e)
 713               {
 714                 removeRedundancyMenuItem_actionPerformed(e);
 715               }
 716             });
 717     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 718     pairwiseAlignmentMenuItem
 719             .addActionListener(new java.awt.event.ActionListener()
 720             {
 721               public void actionPerformed(ActionEvent e)
 722               {
 723                 pairwiseAlignmentMenuItem_actionPerformed(e);
 724               }
 725             });
 726     PCAMenuItem.setText("Principal Component Analysis");
 727     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 728     {
 729       public void actionPerformed(ActionEvent e)
 730       {
 731         PCAMenuItem_actionPerformed(e);
 732       }
 733     });
 734     averageDistanceTreeMenuItem
 735             .setText("Average Distance Using % Identity");
 736     averageDistanceTreeMenuItem
 737             .addActionListener(new java.awt.event.ActionListener()
 738             {
 739               public void actionPerformed(ActionEvent e)
 740               {
 741                 averageDistanceTreeMenuItem_actionPerformed(e);
 742               }
 743             });
 744     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 745     neighbourTreeMenuItem
 746             .addActionListener(new java.awt.event.ActionListener()
 747             {
 748               public void actionPerformed(ActionEvent e)
 749               {
 750                 neighbourTreeMenuItem_actionPerformed(e);
 751               }
 752             });
 753     this.getContentPane().setLayout(borderLayout1);
 754     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 755     statusBar.setBackground(Color.white);
 756     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 757     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 758     statusBar.setText("Status bar");
 759     outputTextboxMenu.setText("Output to Textbox");
 760     clustalColour.setText("Clustalx");
 761
 762     clustalColour.addActionListener(new java.awt.event.ActionListener()
 763     {
 764       public void actionPerformed(ActionEvent e)
 765       {
 766         clustalColour_actionPerformed(e);
 767       }
 768     });
 769     zappoColour.setText("Zappo");
 770     zappoColour.addActionListener(new java.awt.event.ActionListener()
 771     {
 772       public void actionPerformed(ActionEvent e)
 773       {
 774         zappoColour_actionPerformed(e);
 775       }
 776     });
 777     taylorColour.setText("Taylor");
 778     taylorColour.addActionListener(new java.awt.event.ActionListener()
 779     {
 780       public void actionPerformed(ActionEvent e)
 781       {
 782         taylorColour_actionPerformed(e);
 783       }
 784     });
 785     hydrophobicityColour.setText("Hydrophobicity");
 786     hydrophobicityColour
 787             .addActionListener(new java.awt.event.ActionListener()
 788             {
 789               public void actionPerformed(ActionEvent e)
 790               {
 791                 hydrophobicityColour_actionPerformed(e);
 792               }
 793             });
 794     helixColour.setText("Helix Propensity");
 795     helixColour.addActionListener(new java.awt.event.ActionListener()
 796     {
 797       public void actionPerformed(ActionEvent e)
 798       {
 799         helixColour_actionPerformed(e);
 800       }
 801     });
 802     strandColour.setText("Strand Propensity");
 803     strandColour.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       public void actionPerformed(ActionEvent e)
 806       {
 807         strandColour_actionPerformed(e);
 808       }
 809     });
 810     turnColour.setText("Turn Propensity");
 811     turnColour.addActionListener(new java.awt.event.ActionListener()
 812     {
 813       public void actionPerformed(ActionEvent e)
 814       {
 815         turnColour_actionPerformed(e);
 816       }
 817     });
 818     buriedColour.setText("Buried Index");
 819     buriedColour.addActionListener(new java.awt.event.ActionListener()
 820     {
 821       public void actionPerformed(ActionEvent e)
 822       {
 823         buriedColour_actionPerformed(e);
 824       }
 825     });
 826     userDefinedColour.setText("User Defined...");
 827     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 828     {
 829       public void actionPerformed(ActionEvent e)
 830       {
 831         userDefinedColour_actionPerformed(e);
 832       }
 833     });
 834     PIDColour.setText("Percentage Identity");
 835     PIDColour.addActionListener(new java.awt.event.ActionListener()
 836     {
 837       public void actionPerformed(ActionEvent e)
 838       {
 839         PIDColour_actionPerformed(e);
 840       }
 841     });
 842     BLOSUM62Colour.setText("BLOSUM62 Score");
 843     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 844     {
 845       public void actionPerformed(ActionEvent e)
 846       {
 847         BLOSUM62Colour_actionPerformed(e);
 848       }
 849     });
 850     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 851     avDistanceTreeBlosumMenuItem
 852             .addActionListener(new java.awt.event.ActionListener()
 853             {
 854               public void actionPerformed(ActionEvent e)
 855               {
 856                 avTreeBlosumMenuItem_actionPerformed(e);
 857               }
 858             });
 859     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 860     njTreeBlosumMenuItem
 861             .addActionListener(new java.awt.event.ActionListener()
 862             {
 863               public void actionPerformed(ActionEvent e)
 864               {
 865                 njTreeBlosumMenuItem_actionPerformed(e);
 866               }
 867             });
 868     annotationPanelMenuItem.setActionCommand("");
 869     annotationPanelMenuItem.setText("Show Annotations");
 870     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 871             "SHOW_ANNOTATIONS", true));
 872     annotationPanelMenuItem
 873             .addActionListener(new java.awt.event.ActionListener()
 874             {
 875               public void actionPerformed(ActionEvent e)
 876               {
 877                 annotationPanelMenuItem_actionPerformed(e);
 878               }
 879             });
 880     colourTextMenuItem.setText("Colour Text");
 881     colourTextMenuItem
 882             .addActionListener(new java.awt.event.ActionListener()
 883             {
 884               public void actionPerformed(ActionEvent e)
 885               {
 886                 colourTextMenuItem_actionPerformed(e);
 887               }
 888             });
 889     htmlMenuItem.setText("HTML");
 890     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         htmlMenuItem_actionPerformed(e);
 895       }
 896     });
 897     overviewMenuItem.setText("Overview Window");
