src/jalview/jbgui/GAlignFrame.java

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