src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.jbgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 \r
  25 import jalview.schemes.*;\r
  26 \r
  27 public class GAlignFrame\r
  28     extends JInternalFrame\r
  29 {\r
  30   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  31   protected JMenu fileMenu = new JMenu();\r
  32   protected JMenuItem closeMenuItem = new JMenuItem();\r
  33   protected JMenu editMenu = new JMenu();\r
  34   protected JMenu viewMenu = new JMenu();\r
  35   protected JMenu colourMenu = new JMenu();\r
  36   protected JMenu calculateMenu = new JMenu();\r
  37   protected JMenu webService = new JMenu();\r
  38   protected JMenuItem webServiceNoServices;\r
  39   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  40   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  41   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  42   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  43   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  44   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  45   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  46   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  47   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  48   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  49   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  50   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  51   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  52   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  53   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  54   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  55   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  56   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  57   BorderLayout borderLayout1 = new BorderLayout();\r
  58   public JLabel statusBar = new JLabel();\r
  59   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  60   protected JMenu outputTextboxMenu = new JMenu();\r
  61   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  65       JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  73   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  74   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  75   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  76   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  77   JMenuItem htmlMenuItem = new JMenuItem();\r
  78   JMenuItem overviewMenuItem = new JMenuItem();\r
  79   protected JMenuItem undoMenuItem = new JMenuItem();\r
  80   protected JMenuItem redoMenuItem = new JMenuItem();\r
  81   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  82   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  83   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  84   JMenuItem printMenuItem = new JMenuItem();\r
  85   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  86   JMenuItem findMenuItem = new JMenuItem();\r
  87   JMenu searchMenu = new JMenu();\r
  88   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  89   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  90   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  91   JMenuItem deleteGroups = new JMenuItem();\r
  92   JMenuItem delete = new JMenuItem();\r
  93   JMenuItem copy = new JMenuItem();\r
  94   JMenuItem cut = new JMenuItem();\r
  95   JMenu jMenu1 = new JMenu();\r
  96   JMenuItem pasteNew = new JMenuItem();\r
  97   JMenuItem pasteThis = new JMenuItem();\r
  98   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  99   JMenuItem createPNG = new JMenuItem();\r
 100   protected JMenuItem font = new JMenuItem();\r
 101   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 102   JMenuItem epsFile = new JMenuItem();\r
 103   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 104   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 105   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 106   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 107   protected JMenuItem modifyPID = new JMenuItem();\r
 108   protected JMenuItem modifyConservation = new JMenuItem();\r
 109   protected JMenu sortByTreeMenu = new JMenu();\r
 110   protected JMenu sort = new JMenu();\r
 111   JMenu calculate = new JMenu();\r
 112   JMenu jMenu2 = new JMenu();\r
 113   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 114   protected ButtonGroup colours = new ButtonGroup();\r
 115   JMenuItem vamsasStore = new JMenuItem();\r
 116   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
 117   //protected JTabbedPane tabbedPane = new JTabbedPane();\r
 118   public JMenuItem featureSettings = new JMenuItem();\r
 119   JMenuItem fetchSequence = new JMenuItem();\r
 120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 121   JMenuItem annotationColour = new JMenuItem();\r
 122   JMenuItem fetchSeqFeatures = new JMenuItem();\r
 123 \r
 124 \r
 125 \r
 126   JMenuItem associatedData = new JMenuItem();\r
 127   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 128   JMenu addSequenceMenu = new JMenu();\r
 129   JMenuItem addFromFile = new JMenuItem();\r
 130   JMenuItem addFromText = new JMenuItem();\r
 131   JMenuItem addFromURL = new JMenuItem();\r
 132   public GAlignFrame()\r
 133   {\r
 134 \r
 135 \r
 136     try\r
 137     {\r
 138       jbInit();\r
 139       setJMenuBar(alignFrameMenuBar);\r
 140 \r
 141       // dynamically fill save as menu with available formats\r
 142       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 143       {\r
 144         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 145                              elementAt(\r
