src/jalview/jbgui/GAlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.jbgui;
  20
  21 import java.awt.*;
  22 import java.awt.event.*;
  23
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.schemes.*;
  28
  29 public class GAlignFrame extends JInternalFrame
  30 {
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  32
  33   protected JMenu fileMenu = new JMenu();
  34
  35   protected JMenuItem closeMenuItem = new JMenuItem();
  36
  37   protected JMenu editMenu = new JMenu();
  38
  39   protected JMenu viewMenu = new JMenu();
  40
  41   protected JMenu colourMenu = new JMenu();
  42
  43   protected JMenu calculateMenu = new JMenu();
  44
  45   protected JMenu webService = new JMenu();
  46
  47   protected JMenuItem webServiceNoServices;
  48
  49   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  50
  51   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  52
  53   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  54
  55   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  56
  57   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  58
  59   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  60
  61   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  62
  63   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  64
  65   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  66
  67   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  68
  69   protected JMenuItem sortIDMenuItem = new JMenuItem();
  70
  71   protected JMenuItem sortLengthMenuItem = new JMenuItem();
  72
  73   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  74
  75   protected JMenu sortByAnnotScore = new JMenu();
  76
  77   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  78
  79   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  80
  81   protected JMenuItem PCAMenuItem = new JMenuItem();
  82
  83   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  84
  85   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  86
  87   BorderLayout borderLayout1 = new BorderLayout();
  88
  89   public JLabel statusBar = new JLabel();
  90
  91   protected JMenuItem saveAs = new JMenuItem();
  92
  93   protected JMenu outputTextboxMenu = new JMenu();
  94
  95   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  96
  97   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  98
  99   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 112
 113   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 114
 115   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 116
 117   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 118
 119   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
 120
 121   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 122
 123   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 124
 125   public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
 126
 127   JMenuItem htmlMenuItem = new JMenuItem();
 128
 129   JMenuItem overviewMenuItem = new JMenuItem();
 130
 131   protected JMenuItem undoMenuItem = new JMenuItem();
 132
 133   protected JMenuItem redoMenuItem = new JMenuItem();
 134
 135   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 136
 137   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 138
 139   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 140
 141   JMenuItem printMenuItem = new JMenuItem();
 142
 143   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 144
 145   JMenuItem findMenuItem = new JMenuItem();
 146
 147   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 148
 149   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 150   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 151
 152   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 153
 154   JMenuItem deleteGroups = new JMenuItem();
 155
 156   JMenuItem delete = new JMenuItem();
 157
 158   JMenuItem copy = new JMenuItem();
 159
 160   JMenuItem cut = new JMenuItem();
 161
 162   JMenu pasteMenu = new JMenu();
 163
 164   JMenuItem pasteNew = new JMenuItem();
 165
 166   JMenuItem pasteThis = new JMenuItem();
 167
 168   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 169
 170   JMenuItem createPNG = new JMenuItem();
 171
 172   protected JMenuItem font = new JMenuItem();
 173
 174   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 175
 176   JMenuItem epsFile = new JMenuItem();
 177
 178   JMenuItem LoadtreeMenuItem = new JMenuItem();
 179
 180   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 181
 182   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 183
 184   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 185
 186   protected JMenuItem modifyPID = new JMenuItem();
 187
 188   protected JMenuItem modifyConservation = new JMenuItem();
 189
 190   protected JMenu sortByTreeMenu = new JMenu();
 191
 192   protected JMenu sort = new JMenu();
 193
 194   protected JMenu calculateTree = new JMenu();
 195
 196   JMenu jMenu2 = new JMenu();
 197
 198   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 199   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
 200   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 201
 202   protected ButtonGroup colours = new ButtonGroup();
 203
 204   JMenuItem vamsasStore = new JMenuItem();
 205
 206   protected JMenuItem showTranslation = new JMenuItem();
 207
 208   protected JMenuItem extractScores = new JMenuItem();
 209
 210   protected JMenu showProducts = new JMenu();
 211
 212   public JMenuItem featureSettings = new JMenuItem();
 213
 214   JMenuItem fetchSequence = new JMenuItem();
 215
 216   JMenuItem annotationColour = new JMenuItem();
 217
 218   JMenuItem associatedData = new JMenuItem();
 219
 220   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 221
 222   JMenu addSequenceMenu = new JMenu();
 223
 224   JMenuItem addFromFile = new JMenuItem();
 225
 226   JMenuItem addFromText = new JMenuItem();
 227
 228   JMenuItem addFromURL = new JMenuItem();
 229
 230   JMenuItem exportAnnotations = new JMenuItem();
 231
 232   JMenuItem exportFeatures = new JMenuItem();
 233
 234   protected JPanel statusPanel = new JPanel();
 235
 236   GridLayout gridLayout1 = new GridLayout();
 237
 238   JMenu jMenu3 = new JMenu();
 239
 240   JMenuItem showAllSeqs = new JMenuItem();
 241
 242   JMenuItem showAllColumns = new JMenuItem();
 243
 244   JMenu hideMenu = new JMenu();
 245
 246   JMenuItem hideSelSequences = new JMenuItem();
 247
 248   JMenuItem hideSelColumns = new JMenuItem();
 249
 250   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 251
 252   JMenuItem invertColSel = new JMenuItem();
 253
 254   protected JTabbedPane tabbedPane = new JTabbedPane();
 255
 256   JMenuItem save = new JMenuItem();
 257
 258   protected JMenuItem reload = new JMenuItem();
 259
 260   JMenuItem newView = new JMenuItem();
 261
 262   JMenuItem textColour = new JMenuItem();
 263
 264   JMenu formatMenu = new JMenu();
 265
 266   JMenu selectMenu = new JMenu();
 267
 268   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 269
 270   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
 271
 272   protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
 273
 274   protected JMenuItem gatherViews = new JMenuItem();
 275
 276   protected JMenuItem expandViews = new JMenuItem();
 277
 278   JMenuItem pageSetup = new JMenuItem();
 279
 280   JMenuItem alignmentProperties = new JMenuItem();
 281
 282   JMenu tooltipSettingsMenu = new JMenu();
 283
 284   private JMenuItem justifyLeftMenuItem=new JMenuItem();
 285
 286   private JMenuItem justifyRightMenuItem=new JMenuItem();
 287
 288   protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
 289   protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
 290
 291   public GAlignFrame()
 292   {
 293     try
 294     {
 295       jbInit();
 296       setJMenuBar(alignFrameMenuBar);
 297
 298       // dynamically fill save as menu with available formats
 299       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 300       {
 301         JMenuItem item = new JMenuItem(
 302                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 303
 304         item.addActionListener(new java.awt.event.ActionListener()
 305         {
 306           public void actionPerformed(ActionEvent e)
 307           {
 308             outputText_actionPerformed(e);
 309           }
 310         });
 311
 312         outputTextboxMenu.add(item);
 313       }
 314     } catch (Exception e)
 315     {
 316     }
 317
 318     if (!new jalview.util.Platform().isAMac())
 319     {
 320       closeMenuItem.setMnemonic('C');
 321       outputTextboxMenu.setMnemonic('T');
 322       undoMenuItem.setMnemonic('Z');
 323       redoMenuItem.setMnemonic('0');
 324       copy.setMnemonic('C');
 325       cut.setMnemonic('U');
 326       pasteMenu.setMnemonic('P');
 327       reload.setMnemonic('R');
 328     }
 329
 330     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 331     {
 332       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 333               .getUserColourSchemes().keys();