 898     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         overviewMenuItem_actionPerformed(e);
 903       }
 904     });
 905     undoMenuItem.setEnabled(false);
 906     undoMenuItem.setText("Undo");
 907     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 908             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 909                     .getMenuShortcutKeyMask(), false));
 910     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 911     {
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         undoMenuItem_actionPerformed(e);
 915       }
 916     });
 917     redoMenuItem.setEnabled(false);
 918     redoMenuItem.setText("Redo");
 919     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 920             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 921                     .getMenuShortcutKeyMask(), false));
 922     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 923     {
 924       public void actionPerformed(ActionEvent e)
 925       {
 926         redoMenuItem_actionPerformed(e);
 927       }
 928     });
 929     conservationMenuItem.setText("By Conservation");
 930     conservationMenuItem
 931             .addActionListener(new java.awt.event.ActionListener()
 932             {
 933               public void actionPerformed(ActionEvent e)
 934               {
 935                 conservationMenuItem_actionPerformed(e);
 936               }
 937             });
 938     noColourmenuItem.setText("None");
 939     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 940     {
 941       public void actionPerformed(ActionEvent e)
 942       {
 943         noColourmenuItem_actionPerformed(e);
 944       }
 945     });
 946     wrapMenuItem.setText("Wrap");
 947     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 948     {
 949       public void actionPerformed(ActionEvent e)
 950       {
 951         wrapMenuItem_actionPerformed(e);
 952       }
 953     });
 954     printMenuItem.setText("Print ...");
 955     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 956             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 957                     .getMenuShortcutKeyMask(), false));
 958     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 959     {
 960       public void actionPerformed(ActionEvent e)
 961       {
 962         printMenuItem_actionPerformed(e);
 963       }
 964     });
 965     renderGapsMenuItem.setText("Show Gaps");
 966     renderGapsMenuItem.setState(true);
 967     renderGapsMenuItem
 968             .addActionListener(new java.awt.event.ActionListener()
 969             {
 970               public void actionPerformed(ActionEvent e)
 971               {
 972                 renderGapsMenuItem_actionPerformed(e);
 973               }
 974             });
 975     findMenuItem.setText("Find...");
 976     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 977             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 978                     .getMenuShortcutKeyMask(), false));
 979     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 980     {
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         findMenuItem_actionPerformed(e);
 984       }
 985     });
 986     abovePIDThreshold.setText("Above Identity Threshold");
 987     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 988     {
 989       public void actionPerformed(ActionEvent e)
 990       {
 991         abovePIDThreshold_actionPerformed(e);
 992       }
 993     });
 994     showSeqFeatures.setText("Show Sequence Features");
 995     showSeqFeatures.addActionListener(new ActionListener()
 996     {
 997       public void actionPerformed(ActionEvent actionEvent)
 998       {
 999         showSeqFeatures_actionPerformed(actionEvent);
1000       }
1001     });
1002     /*
1003      * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1004      * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1005      * void actionPerformed(ActionEvent actionEvent) {
1006      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1007      */
1008     showDbRefsMenuitem.setText("Show Database Refs");
1009     showDbRefsMenuitem.addActionListener(new ActionListener()
1010     {
1011
1012       public void actionPerformed(ActionEvent e)
1013       {
1014         showDbRefs_actionPerformed(e);
1015       }
1016
1017     });
1018     showNpFeatsMenuitem.setText("Show Non-Positional Features");
1019     showNpFeatsMenuitem.addActionListener(new ActionListener()
1020     {
1021
1022       public void actionPerformed(ActionEvent e)
1023       {
1024         showNpFeats_actionPerformed(e);
1025       }
1026
1027     });
1028     showGroupConservation.setText("Group Conservation");
1029     showGroupConservation.addActionListener(new ActionListener()
1030     {
1031
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         showGroupConservation_actionPerformed(e);
1035       }
1036
1037     });
1038
1039     showGroupConsensus.setText("Group Consensus");
1040     showGroupConsensus.addActionListener(new ActionListener()
1041     {
1042
1043       public void actionPerformed(ActionEvent e)
1044       {
1045         showGroupConsensus_actionPerformed(e);
1046       }
1047
1048     });
1049     showConsensusHistogram.setText("Show Consensus Histogram");
1050     showConsensusHistogram.addActionListener(new ActionListener()
1051     {
1052
1053       public void actionPerformed(ActionEvent e)
1054       {
1055         showConsensusHistogram_actionPerformed(e);
1056       }
1057
1058     });
1059     showSequenceLogo.setText("Show Consensus Logo");
1060     showSequenceLogo.addActionListener(new ActionListener()
1061     {
1062
1063       public void actionPerformed(ActionEvent e)
1064       {
1065         showSequenceLogo_actionPerformed(e);
1066       }
1067
1068     });
1069     applyAutoAnnotationSettings.setText("Apply to all groups");
1070     applyAutoAnnotationSettings.setState(false);
1071     applyAutoAnnotationSettings.setVisible(true);
1072     applyAutoAnnotationSettings.addActionListener(new ActionListener()
1073     {
1074
1075       public void actionPerformed(ActionEvent e)
1076       {
1077         applyAutoAnnotationSettings_actionPerformed(e);
1078       }
1079
1080     });
1081
1082     nucleotideColour.setText("Nucleotide");
1083     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1084     {
1085       public void actionPerformed(ActionEvent e)
1086       {
1087         nucleotideColour_actionPerformed(e);
1088       }
1089     });
1090     deleteGroups.setText("Undefine groups");
1091     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1092             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1093                     .getMenuShortcutKeyMask(), false));
1094     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1095     {