 146                                  i));\r
 147         item.addActionListener(new java.awt.event.ActionListener()\r
 148         {\r
 149           public void actionPerformed(ActionEvent e)\r
 150           {\r
 151             outputText_actionPerformed(e);\r
 152           }\r
 153         });\r
 154 \r
 155         outputTextboxMenu.add(item);\r
 156       }\r
 157     }\r
 158     catch (Exception e)\r
 159     {\r
 160     }\r
 161 \r
 162 \r
 163     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 164     {\r
 165       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 166           getUserColourSchemes().keys();\r
 167 \r
 168       while (userColours.hasMoreElements())\r
 169       {\r
 170         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 171             nextElement().toString());\r
 172         radioItem.setName("USER_DEFINED");\r
 173         radioItem.addMouseListener(new MouseAdapter()\r
 174             {\r
 175               public void mousePressed(MouseEvent evt)\r
 176               {\r
 177                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 178                 {\r
 179                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 180 \r
 181                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 182                       "Remove from default list?",\r
 183                       "Remove user defined colour",\r
 184                       JOptionPane.YES_NO_OPTION);\r
 185                   if(option == JOptionPane.YES_OPTION)\r
 186                   {\r
 187                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 188                     colourMenu.remove(radioItem);\r
 189                   }\r
 190                   else\r
 191                     radioItem.addActionListener(new ActionListener()\r
 192                     {\r
 193                       public void actionPerformed(ActionEvent evt)\r
 194                       {\r
 195                         userDefinedColour_actionPerformed(evt);\r
 196                       }\r
 197                     });\r
 198                 }\r
 199               }\r
 200             });\r
 201         radioItem.addActionListener(new ActionListener()\r
 202         {\r
 203           public void actionPerformed(ActionEvent evt)\r
 204           {\r
 205             userDefinedColour_actionPerformed(evt);\r
 206           }\r
 207         });\r
 208         colourMenu.insert(radioItem, 15);\r
 209         colours.add(radioItem);\r
 210       }\r
 211     }\r
 212     colours.add(noColourmenuItem);\r
 213     colours.add(clustalColour);\r
 214     colours.add(zappoColour);\r
 215     colours.add(taylorColour);\r
 216     colours.add(hydrophobicityColour);\r
 217     colours.add(helixColour);\r
 218     colours.add(strandColour);\r
 219     colours.add(turnColour);\r
 220     colours.add(buriedColour);\r
 221     colours.add(userDefinedColour);\r
 222     colours.add(PIDColour);\r
 223     colours.add(BLOSUM62Colour);\r
 224     colours.add(nucleotideColour);\r
 225 \r
 226     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 227 \r
 228 \r
 229   }\r
 230 \r
 231   public void setColourSelected(String defaultColour)\r
 232   {\r
 233 \r
 234     if (defaultColour != null)\r
 235     {\r
 236       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 237 \r
 238       switch (index)\r
 239       {\r
 240         case ColourSchemeProperty.NONE:\r
 241               noColourmenuItem.setSelected(true);\r
 242               break;\r
 243         case ColourSchemeProperty.CLUSTAL:\r
 244           clustalColour.setSelected(true);\r
 245 \r
 246           break;\r
 247 \r
 248         case ColourSchemeProperty.BLOSUM:\r
 249           BLOSUM62Colour.setSelected(true);\r
 250 \r
 251           break;\r
 252 \r
 253         case ColourSchemeProperty.PID:\r
 254           PIDColour.setSelected(true);\r
 255 \r
 256           break;\r
 257 \r
 258         case ColourSchemeProperty.ZAPPO:\r
 259           zappoColour.setSelected(true);\r
 260 \r
 261           break;\r
 262 \r
 263         case ColourSchemeProperty.TAYLOR:\r
 264           taylorColour.setSelected(true);\r
 265           break;\r
 266 \r
 267         case ColourSchemeProperty.HYDROPHOBIC:\r
 268           hydrophobicityColour.setSelected(true);\r
 269 \r
 270           break;\r
 271 \r
 272         case ColourSchemeProperty.HELIX:\r
 273           helixColour.setSelected(true);\r
 274 \r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.STRAND:\r
 278           strandColour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.TURN:\r
 283           turnColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.BURIED:\r
 288           buriedColour.setSelected(true);\r
 289 \r
 290           break;\r
 291 \r
 292         case ColourSchemeProperty.NUCLEOTIDE:\r
 293           nucleotideColour.setSelected(true);\r
 294 \r
 295           break;\r
 296 \r
 297         case ColourSchemeProperty.USER_DEFINED:\r
 298           userDefinedColour.setSelected(true);\r
 299 \r
 300           break;\r
 301       }\r
 302     }\r
 303 \r
 304   }\r
 305 \r
 306   private void jbInit()\r
 307       throws Exception\r
 308   {\r
 309     fileMenu.setMnemonic('F');\r
 310     fileMenu.setText("File");\r
 311     saveAlignmentMenu.setMnemonic('L');\r
 312     saveAlignmentMenu.setText("Save As");\r
 313     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 314         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 315     saveAlignmentMenu.addActionListener(new ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         saveAlignmentMenu_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     closeMenuItem.setMnemonic('C');\r