 334
 335       while (userColours.hasMoreElements())
 336       {
 337         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
 338                 userColours.nextElement().toString());
 339         radioItem.setName("USER_DEFINED");
 340         radioItem.addMouseListener(new MouseAdapter()
 341         {
 342           public void mousePressed(MouseEvent evt)
 343           {
 344             if (evt.isControlDown()
 345                     || SwingUtilities.isRightMouseButton(evt))
 346             {
 347               radioItem
 348                       .removeActionListener(radioItem.getActionListeners()[0]);
 349
 350               int option = JOptionPane.showInternalConfirmDialog(
 351                       jalview.gui.Desktop.desktop,
 352                       "Remove from default list?",
 353                       "Remove user defined colour",
 354                       JOptionPane.YES_NO_OPTION);
 355               if (option == JOptionPane.YES_OPTION)
 356               {
 357                 jalview.gui.UserDefinedColours
 358                         .removeColourFromDefaults(radioItem.getText());
 359                 colourMenu.remove(radioItem);
 360               }
 361               else
 362               {
 363                 radioItem.addActionListener(new ActionListener()
 364                 {
 365                   public void actionPerformed(ActionEvent evt)
 366                   {
 367                     userDefinedColour_actionPerformed(evt);
 368                   }
 369                 });
 370               }
 371             }
 372           }
 373         });
 374         radioItem.addActionListener(new ActionListener()
 375         {
 376           public void actionPerformed(ActionEvent evt)
 377           {
 378             userDefinedColour_actionPerformed(evt);
 379           }
 380         });
 381         colourMenu.insert(radioItem, 15);
 382         colours.add(radioItem);
 383       }
 384     }
 385     colours.add(noColourmenuItem);
 386     colours.add(clustalColour);
 387     colours.add(zappoColour);
 388     colours.add(taylorColour);
 389     colours.add(hydrophobicityColour);
 390     colours.add(helixColour);
 391     colours.add(strandColour);
 392     colours.add(turnColour);
 393     colours.add(buriedColour);
 394     colours.add(userDefinedColour);
 395     colours.add(PIDColour);
 396     colours.add(BLOSUM62Colour);
 397     colours.add(nucleotideColour);
 398
 399     setColourSelected(jalview.bin.Cache
 400             .getDefault("DEFAULT_COLOUR", "None"));
 401
 402   }
 403
 404   public void setColourSelected(String defaultColour)
 405   {
 406
 407     if (defaultColour != null)
 408     {
 409       int index = ColourSchemeProperty
 410               .getColourIndexFromName(defaultColour);
 411
 412       switch (index)
 413       {
 414       case ColourSchemeProperty.NONE:
 415         noColourmenuItem.setSelected(true);
 416         break;
 417       case ColourSchemeProperty.CLUSTAL:
 418         clustalColour.setSelected(true);
 419
 420         break;
 421
 422       case ColourSchemeProperty.BLOSUM:
 423         BLOSUM62Colour.setSelected(true);
 424
 425         break;
 426
 427       case ColourSchemeProperty.PID:
 428         PIDColour.setSelected(true);
 429
 430         break;
 431
 432       case ColourSchemeProperty.ZAPPO:
 433         zappoColour.setSelected(true);
 434
 435         break;
 436
 437       case ColourSchemeProperty.TAYLOR:
 438         taylorColour.setSelected(true);
 439         break;
 440
 441       case ColourSchemeProperty.HYDROPHOBIC:
 442         hydrophobicityColour.setSelected(true);
 443
 444         break;
 445
 446       case ColourSchemeProperty.HELIX:
 447         helixColour.setSelected(true);
 448
 449         break;
 450
 451       case ColourSchemeProperty.STRAND:
 452         strandColour.setSelected(true);
 453
 454         break;
 455
 456       case ColourSchemeProperty.TURN:
 457         turnColour.setSelected(true);
 458
 459         break;
 460
 461       case ColourSchemeProperty.BURIED:
 462         buriedColour.setSelected(true);
 463
 464         break;
 465
 466       case ColourSchemeProperty.NUCLEOTIDE:
 467         nucleotideColour.setSelected(true);
 468
 469         break;
 470
 471       case ColourSchemeProperty.USER_DEFINED:
 472         userDefinedColour.setSelected(true);
 473
 474         break;
 475       }
 476     }
 477
 478   }
 479
 480   private void jbInit() throws Exception
 481   {
 482     fileMenu.setText("File");
 483     saveAs.setText("Save As...");
 484     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 485             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
 486                     .getMenuShortcutKeyMask()
 487                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 488     saveAs.addActionListener(new ActionListener()
 489     {
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         saveAs_actionPerformed(e);
 493       }
 494     });
 495     closeMenuItem.setText("Close");
 496     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 497             java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
 498                     .getMenuShortcutKeyMask(), false));
 499     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 500     {
 501       public void actionPerformed(ActionEvent e)
 502       {
 503         closeMenuItem_actionPerformed(false);
 504       }
 505     });
 506     editMenu.setText("Edit");
 507     viewMenu.setText("View");
 508     colourMenu.setText("Colour");
 509     calculateMenu.setText("Calculate");
 510     webService.setText("Web Service");
 511     selectAllSequenceMenuItem.setText("Select All");
 512     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 513             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
 514                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 515     selectAllSequenceMenuItem
 516             .addActionListener(new java.awt.event.ActionListener()
 517             {
 518               public void actionPerformed(ActionEvent e)
 519               {
 520                 selectAllSequenceMenuItem_actionPerformed(e);
 521               }
 522             });
 523     deselectAllSequenceMenuItem.setText("Deselect All");
 524     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 525             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
 526     deselectAllSequenceMenuItem
 527             .addActionListener(new java.awt.event.ActionListener()
 528             {
 529               public void actionPerformed(ActionEvent e)
 530               {
 531                 deselectAllSequenceMenuItem_actionPerformed(e);
 532               }
 533             });
 534     invertSequenceMenuItem.setText("Invert Sequence Selection");
 535     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
 536             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
 537                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 538     invertSequenceMenuItem
 539             .addActionListener(new java.awt.event.ActionListener()
 540             {
 541               public void actionPerformed(ActionEvent e)
 542               {
 543                 invertSequenceMenuItem_actionPerformed(e);
 544               }
 545             });
 546     remove2LeftMenuItem.setText("Remove Left");
 547     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 548             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
 549                     .getMenuShortcutKeyMask(), false));
 550     remove2LeftMenuItem
 551             .addActionListener(new java.awt.event.ActionListener()
 552             {
 553               public void actionPerformed(ActionEvent e)
 554               {
 555                 remove2LeftMenuItem_actionPerformed(e);
 556               }
 557             });
 558     remove2RightMenuItem.setText("Remove Right");
 559     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 560             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
 561                     .getMenuShortcutKeyMask(), false));
 562     remove2RightMenuItem
 563             .addActionListener(new java.awt.event.ActionListener()
 564             {
 565               public void actionPerformed(ActionEvent e)
 566               {
 567                 remove2RightMenuItem_actionPerformed(e);
 568               }
 569             });
 570     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 571     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
 572             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 573                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 574     removeGappedColumnMenuItem
 575             .addActionListener(new java.awt.event.ActionListener()
 576             {
 577               public void actionPerformed(ActionEvent e)
 578               {