1096       public void actionPerformed(ActionEvent e)
1097       {
1098         deleteGroups_actionPerformed(e);
1099       }
1100     });
1101     copy.setText("Copy");
1102     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1103             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1104                     .getMenuShortcutKeyMask(), false));
1105
1106     copy.addActionListener(new java.awt.event.ActionListener()
1107     {
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         copy_actionPerformed(e);
1111       }
1112     });
1113     cut.setText("Cut");
1114     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1115             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1116                     .getMenuShortcutKeyMask(), false));
1117     cut.addActionListener(new java.awt.event.ActionListener()
1118     {
1119       public void actionPerformed(ActionEvent e)
1120       {
1121         cut_actionPerformed(e);
1122       }
1123     });
1124     delete.setText("Delete");
1125     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1126             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1127     delete.addActionListener(new java.awt.event.ActionListener()
1128     {
1129       public void actionPerformed(ActionEvent e)
1130       {
1131         delete_actionPerformed(e);
1132       }
1133     });
1134     pasteMenu.setText("Paste");
1135     pasteNew.setText("To New Alignment");
1136     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1137             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1138                     .getMenuShortcutKeyMask()
1139                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1140     pasteNew.addActionListener(new java.awt.event.ActionListener()
1141     {
1142       public void actionPerformed(ActionEvent e)
1143       {
1144         pasteNew_actionPerformed(e);
1145       }
1146     });
1147     pasteThis.setText("Add To This Alignment");
1148     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1149             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1150                     .getMenuShortcutKeyMask(), false));
1151     pasteThis.addActionListener(new java.awt.event.ActionListener()
1152     {
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         pasteThis_actionPerformed(e);
1156       }
1157     });
1158     applyToAllGroups.setText("Apply Colour To All Groups");
1159     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1160     {
1161       public void actionPerformed(ActionEvent e)
1162       {
1163         applyToAllGroups_actionPerformed(e);
1164       }
1165     });
1166     createPNG.addActionListener(new java.awt.event.ActionListener()
1167     {
1168       public void actionPerformed(ActionEvent e)
1169       {
1170         createPNG(null);
1171       }
1172     });
1173     createPNG.setActionCommand("Save As PNG Image");
1174     createPNG.setText("PNG");
1175     font.setText("Font...");
1176     font.addActionListener(new java.awt.event.ActionListener()
1177     {
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         font_actionPerformed(e);
1181       }
1182     });
1183
1184     seqLimits.setText("Show Sequence Limits");
1185     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1186     seqLimits.addActionListener(new java.awt.event.ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         seqLimit_actionPerformed(e);
1191       }
1192     });
1193     epsFile.setText("EPS");
1194     epsFile.addActionListener(new java.awt.event.ActionListener()
1195     {
1196       public void actionPerformed(ActionEvent e)
1197       {
1198         createEPS(null);
1199       }
1200     });
1201     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1202     LoadtreeMenuItem.setText("Load Associated Tree");
1203     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1204     {
1205       public void actionPerformed(ActionEvent e)
1206       {
1207         LoadtreeMenuItem_actionPerformed(e);
1208       }
1209     });
1210     scaleAbove.setVisible(false);
1211     scaleAbove.setText("Scale Above");
1212     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1213     {
1214       public void actionPerformed(ActionEvent e)
1215       {
1216         scaleAbove_actionPerformed(e);
1217       }
1218     });
1219     scaleLeft.setVisible(false);
1220     scaleLeft.setSelected(true);
1221     scaleLeft.setText("Scale Left");
1222     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1223     {
1224       public void actionPerformed(ActionEvent e)
1225       {
1226         scaleLeft_actionPerformed(e);
1227       }
1228     });
1229     scaleRight.setVisible(false);
1230     scaleRight.setSelected(true);
1231     scaleRight.setText("Scale Right");
1232     scaleRight.addActionListener(new java.awt.event.ActionListener()
1233     {
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         scaleRight_actionPerformed(e);
1237       }
1238     });
1239     centreColumnLabelsMenuItem.setVisible(true);
1240     centreColumnLabelsMenuItem.setState(false);
1241     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1242     centreColumnLabelsMenuItem
1243             .addActionListener(new java.awt.event.ActionListener()
1244             {
1245               public void actionPerformed(ActionEvent e)
1246               {
1247                 centreColumnLabels_actionPerformed(e);
1248               }
1249             });
1250     followHighlightMenuItem.setVisible(true);
1251     followHighlightMenuItem.setState(true);
1252     followHighlightMenuItem.setText("Automatic Scrolling");
1253     followHighlightMenuItem.addActionListener(new ActionListener()
1254     {
1255
1256       public void actionPerformed(ActionEvent e)
1257       {
1258         followHighlight_actionPerformed();
1259       }
1260
1261     });
1262
1263     modifyPID.setText("Modify Identity Threshold...");
1264     modifyPID.addActionListener(new java.awt.event.ActionListener()
1265     {
1266       public void actionPerformed(ActionEvent e)
1267       {
1268         modifyPID_actionPerformed(e);
1269       }
1270     });
1271     modifyConservation.setText("Modify Conservation Threshold...");
1272     modifyConservation
1273             .addActionListener(new java.awt.event.ActionListener()
1274             {
1275               public void actionPerformed(ActionEvent e)
1276               {
1277                 modifyConservation_actionPerformed(e);
1278               }
1279             });
1280     sortByTreeMenu.setText("By Tree Order");
1281     sort.setText("Sort");
1282     sort.addMenuListener(new MenuListener()
1283     {
1284       public void menuSelected(MenuEvent e)
1285       {
1286         buildTreeMenu();
1287       }
1288
1289       public void menuDeselected(MenuEvent e)
1290       {
1291       }
1292
1293       public void menuCanceled(MenuEvent e)
1294       {
1295       }
1296     });
1297     sortByAnnotScore.setText("by Score");
1298     sort.add(sortByAnnotScore);
1299     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1300     {
1301
1302       public void menuCanceled(MenuEvent e)
1303       {
1304       }
1305
1306       public void menuDeselected(MenuEvent e)
1307       {
1308       }
1309
1310       public void menuSelected(MenuEvent e)
1311       {
1312         buildSortByAnnotationScoresMenu();
1313       }
1314     });
1315     sortByAnnotScore.setVisible(false);
1316
1317     calculateTree.setText("Calculate Tree");
1318
1319     jMenu2.setText("Export Image");
1320     padGapsMenuitem.setText("Pad Gaps");
1321     padGapsMenuitem.setState(jalview.bin.Cache
1322             .getDefault("PAD_GAPS", false));
1323     padGapsMenuitem.addActionListener(new ActionListener()
1324     {
1325       public void actionPerformed(ActionEvent e)
1326       {
1327         padGapsMenuitem_actionPerformed(e);
1328       }
1329     });
1330     vamsasStore.setVisible(false);
1331     vamsasStore.setText("VAMSAS store");
1332     vamsasStore.addActionListener(new ActionListener()
1333     {
1334       public void actionPerformed(ActionEvent e)
1335       {
1336         vamsasStore_actionPerformed(e);
1337       }
1338     });
1339     showTranslation.setText("Translate cDNA");
1340     showTranslation.addActionListener(new ActionListener()
1341     {
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         showTranslation_actionPerformed(e);
1345       }
1346     });
1347     extractScores.setText("Extract Scores...");
1348     extractScores.addActionListener(new ActionListener()
1349     {
1350       public void actionPerformed(ActionEvent e)
1351       {
1352         extractScores_actionPerformed(e);
1353       }
1354     });
1355     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1356     // score extraction
1357     showProducts.setText("Get Cross References");
1358     /*
1359      * showProducts.addActionListener(new ActionListener() {
1360      *
1361      * public void actionPerformed(ActionEvent e) {
1362      * showProducts_actionPerformed(e); } });
1363      */
1364     featureSettings.setText("Feature Settings...");
1365     featureSettings.addActionListener(new ActionListener()
1366     {
1367       public void actionPerformed(ActionEvent e)
1368       {
1369         featureSettings_actionPerformed(e);
1370       }
1371     });
1372     fetchSequence.setText("Fetch Sequence(s)...");
1373     fetchSequence.addActionListener(new ActionListener()
1374     {
1375       public void actionPerformed(ActionEvent e)
1376       {
1377         fetchSequence_actionPerformed(e);
1378       }
1379     });
1380
1381     annotationColour.setText("By Annotation...");
1382     annotationColour.addActionListener(new ActionListener()
1383     {
1384       public void actionPerformed(ActionEvent e)
1385       {
1386         annotationColour_actionPerformed(e);
1387       }
1388     });
1389     associatedData.setText("Load Features / Annotations");
1390     associatedData.addActionListener(new ActionListener()
1391     {
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         associatedData_actionPerformed(e);
1395       }
1396     });
1397     autoCalculate.setText("Autocalculate Consensus");
1398     autoCalculate.setState(jalview.bin.Cache.getDefault(
1399             "AUTO_CALC_CONSENSUS", true));
1400     autoCalculate.addActionListener(new ActionListener()
1401     {
1402       public void actionPerformed(ActionEvent e)
1403       {
1404         autoCalculate_actionPerformed(e);
1405       }
1406     });
1407     addSequenceMenu.setText("Add Sequences");
1408     addFromFile.setText("From File");
1409     addFromFile.addActionListener(new ActionListener()
1410     {
1411       public void actionPerformed(ActionEvent e)
1412       {
1413         addFromFile_actionPerformed(e);
1414       }
1415     });
1416     addFromText.setText("From Textbox");
1417     addFromText.addActionListener(new ActionListener()
1418     {
1419       public void actionPerformed(ActionEvent e)
1420       {
1421         addFromText_actionPerformed(e);
1422       }
1423     });
1424     addFromURL.setText("From URL");
1425     addFromURL.addActionListener(new ActionListener()
1426     {
1427       public void actionPerformed(ActionEvent e)
1428       {
1429         addFromURL_actionPerformed(e);
1430       }
1431     });
1432     exportFeatures.setText("Export Features...");
1433     exportFeatures.addActionListener(new ActionListener()
1434     {
1435       public void actionPerformed(ActionEvent e)
1436       {
1437         exportFeatures_actionPerformed(e);
1438       }
1439     });
1440     exportAnnotations.setText("Export Annotations...");
1441     exportAnnotations.addActionListener(new ActionListener()
1442     {
1443       public void actionPerformed(ActionEvent e)
1444       {
1445         exportAnnotations_actionPerformed(e);
1446       }
1447     });
1448     statusPanel.setLayout(gridLayout1);
1449     jMenu3.setText("Show");
1450     showAllSeqs.setText("All Sequences");
1451     showAllSeqs.setToolTipText("Shift+H toggles sequence visiblity.");
1452     showAllSeqs.addActionListener(new ActionListener()
1453     {
1454       public void actionPerformed(ActionEvent e)
1455       {
1456         showAllSeqs_actionPerformed(e);
1457       }
1458     });
1459     showAllColumns.setText("All Columns");
1460     showAllColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1461     showAllColumns.addActionListener(new ActionListener()
1462     {
1463       public void actionPerformed(ActionEvent e)
1464       {
1465         showAllColumns_actionPerformed(e);
1466       }
1467     });
1468     hideMenu.setText("Hide");
1469     hideSelSequences.setText("Selected Sequences");
1470     hideSelSequences.setToolTipText("Shift+H toggles sequence visiblity.");
1471     hideSelSequences.addActionListener(new ActionListener()
1472     {
1473       public void actionPerformed(ActionEvent e)
1474       {
1475         hideSelSequences_actionPerformed(e);
1476       }
1477     });
1478     hideSelColumns.setText("Selected Columns");
1479     hideSelColumns.setToolTipText("Ctrl+H toggles column visiblity.");
1480     hideSelColumns.addActionListener(new ActionListener()
1481     {
1482       public void actionPerformed(ActionEvent e)
1483       {
1484         hideSelColumns_actionPerformed(e);
1485       }
1486     });
1487     hideAllSelection.setText("Selected Region");
1488     hideAllSelection.addActionListener(new ActionListener()
1489     {
1490       public void actionPerformed(ActionEvent e)
1491       {
1492         hideAllSelection_actionPerformed(e);
1493       }
1494     });
1495     // TODO: should be hidden if no selection exists.