 579                 removeGappedColumnMenuItem_actionPerformed(e);
 580               }
 581             });
 582     removeAllGapsMenuItem.setText("Remove All Gaps");
 583     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
 584             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
 585                     .getDefaultToolkit().getMenuShortcutKeyMask()
 586                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
 587     removeAllGapsMenuItem
 588             .addActionListener(new java.awt.event.ActionListener()
 589             {
 590               public void actionPerformed(ActionEvent e)
 591               {
 592                 removeAllGapsMenuItem_actionPerformed(e);
 593               }
 594             });
 595     justifyLeftMenuItem.setText("Left Justify Alignment");
 596     justifyLeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 597     {
 598         public void actionPerformed(ActionEvent e)
 599         {
 600           justifyLeftMenuItem_actionPerformed(e);
 601         }
 602     });
 603     justifyRightMenuItem.setText("Right Justify Alignment");
 604     justifyRightMenuItem.addActionListener(new java.awt.event.ActionListener()
 605     {
 606         public void actionPerformed(ActionEvent e)
 607         {
 608           justifyRightMenuItem_actionPerformed(e);
 609         }
 610     });
 611     viewBoxesMenuItem.setText("Boxes");
 612     viewBoxesMenuItem.setState(true);
 613     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 614     {
 615       public void actionPerformed(ActionEvent e)
 616       {
 617         viewBoxesMenuItem_actionPerformed(e);
 618       }
 619     });
 620     viewTextMenuItem.setText("Text");
 621     viewTextMenuItem.setState(true);
 622     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 623     {
 624       public void actionPerformed(ActionEvent e)
 625       {
 626         viewTextMenuItem_actionPerformed(e);
 627       }
 628     });
 629     showUnconservedMenuItem.setText("Show Unconserved");
 630     showUnconservedMenuItem.setState(false);
 631     showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
 632     {
 633       public void actionPerformed(ActionEvent e)
 634       {
 635         showUnconservedMenuItem_actionPerformed(e);
 636       }
 637     });
 638     sortPairwiseMenuItem.setText("by Pairwise Identity");
 639     sortPairwiseMenuItem
 640             .addActionListener(new java.awt.event.ActionListener()
 641             {
 642               public void actionPerformed(ActionEvent e)
 643               {
 644                 sortPairwiseMenuItem_actionPerformed(e);
 645               }
 646             });
 647     sortIDMenuItem.setText("by ID");
 648     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 649     {
 650       public void actionPerformed(ActionEvent e)
 651       {
 652         sortIDMenuItem_actionPerformed(e);
 653       }
 654     });
 655     sortLengthMenuItem.setText("By Length");
 656     sortLengthMenuItem.addActionListener(new java.awt.event.ActionListener()
 657     {
 658       public void actionPerformed(ActionEvent e)
 659       {
 660         sortLengthMenuItem_actionPerformed(e);
 661       }
 662     });
 663     sortGroupMenuItem.setText("by Group");
 664     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 665     {
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         sortGroupMenuItem_actionPerformed(e);
 669       }
 670     });
 671     removeRedundancyMenuItem.setText("Remove Redundancy...");
 672     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
 673             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
 674                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
 675     removeRedundancyMenuItem
 676             .addActionListener(new java.awt.event.ActionListener()
 677             {
 678               public void actionPerformed(ActionEvent e)
 679               {
 680                 removeRedundancyMenuItem_actionPerformed(e);
 681               }
 682             });
 683     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 684     pairwiseAlignmentMenuItem
 685             .addActionListener(new java.awt.event.ActionListener()
 686             {
 687               public void actionPerformed(ActionEvent e)
 688               {
 689                 pairwiseAlignmentMenuItem_actionPerformed(e);
 690               }
 691             });
 692     PCAMenuItem.setText("Principal Component Analysis");
 693     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 694     {
 695       public void actionPerformed(ActionEvent e)
 696       {
 697         PCAMenuItem_actionPerformed(e);
 698       }
 699     });
 700     averageDistanceTreeMenuItem
 701             .setText("Average Distance Using % Identity");
 702     averageDistanceTreeMenuItem
 703             .addActionListener(new java.awt.event.ActionListener()
 704             {
 705               public void actionPerformed(ActionEvent e)
 706               {
 707                 averageDistanceTreeMenuItem_actionPerformed(e);
 708               }
 709             });
 710     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
 711     neighbourTreeMenuItem
 712             .addActionListener(new java.awt.event.ActionListener()
 713             {
 714               public void actionPerformed(ActionEvent e)
 715               {
 716                 neighbourTreeMenuItem_actionPerformed(e);
 717               }
 718             });
 719     this.getContentPane().setLayout(borderLayout1);
 720     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 721     statusBar.setBackground(Color.white);
 722     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 723     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 724     statusBar.setText("Status bar");
 725     outputTextboxMenu.setText("Output to Textbox");
 726     clustalColour.setText("Clustalx");
 727
 728     clustalColour.addActionListener(new java.awt.event.ActionListener()
 729     {
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         clustalColour_actionPerformed(e);
 733       }
 734     });
 735     zappoColour.setText("Zappo");
 736     zappoColour.addActionListener(new java.awt.event.ActionListener()
 737     {
 738       public void actionPerformed(ActionEvent e)
 739       {
 740         zappoColour_actionPerformed(e);
 741       }
 742     });
 743     taylorColour.setText("Taylor");
 744     taylorColour.addActionListener(new java.awt.event.ActionListener()
 745     {
 746       public void actionPerformed(ActionEvent e)
 747       {
 748         taylorColour_actionPerformed(e);
 749       }
 750     });
 751     hydrophobicityColour.setText("Hydrophobicity");
 752     hydrophobicityColour
 753             .addActionListener(new java.awt.event.ActionListener()
 754             {
 755               public void actionPerformed(ActionEvent e)
 756               {
 757                 hydrophobicityColour_actionPerformed(e);
 758               }
 759             });
 760     helixColour.setText("Helix Propensity");
 761     helixColour.addActionListener(new java.awt.event.ActionListener()
 762     {
 763       public void actionPerformed(ActionEvent e)
 764       {
 765         helixColour_actionPerformed(e);
 766       }
 767     });
 768     strandColour.setText("Strand Propensity");
 769     strandColour.addActionListener(new java.awt.event.ActionListener()
 770     {
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         strandColour_actionPerformed(e);
 774       }
 775     });
 776     turnColour.setText("Turn Propensity");
 777     turnColour.addActionListener(new java.awt.event.ActionListener()
 778     {
 779       public void actionPerformed(ActionEvent e)
 780       {
 781         turnColour_actionPerformed(e);
 782       }
 783     });
 784     buriedColour.setText("Buried Index");
 785     buriedColour.addActionListener(new java.awt.event.ActionListener()
 786     {
 787       public void actionPerformed(ActionEvent e)
 788       {
 789         buriedColour_actionPerformed(e);
 790       }
 791     });
 792     userDefinedColour.setText("User Defined...");
 793     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 794     {
 795       public void actionPerformed(ActionEvent e)
 796       {
 797         userDefinedColour_actionPerformed(e);
 798       }
 799     });
 800     PIDColour.setText("Percentage Identity");
 801     PIDColour.addActionListener(new java.awt.event.ActionListener()
 802     {
 803       public void actionPerformed(ActionEvent e)
 804       {
 805         PIDColour_actionPerformed(e);
 806       }
 807     });
 808     BLOSUM62Colour.setText("BLOSUM62 Score");
 809     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 810     {
 811       public void actionPerformed(ActionEvent e)
 812       {
 813         BLOSUM62Colour_actionPerformed(e);
 814       }
 815     });
 816     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
 817     avDistanceTreeBlosumMenuItem
 818             .addActionListener(new java.awt.event.ActionListener()
 819             {
 820               public void actionPerformed(ActionEvent e)
 821               {
 822                 avTreeBlosumMenuItem_actionPerformed(e);
 823               }
 824             });
 825     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
 826     njTreeBlosumMenuItem
 827             .addActionListener(new java.awt.event.ActionListener()
 828             {
 829               public void actionPerformed(ActionEvent e)
 830               {
 831                 njTreeBlosumMenuItem_actionPerformed(e);
 832               }
 833             });
 834     annotationPanelMenuItem.setActionCommand("");
 835     annotationPanelMenuItem.setText("Show Annotations");
 836     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
 837             "SHOW_ANNOTATIONS", true));
 838     annotationPanelMenuItem
 839             .addActionListener(new java.awt.event.ActionListener()
 840             {
 841               public void actionPerformed(ActionEvent e)
 842               {
 843                 annotationPanelMenuItem_actionPerformed(e);
 844               }
 845             });
 846     colourTextMenuItem.setText("Colour Text");
 847     colourTextMenuItem
 848             .addActionListener(new java.awt.event.ActionListener()
 849             {
 850               public void actionPerformed(ActionEvent e)
 851               {
 852                 colourTextMenuItem_actionPerformed(e);
 853               }
 854             });
 855     htmlMenuItem.setText("HTML");
 856     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 857     {
 858       public void actionPerformed(ActionEvent e)
 859       {
 860         htmlMenuItem_actionPerformed(e);
 861       }
 862     });
 863     overviewMenuItem.setText("Overview Window");
 864     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 865     {
 866       public void actionPerformed(ActionEvent e)
 867       {
 868         overviewMenuItem_actionPerformed(e);
 869       }
 870     });
 871     undoMenuItem.setEnabled(false);
 872     undoMenuItem.setText("Undo");
 873     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 874             java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
 875                     .getMenuShortcutKeyMask(), false));
 876     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 877     {
 878       public void actionPerformed(ActionEvent e)
 879       {
 880         undoMenuItem_actionPerformed(e);
 881       }
 882     });
 883     redoMenuItem.setEnabled(false);
 884     redoMenuItem.setText("Redo");
 885     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 886             java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
 887                     .getMenuShortcutKeyMask(), false));
 888     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 889     {
 890       public void actionPerformed(ActionEvent e)
 891       {
 892         redoMenuItem_actionPerformed(e);
 893       }
 894     });
 895     conservationMenuItem.setText("By Conservation");
 896     conservationMenuItem
 897             .addActionListener(new java.awt.event.ActionListener()
 898             {
 899               public void actionPerformed(ActionEvent e)
 900               {
 901                 conservationMenuItem_actionPerformed(e);
 902               }
 903             });
 904     noColourmenuItem.setText("None");
 905     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 906     {
 907       public void actionPerformed(ActionEvent e)
 908       {
 909         noColourmenuItem_actionPerformed(e);
 910       }
 911     });
 912     wrapMenuItem.setText("Wrap");
 913     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 914     {
 915       public void actionPerformed(ActionEvent e)
 916       {
 917         wrapMenuItem_actionPerformed(e);
 918       }
 919     });
 920     printMenuItem.setText("Print ...");
 921     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 922             java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
 923                     .getMenuShortcutKeyMask(), false));
 924     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 925     {
 926       public void actionPerformed(ActionEvent e)
 927       {
 928         printMenuItem_actionPerformed(e);
 929       }
 930     });
 931     renderGapsMenuItem.setText("Show Gaps");
 932     renderGapsMenuItem.setState(true);
 933     renderGapsMenuItem
 934             .addActionListener(new java.awt.event.ActionListener()
 935             {
 936               public void actionPerformed(ActionEvent e)
 937               {
 938                 renderGapsMenuItem_actionPerformed(e);
 939               }
 940             });
 941     findMenuItem.setText("Find...");
 942     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 943             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
 944                     .getMenuShortcutKeyMask(), false));
 945     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 946     {
 947       public void actionPerformed(ActionEvent e)
 948       {
 949         findMenuItem_actionPerformed(e);
 950       }
 951     });
 952     abovePIDThreshold.setText("Above Identity Threshold");
 953     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
 954     {
 955       public void actionPerformed(ActionEvent e)
 956       {
 957         abovePIDThreshold_actionPerformed(e);
 958       }
 959     });
 960     showSeqFeatures.setText("Show Sequence Features");
 961     showSeqFeatures.addActionListener(new ActionListener()
 962     {
 963       public void actionPerformed(ActionEvent actionEvent)
 964       {
 965         showSeqFeatures_actionPerformed(actionEvent);
 966       }
 967     });
 968     showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
 969     showSeqFeaturesHeight.addActionListener(new ActionListener()
 970     {
 971       public void actionPerformed(ActionEvent actionEvent)
 972       {
 973         showSeqFeaturesHeight_actionPerformed(actionEvent);
 974       }
 975     });
 976     showDbRefsMenuitem.setText("Show Database Refs");
 977     showDbRefsMenuitem.addActionListener(new ActionListener()
 978     {
 979
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         showDbRefs_actionPerformed(e);
 983       }
 984
 985     });
 986     showNpFeatsMenuitem.setText("Show Non-Positional Features");
 987     showNpFeatsMenuitem.addActionListener(new ActionListener()
 988     {
 989
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         showNpFeats_actionPerformed(e);
 993       }
 994
 995     });
 996     showGroupConservation.setText("Group Conservation");
 997     showGroupConservation.addActionListener(new ActionListener()
 998     {
 999
1000       public void actionPerformed(ActionEvent e)
1001       {
1002         showGroupConservation_actionPerformed(e);
1003       }
1004
1005     });
1006
1007     showGroupConsensus.setText("Group Consensus");
1008     showGroupConsensus.addActionListener(new ActionListener()
1009     {
1010
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         showGroupConsensus_actionPerformed(e);
1014       }
1015
1016     });
1017
1018     nucleotideColour.setText("Nucleotide");
1019     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         nucleotideColour_actionPerformed(e);
1024       }
1025     });
1026     deleteGroups.setText("Undefine groups");
1027     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1028             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1029                     .getMenuShortcutKeyMask(), false));
1030     deleteGroups.addActionListener(new java.awt.event.ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         deleteGroups_actionPerformed(e);
1035       }
1036     });
1037     copy.setText("Copy");
1038     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1039             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1040                     .getMenuShortcutKeyMask(), false));
1041
1042     copy.addActionListener(new java.awt.event.ActionListener()
1043     {
1044       public void actionPerformed(ActionEvent e)
1045       {
1046         copy_actionPerformed(e);
1047       }
1048     });
1049     cut.setText("Cut");
1050     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1051             java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1052                     .getMenuShortcutKeyMask(), false));
1053     cut.addActionListener(new java.awt.event.ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         cut_actionPerformed(e);
1058       }
1059     });
1060     delete.setText("Delete");
1061     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1062             java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1063     delete.addActionListener(new java.awt.event.ActionListener()
1064     {
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         delete_actionPerformed(e);