1496     hideAllButSelection.setText("All but Selected Region (Shift+Ctrl+H)");
1497     hideAllButSelection.addActionListener(new ActionListener()
1498     {
1499       public void actionPerformed(ActionEvent e)
1500       {
1501         hideAllButSelection_actionPerformed(e);
1502       }
1503     });
1504     showAllhidden.setText("All Sequences and Columns");
1505     showAllhidden
1506             .setToolTipText("H toggles visibility of hidden or selected regions.");
1507     showAllhidden.addActionListener(new ActionListener()
1508     {
1509       public void actionPerformed(ActionEvent e)
1510       {
1511         showAllhidden_actionPerformed(e);
1512       }
1513     });
1514
1515     hiddenMarkers.setText("Show Hidden Markers");
1516     hiddenMarkers.addActionListener(new ActionListener()
1517     {
1518       public void actionPerformed(ActionEvent e)
1519       {
1520         hiddenMarkers_actionPerformed(e);
1521       }
1522     });
1523     invertColSel.setText("Invert Column Selection");
1524     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1525             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1526                     .getMenuShortcutKeyMask()
1527                     | java.awt.event.KeyEvent.ALT_MASK, false));
1528     invertColSel.addActionListener(new ActionListener()
1529     {
1530       public void actionPerformed(ActionEvent e)
1531       {
1532         invertColSel_actionPerformed(e);
1533       }
1534     });
1535     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1536     {
1537       public void stateChanged(ChangeEvent evt)
1538       {
1539         JTabbedPane pane = (JTabbedPane) evt.getSource();
1540         int sel = pane.getSelectedIndex();
1541         tabSelectionChanged(sel);
1542       }
1543     });
1544     tabbedPane.addMouseListener(new MouseAdapter()
1545     {
1546       public void mousePressed(MouseEvent e)
1547       {
1548         tabbedPane_mousePressed(e);
1549       }
1550     });
1551     tabbedPane.addFocusListener(new FocusAdapter()
1552     {
1553       public void focusGained(FocusEvent e)
1554       {
1555         tabbedPane_focusGained(e);
1556       }
1557     });
1558     save.setText("Save");
1559     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1560             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1561                     .getMenuShortcutKeyMask(), false));
1562     save.addActionListener(new ActionListener()
1563     {
1564       public void actionPerformed(ActionEvent e)
1565       {
1566         save_actionPerformed(e);
1567       }
1568     });
1569     reload.setEnabled(false);
1570     reload.setText("Reload");
1571     reload.addActionListener(new ActionListener()
1572     {
1573       public void actionPerformed(ActionEvent e)
1574       {
1575         reload_actionPerformed(e);
1576       }
1577     });
1578     newView.setText("New View");
1579     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1580             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1581                     .getMenuShortcutKeyMask(), false));
1582     newView.addActionListener(new ActionListener()
1583     {
1584       public void actionPerformed(ActionEvent e)
1585       {
1586         newView_actionPerformed(e);
1587       }
1588     });
1589     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1590             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1591     textColour.setText("Colour Text ...");
1592     textColour.addActionListener(new ActionListener()
1593     {
1594       public void actionPerformed(ActionEvent e)
1595       {
1596         textColour_actionPerformed(e);
1597       }
1598     });
1599     formatMenu.setText("Format");
1600     selectMenu.setText("Select");
1601     idRightAlign.setText("Right Align Sequence Id");
1602     idRightAlign.addActionListener(new ActionListener()
1603     {
1604       public void actionPerformed(ActionEvent e)
1605       {
1606         idRightAlign_actionPerformed(e);
1607       }
1608     });
1609     gatherViews.setEnabled(false);
1610     gatherViews.setText("Gather Views");
1611     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1612             java.awt.event.KeyEvent.VK_G, 0, false));
1613     gatherViews.addActionListener(new ActionListener()
1614     {
1615       public void actionPerformed(ActionEvent e)
1616       {
1617         gatherViews_actionPerformed(e);
1618       }
1619     });
1620     expandViews.setEnabled(false);
1621     expandViews.setText("Expand Views");
1622     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1623             java.awt.event.KeyEvent.VK_X, 0, false));
1624     expandViews.addActionListener(new ActionListener()
1625     {
1626       public void actionPerformed(ActionEvent e)
1627       {
1628         expandViews_actionPerformed(e);
1629       }
1630     });
1631     pageSetup.setText("Page Setup ...");
1632     pageSetup.addActionListener(new ActionListener()
1633     {
1634       public void actionPerformed(ActionEvent e)
1635       {
1636         pageSetup_actionPerformed(e);
1637       }
1638     });
1639     alignmentProperties.setText("Alignment Properties...");
1640     alignmentProperties.addActionListener(new ActionListener()
1641     {
1642       public void actionPerformed(ActionEvent actionEvent)
1643       {
1644         alignmentProperties();
1645       }
1646     });
1647     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1648     autoAnnMenu.setText("Autocalculated Annotation");
1649     alignFrameMenuBar.add(fileMenu);
1650     alignFrameMenuBar.add(editMenu);
1651     alignFrameMenuBar.add(selectMenu);
1652     alignFrameMenuBar.add(viewMenu);
1653     alignFrameMenuBar.add(formatMenu);
1654     alignFrameMenuBar.add(colourMenu);
1655     alignFrameMenuBar.add(calculateMenu);
1656     alignFrameMenuBar.add(webService);
1657     fileMenu.add(fetchSequence);
1658     fileMenu.add(addSequenceMenu);
1659     fileMenu.add(reload);
1660     fileMenu.addSeparator();
1661     fileMenu.add(vamsasStore);
1662     fileMenu.add(save);
1663     fileMenu.add(saveAs);
1664     fileMenu.add(outputTextboxMenu);
1665     fileMenu.add(pageSetup);
1666     fileMenu.add(printMenuItem);
1667     fileMenu.addSeparator();
1668     fileMenu.add(jMenu2);
1669     fileMenu.add(exportFeatures);
1670     fileMenu.add(exportAnnotations);
1671     fileMenu.add(LoadtreeMenuItem);
1672     fileMenu.add(associatedData);
1673     fileMenu.addSeparator();
1674     fileMenu.add(closeMenuItem);
1675     editMenu.add(undoMenuItem);
1676     editMenu.add(redoMenuItem);
1677     editMenu.add(cut);
1678     editMenu.add(copy);
1679     editMenu.add(pasteMenu);
1680     editMenu.add(delete);
1681     editMenu.addSeparator();
1682     editMenu.add(remove2LeftMenuItem);
1683     editMenu.add(remove2RightMenuItem);
1684     editMenu.add(removeGappedColumnMenuItem);
1685     editMenu.add(removeAllGapsMenuItem);
1686     editMenu.add(removeRedundancyMenuItem);
1687     editMenu.addSeparator();
1688     // dont add these yet in the CVS build - they cannot be undone!
1689     // Excluded from Jalview 2.5 release - undo needs to be implemented.
1690     // editMenu.add(justifyLeftMenuItem);
1691     // editMenu.add(justifyRightMenuItem);
1692     // editMenu.addSeparator();
1693     editMenu.add(padGapsMenuitem);
1694     viewMenu.add(newView);
1695     viewMenu.add(expandViews);
1696     viewMenu.add(gatherViews);
1697     viewMenu.addSeparator();
1698     viewMenu.add(jMenu3);
1699     viewMenu.add(hideMenu);
1700     viewMenu.addSeparator();
1701     viewMenu.add(followHighlightMenuItem);
1702     viewMenu.add(annotationPanelMenuItem);
1703     autoAnnMenu.add(applyAutoAnnotationSettings);
1704     autoAnnMenu.add(showConsensusHistogram);
1705     autoAnnMenu.add(showSequenceLogo);
1706     autoAnnMenu.addSeparator();
1707     autoAnnMenu.add(showGroupConservation);
1708     autoAnnMenu.add(showGroupConsensus);
1709     viewMenu.add(autoAnnMenu);
1710     viewMenu.addSeparator();
1711     viewMenu.add(showSeqFeatures);
1712     // viewMenu.add(showSeqFeaturesHeight);
1713
1714     viewMenu.add(featureSettings);
1715     tooltipSettingsMenu.add(showDbRefsMenuitem);
1716     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1717     viewMenu.add(tooltipSettingsMenu);
1718     viewMenu.addSeparator();
1719     viewMenu.add(alignmentProperties);
1720     viewMenu.addSeparator();
1721     viewMenu.add(overviewMenuItem);
1722     colourMenu.add(applyToAllGroups);
1723     colourMenu.add(textColour);
1724     colourMenu.addSeparator();
1725     colourMenu.add(noColourmenuItem);
1726     colourMenu.add(clustalColour);
1727     colourMenu.add(BLOSUM62Colour);
1728     colourMenu.add(PIDColour);
1729     colourMenu.add(zappoColour);
1730     colourMenu.add(taylorColour);
1731     colourMenu.add(hydrophobicityColour);
1732     colourMenu.add(helixColour);
1733     colourMenu.add(strandColour);
1734     colourMenu.add(turnColour);
1735     colourMenu.add(buriedColour);
1736     colourMenu.add(nucleotideColour);
1737     colourMenu.add(userDefinedColour);
1738     colourMenu.addSeparator();
1739     colourMenu.add(conservationMenuItem);
1740     colourMenu.add(modifyConservation);
1741     colourMenu.add(abovePIDThreshold);
1742     colourMenu.add(modifyPID);
1743     colourMenu.add(annotationColour);
1744     calculateMenu.add(sort);
1745     calculateMenu.add(calculateTree);
1746     calculateMenu.addSeparator();
1747     calculateMenu.add(pairwiseAlignmentMenuItem);
1748     calculateMenu.add(PCAMenuItem);
1749     calculateMenu.addSeparator();
1750     calculateMenu.add(showTranslation);
1751     calculateMenu.add(showProducts);
1752     calculateMenu.add(autoCalculate);
1753     calculateMenu.addSeparator();
1754     calculateMenu.add(extractScores);
1755     webServiceNoServices = new JMenuItem("<No Services>");
1756     webService.add(webServiceNoServices);
1757     pasteMenu.add(pasteNew);
1758     pasteMenu.add(pasteThis);
1759     sort.add(sortIDMenuItem);
1760     sort.add(sortLengthMenuItem);
1761     sort.add(sortGroupMenuItem);
1762     sort.add(sortPairwiseMenuItem);
1763     sort.add(sortByTreeMenu);
1764     calculateTree.add(averageDistanceTreeMenuItem);
1765     calculateTree.add(neighbourTreeMenuItem);
1766     calculateTree.add(avDistanceTreeBlosumMenuItem);
1767     calculateTree.add(njTreeBlosumMenuItem);
1768     jMenu2.add(htmlMenuItem);
1769     jMenu2.add(epsFile);
1770     jMenu2.add(createPNG);
1771     addSequenceMenu.add(addFromFile);
1772     addSequenceMenu.add(addFromText);
1773     addSequenceMenu.add(addFromURL);
1774     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1775     statusPanel.add(statusBar, null);
1776     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1777     jMenu3.add(showAllColumns);
1778     jMenu3.add(showAllSeqs);
1779     jMenu3.add(showAllhidden);
1780     hideMenu.add(hideSelColumns);
1781     hideMenu.add(hideSelSequences);
1782     hideMenu.add(hideAllSelection);
1783     hideMenu.add(hideAllButSelection);
1784
1785     formatMenu.add(font);
1786     formatMenu.addSeparator();
1787     formatMenu.add(wrapMenuItem);
1788     formatMenu.add(scaleAbove);
1789     formatMenu.add(scaleLeft);
1790     formatMenu.add(scaleRight);
1791     formatMenu.add(seqLimits);
1792     formatMenu.add(idRightAlign);
1793     formatMenu.add(hiddenMarkers);
1794     formatMenu.add(viewBoxesMenuItem);
1795     formatMenu.add(viewTextMenuItem);
1796     formatMenu.add(colourTextMenuItem);
1797     formatMenu.add(renderGapsMenuItem);
1798     formatMenu.add(centreColumnLabelsMenuItem);
1799     formatMenu.add(showNonconservedMenuItem);
1800     selectMenu.add(findMenuItem);
1801     selectMenu.addSeparator();
1802     selectMenu.add(selectAllSequenceMenuItem);
1803     selectMenu.add(deselectAllSequenceMenuItem);
1804     selectMenu.add(invertSequenceMenuItem);
1805     selectMenu.add(invertColSel);
1806     selectMenu.add(deleteGroups);
1807     selectMenu.add(grpsFromSelection);
1808   }
1809
1810   protected void showAllhidden_actionPerformed(ActionEvent e)
1811   {
1812     // TODO Auto-generated method stub
1813
1814   }
1815
1816   protected void hideAllButSelection_actionPerformed(ActionEvent e)
1817   {
1818     // TODO Auto-generated method stub
1819
1820   }
1821
1822   protected void hideAllSelection_actionPerformed(ActionEvent e)
1823   {
1824     // TODO Auto-generated method stub
1825
1826   }
1827
1828   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
1829   {
1830     // TODO Auto-generated method stub
1831
1832   }
1833