1068       }
1069     });
1070     pasteMenu.setText("Paste");
1071     pasteNew.setText("To New Alignment");
1072     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1073             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1074                     .getMenuShortcutKeyMask()
1075                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
1076     pasteNew.addActionListener(new java.awt.event.ActionListener()
1077     {
1078       public void actionPerformed(ActionEvent e)
1079       {
1080         pasteNew_actionPerformed(e);
1081       }
1082     });
1083     pasteThis.setText("Add To This Alignment");
1084     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1085             java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1086                     .getMenuShortcutKeyMask(), false));
1087     pasteThis.addActionListener(new java.awt.event.ActionListener()
1088     {
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         pasteThis_actionPerformed(e);
1092       }
1093     });
1094     applyToAllGroups.setText("Apply Colour To All Groups");
1095     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1096     {
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         applyToAllGroups_actionPerformed(e);
1100       }
1101     });
1102     createPNG.addActionListener(new java.awt.event.ActionListener()
1103     {
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         createPNG(null);
1107       }
1108     });
1109     createPNG.setActionCommand("Save As PNG Image");
1110     createPNG.setText("PNG");
1111     font.setText("Font...");
1112     font.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         font_actionPerformed(e);
1117       }
1118     });
1119
1120     seqLimits.setText("Show Sequence Limits");
1121     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1122     seqLimits.addActionListener(new java.awt.event.ActionListener()
1123     {
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         seqLimit_actionPerformed(e);
1127       }
1128     });
1129     epsFile.setText("EPS");
1130     epsFile.addActionListener(new java.awt.event.ActionListener()
1131     {
1132       public void actionPerformed(ActionEvent e)
1133       {
1134         createEPS(null);
1135       }
1136     });
1137     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
1138     LoadtreeMenuItem.setText("Load Associated Tree");
1139     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1140     {
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         LoadtreeMenuItem_actionPerformed(e);
1144       }
1145     });
1146     scaleAbove.setVisible(false);
1147     scaleAbove.setText("Scale Above");
1148     scaleAbove.addActionListener(new java.awt.event.ActionListener()
1149     {
1150       public void actionPerformed(ActionEvent e)
1151       {
1152         scaleAbove_actionPerformed(e);
1153       }
1154     });
1155     scaleLeft.setVisible(false);
1156     scaleLeft.setSelected(true);
1157     scaleLeft.setText("Scale Left");
1158     scaleLeft.addActionListener(new java.awt.event.ActionListener()
1159     {
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         scaleLeft_actionPerformed(e);
1163       }
1164     });
1165     scaleRight.setVisible(false);
1166     scaleRight.setSelected(true);
1167     scaleRight.setText("Scale Right");
1168     scaleRight.addActionListener(new java.awt.event.ActionListener()
1169     {
1170       public void actionPerformed(ActionEvent e)
1171       {
1172         scaleRight_actionPerformed(e);
1173       }
1174     });
1175     centreColumnLabelsMenuItem.setVisible(true);
1176     centreColumnLabelsMenuItem.setState(false);
1177     centreColumnLabelsMenuItem.setText("Centre Column Labels");
1178     centreColumnLabelsMenuItem
1179             .addActionListener(new java.awt.event.ActionListener()
1180             {
1181               public void actionPerformed(ActionEvent e)
1182               {
1183                 centreColumnLabels_actionPerformed(e);
1184               }
1185             });
1186     followHighlightMenuItem.setVisible(true);
1187     followHighlightMenuItem.setState(true);
1188     followHighlightMenuItem.setText("Automatic Scrolling");
1189     followHighlightMenuItem.addActionListener(new ActionListener()
1190     {
1191
1192       public void actionPerformed(ActionEvent e)
1193       {
1194         followHighlight_actionPerformed();
1195       }
1196
1197     });
1198
1199     modifyPID.setText("Modify Identity Threshold...");
1200     modifyPID.addActionListener(new java.awt.event.ActionListener()
1201     {
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         modifyPID_actionPerformed(e);
1205       }
1206     });
1207     modifyConservation.setText("Modify Conservation Threshold...");
1208     modifyConservation
1209             .addActionListener(new java.awt.event.ActionListener()
1210             {
1211               public void actionPerformed(ActionEvent e)
1212               {
1213                 modifyConservation_actionPerformed(e);
1214               }
1215             });
1216     sortByTreeMenu.setText("By Tree Order");
1217     sort.setText("Sort");
1218     sort.addMenuListener(new MenuListener()
1219     {
1220       public void menuSelected(MenuEvent e)
1221       {
1222         buildTreeMenu();
1223       }
1224
1225       public void menuDeselected(MenuEvent e)
1226       {
1227       }
1228
1229       public void menuCanceled(MenuEvent e)
1230       {
1231       }
1232     });
1233     sortByAnnotScore.setText("by Score");
1234     sort.add(sortByAnnotScore);
1235     sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1236     {
1237
1238       public void menuCanceled(MenuEvent e)
1239       {
1240       }
1241
1242       public void menuDeselected(MenuEvent e)
1243       {
1244       }
1245
1246       public void menuSelected(MenuEvent e)
1247       {
1248         buildSortByAnnotationScoresMenu();
1249       }
1250     });
1251     sortByAnnotScore.setVisible(false);
1252
1253     calculateTree.setText("Calculate Tree");
1254
1255     jMenu2.setText("Export Image");
1256     padGapsMenuitem.setText("Pad Gaps");
1257     padGapsMenuitem.setState(jalview.bin.Cache
1258             .getDefault("PAD_GAPS", false));
1259     padGapsMenuitem.addActionListener(new ActionListener()
1260     {
1261       public void actionPerformed(ActionEvent e)
1262       {
1263         padGapsMenuitem_actionPerformed(e);
1264       }
1265     });
1266     vamsasStore.setVisible(false);
1267     vamsasStore.setText("VAMSAS store");
1268     vamsasStore.addActionListener(new ActionListener()
1269     {
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         vamsasStore_actionPerformed(e);
1273       }
1274     });
1275     showTranslation.setText("Translate cDNA");
1276     showTranslation.addActionListener(new ActionListener()
1277     {
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         showTranslation_actionPerformed(e);
1281       }
1282     });
1283     extractScores.setText("Extract Scores...");
1284     extractScores.addActionListener(new ActionListener()
1285     {
1286       public void actionPerformed(ActionEvent e)
1287       {
1288         extractScores_actionPerformed(e);
1289       }
1290     });
1291     extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1292                                     // score extraction
1293     showProducts.setText("Get Cross References");
1294     /*
1295      * showProducts.addActionListener(new ActionListener() {
1296      *
1297      * public void actionPerformed(ActionEvent e) {
1298      * showProducts_actionPerformed(e); } });
1299      */
1300     featureSettings.setText("Feature Settings...");
1301     featureSettings.addActionListener(new ActionListener()
1302     {
1303       public void actionPerformed(ActionEvent e)
1304       {
1305         featureSettings_actionPerformed(e);
1306       }
1307     });
1308     fetchSequence.setText("Fetch Sequence(s)...");
1309     fetchSequence.addActionListener(new ActionListener()
1310     {
1311       public void actionPerformed(ActionEvent e)
1312       {
1313         fetchSequence_actionPerformed(e);
1314       }
1315     });
1316
1317     annotationColour.setText("By Annotation...");
1318     annotationColour.addActionListener(new ActionListener()
1319     {
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         annotationColour_actionPerformed(e);
1323       }
1324     });
1325     associatedData.setText("Load Features / Annotations");
1326     associatedData.addActionListener(new ActionListener()
1327     {
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         associatedData_actionPerformed(e);
1331       }
1332     });
1333     autoCalculate.setText("Autocalculate Consensus");
1334     autoCalculate.setState(jalview.bin.Cache.getDefault(
1335             "AUTO_CALC_CONSENSUS", true));
1336     autoCalculate.addActionListener(new ActionListener()
1337     {
1338       public void actionPerformed(ActionEvent e)
1339       {
1340         autoCalculate_actionPerformed(e);
1341       }
1342     });
1343     addSequenceMenu.setText("Add Sequences");
1344     addFromFile.setText("From File");
1345     addFromFile.addActionListener(new ActionListener()
1346     {
1347       public void actionPerformed(ActionEvent e)
1348       {
1349         addFromFile_actionPerformed(e);
1350       }
1351     });
1352     addFromText.setText("From Textbox");
1353     addFromText.addActionListener(new ActionListener()
1354     {
1355       public void actionPerformed(ActionEvent e)
1356       {
1357         addFromText_actionPerformed(e);
1358       }
1359     });
1360     addFromURL.setText("From URL");
1361     addFromURL.addActionListener(new ActionListener()
1362     {
1363       public void actionPerformed(ActionEvent e)
1364       {
1365         addFromURL_actionPerformed(e);
1366       }
1367     });
1368     exportFeatures.setText("Export Features...");
1369     exportFeatures.addActionListener(new ActionListener()
1370     {
1371       public void actionPerformed(ActionEvent e)
1372       {
1373         exportFeatures_actionPerformed(e);
1374       }
1375     });
1376     exportAnnotations.setText("Export Annotations...");
1377     exportAnnotations.addActionListener(new ActionListener()
1378     {
1379       public void actionPerformed(ActionEvent e)
1380       {
1381         exportAnnotations_actionPerformed(e);
1382       }
1383     });
1384     statusPanel.setLayout(gridLayout1);
1385     jMenu3.setText("Show");
1386     showAllSeqs.setText("All Sequences");
1387     showAllSeqs.addActionListener(new ActionListener()
1388     {
1389       public void actionPerformed(ActionEvent e)
1390       {
1391         showAllSeqs_actionPerformed(e);
1392       }
1393     });
1394     showAllColumns.setText("All Columns");
1395     showAllColumns.addActionListener(new ActionListener()
1396     {
1397       public void actionPerformed(ActionEvent e)
1398       {
1399         showAllColumns_actionPerformed(e);
1400       }
1401     });
1402     hideMenu.setText("Hide");
1403     hideSelSequences.setText("Selected Sequences");
1404     hideSelSequences.addActionListener(new ActionListener()
1405     {
1406       public void actionPerformed(ActionEvent e)
1407       {
1408         hideSelSequences_actionPerformed(e);
1409       }
1410     });
1411     hideSelColumns.setText("Selected Columns");
1412     hideSelColumns.addActionListener(new ActionListener()
1413     {
1414       public void actionPerformed(ActionEvent e)
1415       {
1416         hideSelColumns_actionPerformed(e);
1417       }
1418     });
1419     hiddenMarkers.setText("Show Hidden Markers");
1420     hiddenMarkers.addActionListener(new ActionListener()
1421     {
1422       public void actionPerformed(ActionEvent e)
1423       {
1424         hiddenMarkers_actionPerformed(e);
1425       }
1426     });
1427     invertColSel.setText("Invert Column Selection");
1428     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1429             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1430                     .getMenuShortcutKeyMask()
1431                     | java.awt.event.KeyEvent.ALT_MASK, false));
1432     invertColSel.addActionListener(new ActionListener()
1433     {
1434       public void actionPerformed(ActionEvent e)
1435       {
1436         invertColSel_actionPerformed(e);
1437       }
1438     });
1439     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1440     {
1441       public void stateChanged(ChangeEvent evt)
1442       {
1443         JTabbedPane pane = (JTabbedPane) evt.getSource();
1444         int sel = pane.getSelectedIndex();
1445         tabSelectionChanged(sel);
1446       }
1447     });
1448     tabbedPane.addMouseListener(new MouseAdapter()
1449     {
1450       public void mousePressed(MouseEvent e)
1451       {
1452         tabbedPane_mousePressed(e);
1453       }
1454     });
1455     tabbedPane.addFocusListener(new FocusAdapter()
1456     {
1457       public void focusGained(FocusEvent e)
1458       {
1459         tabbedPane_focusGained(e);
1460       }
1461     });
1462     save.setText("Save");
1463     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1464             java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1465                     .getMenuShortcutKeyMask(), false));
1466     save.addActionListener(new ActionListener()
1467     {
1468       public void actionPerformed(ActionEvent e)
1469       {
1470         save_actionPerformed(e);
1471       }
1472     });
1473     reload.setEnabled(false);
1474     reload.setText("Reload");
1475     reload.addActionListener(new ActionListener()
1476     {
1477       public void actionPerformed(ActionEvent e)
1478       {
1479         reload_actionPerformed(e);
1480       }
1481     });
1482     newView.setText("New View");
1483     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1484             java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1485                     .getMenuShortcutKeyMask(), false));
1486     newView.addActionListener(new ActionListener()
1487     {
1488       public void actionPerformed(ActionEvent e)
1489       {
1490         newView_actionPerformed(e);
1491       }
1492     });
1493     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
1494             + "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
1495     textColour.setText("Colour Text ...");
1496     textColour.addActionListener(new ActionListener()
1497     {
1498       public void actionPerformed(ActionEvent e)
1499       {
1500         textColour_actionPerformed(e);
1501       }
1502     });
1503     formatMenu.setText("Format");
1504     selectMenu.setText("Select");
1505     idRightAlign.setText("Right Align Sequence Id");
1506     idRightAlign.addActionListener(new ActionListener()
1507     {
1508       public void actionPerformed(ActionEvent e)
1509       {
1510         idRightAlign_actionPerformed(e);
1511       }
1512     });
1513     gatherViews.setEnabled(false);
1514     gatherViews.setText("Gather Views");
1515     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1516             java.awt.event.KeyEvent.VK_G, 0, false));
1517     gatherViews.addActionListener(new ActionListener()
1518     {
1519       public void actionPerformed(ActionEvent e)
1520       {
1521         gatherViews_actionPerformed(e);
1522       }
1523     });
1524     expandViews.setEnabled(false);
1525     expandViews.setText("Expand Views");
1526     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1527             java.awt.event.KeyEvent.VK_X, 0, false));
1528     expandViews.addActionListener(new ActionListener()
1529     {
1530       public void actionPerformed(ActionEvent e)
1531       {
1532         expandViews_actionPerformed(e);
1533       }
1534     });
1535     pageSetup.setText("Page Setup ...");
1536     pageSetup.addActionListener(new ActionListener()
1537     {
1538       public void actionPerformed(ActionEvent e)
1539       {
1540         pageSetup_actionPerformed(e);
1541       }
1542     });
1543     alignmentProperties.setText("Alignment Properties...");
1544     alignmentProperties.addActionListener(new ActionListener()
1545     {
1546       public void actionPerformed(ActionEvent actionEvent)
1547       {
1548         alignmentProperties();
1549       }
1550     });
1551     tooltipSettingsMenu.setText("Sequence ID Tooltip");
1552     alignFrameMenuBar.add(fileMenu);
1553     alignFrameMenuBar.add(editMenu);
1554     alignFrameMenuBar.add(selectMenu);
1555     alignFrameMenuBar.add(viewMenu);
1556     alignFrameMenuBar.add(formatMenu);
1557     alignFrameMenuBar.add(colourMenu);
1558     alignFrameMenuBar.add(calculateMenu);
1559     alignFrameMenuBar.add(webService);
1560     fileMenu.add(fetchSequence);
1561     fileMenu.add(addSequenceMenu);
1562     fileMenu.add(reload);
1563     fileMenu.addSeparator();
1564     fileMenu.add(vamsasStore);
1565     fileMenu.add(save);
1566     fileMenu.add(saveAs);
1567     fileMenu.add(outputTextboxMenu);
1568     fileMenu.add(pageSetup);
1569     fileMenu.add(printMenuItem);
1570     fileMenu.addSeparator();
1571     fileMenu.add(jMenu2);
1572     fileMenu.add(exportFeatures);
1573     fileMenu.add(exportAnnotations);
1574     fileMenu.add(LoadtreeMenuItem);
1575     fileMenu.add(associatedData);
1576     fileMenu.addSeparator();
1577     fileMenu.add(closeMenuItem);
1578     editMenu.add(undoMenuItem);
1579     editMenu.add(redoMenuItem);
1580     editMenu.add(cut);
1581     editMenu.add(copy);
1582     editMenu.add(pasteMenu);
1583     editMenu.add(delete);
1584     editMenu.addSeparator();
1585     editMenu.add(remove2LeftMenuItem);
1586     editMenu.add(remove2RightMenuItem);
1587     editMenu.add(removeGappedColumnMenuItem);
1588     editMenu.add(removeAllGapsMenuItem);
1589     editMenu.add(removeRedundancyMenuItem);
1590     editMenu.addSeparator();
1591     // dont add these yet in the CVS build - they cannot be undone!