1834   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
1835   {
1836     // TODO Auto-generated method stub
1837
1838   }
1839
1840   protected void showSequenceLogo_actionPerformed(ActionEvent e)
1841   {
1842     // TODO Auto-generated method stub
1843
1844   }
1845
1846   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
1847   {
1848     // TODO Auto-generated method stub
1849
1850   }
1851
1852   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1853   {
1854     // TODO Auto-generated method stub
1855
1856   }
1857
1858   protected void showGroupConservation_actionPerformed(ActionEvent e)
1859   {
1860     // TODO Auto-generated method stub
1861
1862   }
1863
1864   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1865   {
1866     // TODO Auto-generated method stub
1867
1868   }
1869
1870   protected void showSeqFeaturesHeight_actionPerformed(
1871           ActionEvent actionEvent)
1872   {
1873     // TODO Auto-generated method stub
1874
1875   }
1876
1877   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1878   {
1879     // TODO Auto-generated method stub
1880
1881   }
1882
1883   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1884   {
1885     // TODO Auto-generated method stub
1886
1887   }
1888
1889   protected void followHighlight_actionPerformed()
1890   {
1891     // TODO Auto-generated method stub
1892
1893   }
1894
1895   protected void showNpFeats_actionPerformed(ActionEvent e)
1896   {
1897     // TODO Auto-generated method stub
1898
1899   }
1900
1901   protected void showDbRefs_actionPerformed(ActionEvent e)
1902   {
1903     // TODO Auto-generated method stub
1904
1905   }
1906
1907   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1908   {
1909   }
1910
1911   protected void showProducts_actionPerformed(ActionEvent e)
1912   {
1913   }
1914
1915   protected void buildSortByAnnotationScoresMenu()
1916   {
1917   }
1918
1919   protected void extractScores_actionPerformed(ActionEvent e)
1920   {
1921   }
1922
1923   protected void outputText_actionPerformed(ActionEvent e)
1924   {
1925   }
1926
1927   public void addFromFile_actionPerformed(ActionEvent e)
1928   {
1929
1930   }
1931
1932   public void addFromText_actionPerformed(ActionEvent e)
1933   {
1934
1935   }
1936
1937   public void addFromURL_actionPerformed(ActionEvent e)
1938   {
1939
1940   }
1941
1942   public void exportFeatures_actionPerformed(ActionEvent e)
1943   {
1944
1945   }
1946
1947   public void exportAnnotations_actionPerformed(ActionEvent e)
1948   {
1949
1950   }
1951
1952   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1953   {
1954   }
1955
1956   protected void closeMenuItem_actionPerformed(boolean b)
1957   {
1958   }
1959
1960   protected void redoMenuItem_actionPerformed(ActionEvent e)
1961   {
1962   }
1963
1964   protected void undoMenuItem_actionPerformed(ActionEvent e)
1965   {
1966   }
1967
1968   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1969   {
1970   }
1971
1972   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1973   {
1974   }
1975
1976   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1977   {
1978   }
1979
1980   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1981   {
1982   }
1983
1984   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1985   {
1986   }
1987
1988   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1989   {
1990   }
1991
1992   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1993   {
1994   }
1995
1996   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1997   {
1998   }
1999
2000   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2001   {
2002   }
2003
2004   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2005   {
2006   }
2007
2008   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2009   {
2010   }
2011
2012   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2013   {
2014   }
2015
2016   protected void overviewMenuItem_actionPerformed(ActionEvent e)
2017   {
2018   }
2019
2020   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2021   {
2022   }
2023
2024   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2025   {
2026   }
2027
2028   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2029   {
2030   }
2031
2032   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2033   {
2034   }
2035
2036   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2037   {
2038   }
2039
2040   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2041   {
2042   }
2043
2044   protected void PCAMenuItem_actionPerformed(ActionEvent e)
2045   {
2046   }
2047
2048   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2049   {
2050   }
2051
2052   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2053   {
2054   }
2055
2056   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2057   {
2058   }
2059
2060   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2061   {
2062   }
2063
2064   protected void clustalColour_actionPerformed(ActionEvent e)
2065   {
2066   }
2067
2068   protected void zappoColour_actionPerformed(ActionEvent e)
2069   {
2070   }
2071
2072   protected void taylorColour_actionPerformed(ActionEvent e)
2073   {
2074   }
2075
2076   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2077   {
2078   }
2079
2080   protected void helixColour_actionPerformed(ActionEvent e)
2081   {
2082   }
2083
2084   protected void strandColour_actionPerformed(ActionEvent e)
2085   {
2086   }
2087
2088   protected void turnColour_actionPerformed(ActionEvent e)
2089   {
2090   }
2091