1592     editMenu.add(justifyLeftMenuItem);
1593     editMenu.add(justifyRightMenuItem);
1594     editMenu.addSeparator();
1595     editMenu.add(padGapsMenuitem);
1596     viewMenu.add(newView);
1597     viewMenu.add(expandViews);
1598     viewMenu.add(gatherViews);
1599     viewMenu.addSeparator();
1600     viewMenu.add(jMenu3);
1601     viewMenu.add(hideMenu);
1602     viewMenu.addSeparator();
1603     viewMenu.add(followHighlightMenuItem);
1604     viewMenu.add(annotationPanelMenuItem);
1605     viewMenu.add(showGroupConservation);
1606     viewMenu.add(showGroupConsensus);
1607     viewMenu.addSeparator();
1608     viewMenu.add(showSeqFeatures);
1609     viewMenu.add(showSeqFeaturesHeight);
1610
1611     viewMenu.add(featureSettings);
1612     tooltipSettingsMenu.add(showDbRefsMenuitem);
1613     tooltipSettingsMenu.add(showNpFeatsMenuitem);
1614     viewMenu.add(tooltipSettingsMenu);
1615     viewMenu.addSeparator();
1616     viewMenu.add(alignmentProperties);
1617     viewMenu.addSeparator();
1618     viewMenu.add(overviewMenuItem);
1619     colourMenu.add(applyToAllGroups);
1620     colourMenu.add(textColour);
1621     colourMenu.addSeparator();
1622     colourMenu.add(noColourmenuItem);
1623     colourMenu.add(clustalColour);
1624     colourMenu.add(BLOSUM62Colour);
1625     colourMenu.add(PIDColour);
1626     colourMenu.add(zappoColour);
1627     colourMenu.add(taylorColour);
1628     colourMenu.add(hydrophobicityColour);
1629     colourMenu.add(helixColour);
1630     colourMenu.add(strandColour);
1631     colourMenu.add(turnColour);
1632     colourMenu.add(buriedColour);
1633     colourMenu.add(nucleotideColour);
1634     colourMenu.add(userDefinedColour);
1635     colourMenu.addSeparator();
1636     colourMenu.add(conservationMenuItem);
1637     colourMenu.add(modifyConservation);
1638     colourMenu.add(abovePIDThreshold);
1639     colourMenu.add(modifyPID);
1640     colourMenu.add(annotationColour);
1641     calculateMenu.add(sort);
1642     calculateMenu.add(calculateTree);
1643     calculateMenu.addSeparator();
1644     calculateMenu.add(pairwiseAlignmentMenuItem);
1645     calculateMenu.add(PCAMenuItem);
1646     calculateMenu.addSeparator();
1647     calculateMenu.add(showTranslation);
1648     calculateMenu.add(showProducts);
1649     calculateMenu.add(autoCalculate);
1650     calculateMenu.addSeparator();
1651     calculateMenu.add(extractScores);
1652     webServiceNoServices = new JMenuItem("<No Services>");
1653     webService.add(webServiceNoServices);
1654     pasteMenu.add(pasteNew);
1655     pasteMenu.add(pasteThis);
1656     sort.add(sortIDMenuItem);
1657     sort.add(sortLengthMenuItem);
1658     sort.add(sortGroupMenuItem);
1659     sort.add(sortPairwiseMenuItem);
1660     sort.add(sortByTreeMenu);
1661     calculateTree.add(averageDistanceTreeMenuItem);
1662     calculateTree.add(neighbourTreeMenuItem);
1663     calculateTree.add(avDistanceTreeBlosumMenuItem);
1664     calculateTree.add(njTreeBlosumMenuItem);
1665     jMenu2.add(htmlMenuItem);
1666     jMenu2.add(epsFile);
1667     jMenu2.add(createPNG);
1668     addSequenceMenu.add(addFromFile);
1669     addSequenceMenu.add(addFromText);
1670     addSequenceMenu.add(addFromURL);
1671     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1672     statusPanel.add(statusBar, null);
1673     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1674     jMenu3.add(showAllColumns);
1675     jMenu3.add(showAllSeqs);
1676     hideMenu.add(hideSelColumns);
1677     hideMenu.add(hideSelSequences);
1678     formatMenu.add(font);
1679     formatMenu.addSeparator();
1680     formatMenu.add(wrapMenuItem);
1681     formatMenu.add(scaleAbove);
1682     formatMenu.add(scaleLeft);
1683     formatMenu.add(scaleRight);
1684     formatMenu.add(seqLimits);
1685     formatMenu.add(idRightAlign);
1686     formatMenu.add(hiddenMarkers);
1687     formatMenu.add(viewBoxesMenuItem);
1688     formatMenu.add(viewTextMenuItem);
1689     formatMenu.add(colourTextMenuItem);
1690     formatMenu.add(renderGapsMenuItem);
1691     formatMenu.add(centreColumnLabelsMenuItem);
1692     formatMenu.add(showUnconservedMenuItem);
1693     selectMenu.add(findMenuItem);
1694     selectMenu.addSeparator();
1695     selectMenu.add(selectAllSequenceMenuItem);
1696     selectMenu.add(deselectAllSequenceMenuItem);
1697     selectMenu.add(invertSequenceMenuItem);
1698     selectMenu.add(invertColSel);
1699     selectMenu.add(deleteGroups);
1700   }
1701
1702   protected void showGroupConsensus_actionPerformed(ActionEvent e)
1703   {
1704     // TODO Auto-generated method stub
1705
1706   }
1707
1708   protected void showGroupConservation_actionPerformed(ActionEvent e)
1709   {
1710     // TODO Auto-generated method stub
1711
1712   }
1713
1714   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
1715   {
1716     // TODO Auto-generated method stub
1717
1718   }
1719
1720   protected void showSeqFeaturesHeight_actionPerformed(
1721           ActionEvent actionEvent)
1722   {
1723     // TODO Auto-generated method stub
1724
1725   }
1726
1727   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
1728   {
1729     // TODO Auto-generated method stub
1730
1731   }
1732
1733   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
1734   {
1735     // TODO Auto-generated method stub
1736
1737   }
1738
1739   protected void followHighlight_actionPerformed()
1740   {
1741     // TODO Auto-generated method stub
1742
1743   }
1744
1745   protected void showNpFeats_actionPerformed(ActionEvent e)
1746   {
1747     // TODO Auto-generated method stub
1748
1749   }
1750
1751   protected void showDbRefs_actionPerformed(ActionEvent e)
1752   {
1753     // TODO Auto-generated method stub
1754
1755   }
1756
1757   protected void centreColumnLabels_actionPerformed(ActionEvent e)
1758   {
1759   }
1760
1761   protected void showProducts_actionPerformed(ActionEvent e)
1762   {
1763   }
1764
1765   protected void buildSortByAnnotationScoresMenu()
1766   {
1767   }
1768
1769   protected void extractScores_actionPerformed(ActionEvent e)
1770   {
1771   }
1772
1773   protected void outputText_actionPerformed(ActionEvent e)
1774   {
1775   }
1776
1777   public void addFromFile_actionPerformed(ActionEvent e)
1778   {
1779
1780   }
1781
1782   public void addFromText_actionPerformed(ActionEvent e)
1783   {
1784
1785   }
1786
1787   public void addFromURL_actionPerformed(ActionEvent e)
1788   {
1789
1790   }
1791
1792   public void exportFeatures_actionPerformed(ActionEvent e)
1793   {
1794
1795   }
1796
1797   public void exportAnnotations_actionPerformed(ActionEvent e)
1798   {
1799
1800   }
1801
1802   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1803   {
1804   }
1805
1806   protected void closeMenuItem_actionPerformed(boolean b)
1807   {
1808   }
1809
1810   protected void redoMenuItem_actionPerformed(ActionEvent e)
1811   {
1812   }
1813
1814   protected void undoMenuItem_actionPerformed(ActionEvent e)
1815   {
1816   }
1817
1818   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1819   {
1820   }
1821
1822   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1823   {
1824   }
1825
1826   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1827   {
1828   }
1829
1830   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1831   {
1832   }
1833
1834   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
1835   {
1836   }
1837
1838   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1839   {
1840   }
1841
1842   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1843   {
1844   }
1845
1846   protected void wrapMenuItem_actionPerformed(ActionEvent e)