2092   protected void buriedColour_actionPerformed(ActionEvent e)
2093   {
2094   }
2095
2096   protected void userDefinedColour_actionPerformed(ActionEvent e)
2097   {
2098   }
2099
2100   protected void PIDColour_actionPerformed(ActionEvent e)
2101   {
2102   }
2103
2104   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2105   {
2106   }
2107
2108   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2109   {
2110   }
2111
2112   protected void conservationMenuItem_actionPerformed(ActionEvent e)
2113   {
2114   }
2115
2116   protected void printMenuItem_actionPerformed(ActionEvent e)
2117   {
2118   }
2119
2120   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2121   {
2122   }
2123
2124   protected void findMenuItem_actionPerformed(ActionEvent e)
2125   {
2126   }
2127
2128   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2129   {
2130   }
2131
2132   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2133   {
2134   }
2135
2136   protected void nucleotideColour_actionPerformed(ActionEvent e)
2137   {
2138   }
2139
2140   protected void deleteGroups_actionPerformed(ActionEvent e)
2141   {
2142   }
2143
2144   protected void copy_actionPerformed(ActionEvent e)
2145   {
2146   }
2147
2148   protected void cut_actionPerformed(ActionEvent e)
2149   {
2150   }
2151
2152   protected void delete_actionPerformed(ActionEvent e)
2153   {
2154   }
2155
2156   protected void pasteNew_actionPerformed(ActionEvent e)
2157   {
2158   }
2159
2160   protected void pasteThis_actionPerformed(ActionEvent e)
2161   {
2162   }
2163
2164   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2165   {
2166   }
2167
2168   public void createPNG(java.io.File f)
2169   {
2170   }
2171
2172   protected void font_actionPerformed(ActionEvent e)
2173   {
2174   }
2175
2176   protected void seqLimit_actionPerformed(ActionEvent e)
2177   {
2178   }
2179
2180   public void seqDBRef_actionPerformed(ActionEvent e)
2181   {
2182
2183   }
2184
2185   public void createEPS(java.io.File f)
2186   {
2187   }
2188
2189   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2190   {
2191   }
2192
2193   protected void jpred_actionPerformed(ActionEvent e)
2194   {
2195   }
2196
2197   protected void scaleAbove_actionPerformed(ActionEvent e)
2198   {
2199   }
2200
2201   protected void scaleLeft_actionPerformed(ActionEvent e)
2202   {
2203   }
2204
2205   protected void scaleRight_actionPerformed(ActionEvent e)
2206   {
2207   }
2208
2209   protected void modifyPID_actionPerformed(ActionEvent e)
2210   {
2211   }
2212
2213   protected void modifyConservation_actionPerformed(ActionEvent e)
2214   {
2215   }
2216
2217   protected void saveAs_actionPerformed(ActionEvent e)
2218   {
2219   }
2220
2221   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2222   {
2223   }
2224
2225   public void vamsasStore_actionPerformed(ActionEvent e)
2226   {
2227
2228   }
2229
2230   public void vamsasLoad_actionPerformed(ActionEvent e)
2231   {
2232
2233   }
2234
2235   public void showTranslation_actionPerformed(ActionEvent e)
2236   {
2237
2238   }
2239
2240   public void featureSettings_actionPerformed(ActionEvent e)
2241   {
2242
2243   }
2244
2245   public void fetchSequence_actionPerformed(ActionEvent e)
2246   {
2247
2248   }
2249
2250   public void smoothFont_actionPerformed(ActionEvent e)
2251   {
2252
2253   }
2254
2255   public void annotationColour_actionPerformed(ActionEvent e)
2256   {
2257
2258   }
2259
2260   public void associatedData_actionPerformed(ActionEvent e)
2261   {
2262
2263   }
2264
2265   public void autoCalculate_actionPerformed(ActionEvent e)
2266   {
2267
2268   }
2269
2270   public void showAllSeqs_actionPerformed(ActionEvent e)
2271   {
2272
2273   }
2274
2275   public void showAllColumns_actionPerformed(ActionEvent e)
2276   {
2277
2278   }
2279
2280   public void hideSelSequences_actionPerformed(ActionEvent e)
2281   {
2282
2283   }
2284
2285   public void hideSelColumns_actionPerformed(ActionEvent e)
2286   {
2287
2288   }
2289
2290   public void hiddenMarkers_actionPerformed(ActionEvent e)
2291   {
2292
2293   }
2294
2295   public void findPdbId_actionPerformed(ActionEvent e)
2296   {
2297
2298   }
2299
2300   public void enterPdbId_actionPerformed(ActionEvent e)
2301   {
2302
2303   }
2304
2305   public void pdbFile_actionPerformed(ActionEvent e)
2306   {
2307
2308   }
2309
2310   public void invertColSel_actionPerformed(ActionEvent e)
2311   {
2312
2313   }
2314
2315   public void tabSelectionChanged(int sel)
2316   {
2317
2318   }
2319
2320   public void tabbedPane_mousePressed(MouseEvent e)
2321   {
2322
2323   }
2324
2325   public void tabbedPane_focusGained(FocusEvent e)
2326   {
2327     requestFocus();
2328   }
2329
2330   public void save_actionPerformed(ActionEvent e)
2331   {
2332
2333   }
2334
2335   public void reload_actionPerformed(ActionEvent e)
2336   {
2337
2338   }
2339
2340   public void newView_actionPerformed(ActionEvent e)
2341   {
2342
2343   }
2344
2345   public void textColour_actionPerformed(ActionEvent e)
2346   {
2347
2348   }
2349
2350   public void idRightAlign_actionPerformed(ActionEvent e)
2351   {
2352
2353   }
2354
2355   public void expandViews_actionPerformed(ActionEvent e)
2356   {
2357
2358   }
2359
2360   public void gatherViews_actionPerformed(ActionEvent e)
2361   {
2362
2363   }
2364
2365   public void buildTreeMenu()
2366   {
2367
2368   }
2369
2370   public void pageSetup_actionPerformed(ActionEvent e)
2371   {
2372
2373   }
2374
2375   public void alignmentProperties()
2376   {
2377
2378   }
2379 }