1847   {
1848   }
1849
1850   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1851   {
1852   }
1853
1854   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
1855   {
1856   }
1857
1858   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1859   {
1860   }
1861
1862   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1863   {
1864   }
1865
1866   protected void overviewMenuItem_actionPerformed(ActionEvent e)
1867   {
1868   }
1869
1870   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
1871   {
1872   }
1873
1874   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
1875   {
1876   }
1877
1878   protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
1879   {
1880   }
1881
1882   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
1883   {
1884   }
1885
1886   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
1887   {
1888   }
1889
1890   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
1891   {
1892   }
1893
1894   protected void PCAMenuItem_actionPerformed(ActionEvent e)
1895   {
1896   }
1897
1898   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
1899   {
1900   }
1901
1902   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
1903   {
1904   }
1905
1906   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1907   {
1908   }
1909
1910   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1911   {
1912   }
1913
1914   protected void clustalColour_actionPerformed(ActionEvent e)
1915   {
1916   }
1917
1918   protected void zappoColour_actionPerformed(ActionEvent e)
1919   {
1920   }
1921
1922   protected void taylorColour_actionPerformed(ActionEvent e)
1923   {
1924   }
1925
1926   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1927   {
1928   }
1929
1930   protected void helixColour_actionPerformed(ActionEvent e)
1931   {
1932   }
1933
1934   protected void strandColour_actionPerformed(ActionEvent e)
1935   {
1936   }
1937
1938   protected void turnColour_actionPerformed(ActionEvent e)
1939   {
1940   }
1941
1942   protected void buriedColour_actionPerformed(ActionEvent e)
1943   {
1944   }
1945
1946   protected void userDefinedColour_actionPerformed(ActionEvent e)
1947   {
1948   }
1949
1950   protected void PIDColour_actionPerformed(ActionEvent e)
1951   {
1952   }
1953
1954   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1955   {
1956   }
1957
1958   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1959   {
1960   }
1961
1962   protected void conservationMenuItem_actionPerformed(ActionEvent e)
1963   {
1964   }
1965
1966   protected void printMenuItem_actionPerformed(ActionEvent e)
1967   {
1968   }
1969
1970   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1971   {
1972   }
1973
1974   protected void findMenuItem_actionPerformed(ActionEvent e)
1975   {
1976   }
1977
1978   protected void abovePIDThreshold_actionPerformed(ActionEvent e)
1979   {
1980   }
1981
1982   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
1983   {
1984   }
1985
1986   protected void nucleotideColour_actionPerformed(ActionEvent e)
1987   {
1988   }
1989
1990   protected void deleteGroups_actionPerformed(ActionEvent e)
1991   {
1992   }
1993
1994   protected void copy_actionPerformed(ActionEvent e)
1995   {
1996   }
1997
1998   protected void cut_actionPerformed(ActionEvent e)
1999   {
2000   }
2001
2002   protected void delete_actionPerformed(ActionEvent e)
2003   {
2004   }
2005
2006   protected void pasteNew_actionPerformed(ActionEvent e)
2007   {
2008   }
2009
2010   protected void pasteThis_actionPerformed(ActionEvent e)
2011   {
2012   }
2013
2014   protected void applyToAllGroups_actionPerformed(ActionEvent e)
2015   {
2016   }
2017
2018   public void createPNG(java.io.File f)
2019   {
2020   }
2021
2022   protected void font_actionPerformed(ActionEvent e)
2023   {
2024   }
2025
2026   protected void seqLimit_actionPerformed(ActionEvent e)
2027   {
2028   }
2029
2030   public void seqDBRef_actionPerformed(ActionEvent e)
2031   {
2032
2033   }
2034
2035   public void createEPS(java.io.File f)
2036   {
2037   }
2038
2039   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2040   {
2041   }
2042
2043   protected void jpred_actionPerformed(ActionEvent e)
2044   {
2045   }
2046
2047   protected void scaleAbove_actionPerformed(ActionEvent e)
2048   {
2049   }
2050
2051   protected void scaleLeft_actionPerformed(ActionEvent e)
2052   {
2053   }
2054
2055   protected void scaleRight_actionPerformed(ActionEvent e)
2056   {
2057   }
2058
2059   protected void modifyPID_actionPerformed(ActionEvent e)
2060   {
2061   }
2062
2063   protected void modifyConservation_actionPerformed(ActionEvent e)
2064   {
2065   }
2066
2067   protected void saveAs_actionPerformed(ActionEvent e)
2068   {
2069   }
2070
2071   protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2072   {
2073   }
2074
2075   public void vamsasStore_actionPerformed(ActionEvent e)
2076   {
2077
2078   }
2079
2080   public void vamsasLoad_actionPerformed(ActionEvent e)
2081   {
2082
2083   }
2084
2085   public void showTranslation_actionPerformed(ActionEvent e)
2086   {
2087
2088   }
2089
2090   public void featureSettings_actionPerformed(ActionEvent e)
2091   {
2092
2093   }
2094
2095   public void fetchSequence_actionPerformed(ActionEvent e)
2096   {
2097
2098   }
2099
2100   public void smoothFont_actionPerformed(ActionEvent e)
2101   {
2102
2103   }
2104
2105   public void annotationColour_actionPerformed(ActionEvent e)
2106   {
2107
2108   }
2109
2110   public void associatedData_actionPerformed(ActionEvent e)
2111   {
2112
2113   }
2114
2115   public void autoCalculate_actionPerformed(ActionEvent e)
2116   {
2117
2118   }
2119
2120   public void showAllSeqs_actionPerformed(ActionEvent e)
2121   {
2122
2123   }
2124
2125   public void showAllColumns_actionPerformed(ActionEvent e)
2126   {
2127
2128   }
2129
2130   public void hideSelSequences_actionPerformed(ActionEvent e)
2131   {
2132
2133   }
2134
2135   public void hideSelColumns_actionPerformed(ActionEvent e)
2136   {
2137
2138   }
2139
2140   public void hiddenMarkers_actionPerformed(ActionEvent e)
2141   {
2142
2143   }
2144
2145   public void findPdbId_actionPerformed(ActionEvent e)
2146   {
2147
2148   }
2149
2150   public void enterPdbId_actionPerformed(ActionEvent e)
2151   {
2152
2153   }
2154
2155   public void pdbFile_actionPerformed(ActionEvent e)
2156   {
2157
2158   }
2159
2160   public void invertColSel_actionPerformed(ActionEvent e)
2161   {
2162
2163   }
2164
2165   public void tabSelectionChanged(int sel)
2166   {
2167
2168   }
2169
2170   public void tabbedPane_mousePressed(MouseEvent e)
2171   {
2172
2173   }
2174
2175   public void tabbedPane_focusGained(FocusEvent e)
2176   {
2177     requestFocus();
2178   }
2179
2180   public void save_actionPerformed(ActionEvent e)
2181   {
2182
2183   }
2184
2185   public void reload_actionPerformed(ActionEvent e)
2186   {
2187
2188   }
2189
2190   public void newView_actionPerformed(ActionEvent e)
2191   {
2192
2193   }
2194
2195   public void textColour_actionPerformed(ActionEvent e)
2196   {
2197
2198   }
2199
2200   public void idRightAlign_actionPerformed(ActionEvent e)
2201   {
2202
2203   }
2204
2205   public void expandViews_actionPerformed(ActionEvent e)
2206   {
2207
2208   }
2209
2210   public void gatherViews_actionPerformed(ActionEvent e)
2211   {
2212
2213   }
2214
2215   public void buildTreeMenu()
2216   {
2217
2218   }
2219
2220   public void pageSetup_actionPerformed(ActionEvent e)
2221   {
2222
2223   }
2224
2225   public void alignmentProperties()
2226   {
2227
2228   }
2229 }