 323     closeMenuItem.setText("Close");\r
 324     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         closeMenuItem_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     editMenu.setText("Edit");\r
 332     viewMenu.setText("View");\r
 333     colourMenu.setText("Colour");\r
 334     calculateMenu.setText("Calculate");\r
 335     webService.setText("Web Service");\r
 336     selectAllSequenceMenuItem.setText("Select all");\r
 337     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 338         java.awt.event.KeyEvent.VK_A,\r
 339         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 340     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 341                                                 ActionListener()\r
 342     {\r
 343       public void actionPerformed(ActionEvent e)\r
 344       {\r
 345         selectAllSequenceMenuItem_actionPerformed(e);\r
 346       }\r
 347     });\r
 348     deselectAllSequenceMenuItem.setText("Deselect All");\r
 349     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 350                                                getKeyStroke(\r
 351         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 352     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 353                                                   ActionListener()\r
 354     {\r
 355       public void actionPerformed(ActionEvent e)\r
 356       {\r
 357         deselectAllSequenceMenuItem_actionPerformed(e);\r
 358       }\r
 359     });\r
 360     invertSequenceMenuItem.setText("Invert Selection");\r
 361     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 362     {\r
 363       public void actionPerformed(ActionEvent e)\r
 364       {\r
 365         invertSequenceMenuItem_actionPerformed(e);\r
 366       }\r
 367     });\r
 368     remove2LeftMenuItem.setText("Remove Left");\r
 369     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 370     {\r
 371       public void actionPerformed(ActionEvent e)\r
 372       {\r
 373         remove2LeftMenuItem_actionPerformed(e);\r
 374       }\r
 375     });\r
 376     remove2RightMenuItem.setText("Remove Right");\r
 377     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 378     {\r
 379       public void actionPerformed(ActionEvent e)\r
 380       {\r
 381         remove2RightMenuItem_actionPerformed(e);\r
 382       }\r
 383     });\r
 384     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 385     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 386                                                  ActionListener()\r
 387     {\r
 388       public void actionPerformed(ActionEvent e)\r
 389       {\r
 390         removeGappedColumnMenuItem_actionPerformed(e);\r
 391       }\r
 392     });\r
 393     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 394     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         removeAllGapsMenuItem_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     viewBoxesMenuItem.setText("Boxes");\r
 402     viewBoxesMenuItem.setState(true);\r
 403     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         viewBoxesMenuItem_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     viewTextMenuItem.setText("Text");\r
 411     viewTextMenuItem.setState(true);\r
 412     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 413     {\r
 414       public void actionPerformed(ActionEvent e)\r
 415       {\r
 416         viewTextMenuItem_actionPerformed(e);\r
 417       }\r
 418     });\r
 419     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 420     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 421     {\r
 422       public void actionPerformed(ActionEvent e)\r
 423       {\r
 424         sortPairwiseMenuItem_actionPerformed(e);\r
 425       }\r
 426     });\r
 427     sortIDMenuItem.setText("by ID");\r
 428     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         sortIDMenuItem_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     sortGroupMenuItem.setText("by Group");\r
 436     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 437     {\r
 438       public void actionPerformed(ActionEvent e)\r
 439       {\r
 440         sortGroupMenuItem_actionPerformed(e);\r
 441       }\r
 442     });\r
 443     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 444     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 445                                                ActionListener()\r
 446     {\r
 447       public void actionPerformed(ActionEvent e)\r
 448       {\r
 449         removeRedundancyMenuItem_actionPerformed(e);\r
 450       }\r
 451     });\r
 452     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 453     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 454                                                 ActionListener()\r
 455     {\r
 456       public void actionPerformed(ActionEvent e)\r
 457       {\r
 458         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 459       }\r
 460     });\r
 461     PCAMenuItem.setText("Principal Component Analysis");\r
 462     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         PCAMenuItem_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     averageDistanceTreeMenuItem.setText(\r
 470         "Average Distance Using % Identity");\r
 471     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 472                                                   ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         averageDistanceTreeMenuItem_actionPerformed(e);\r
 477       }\r
 478     });\r
 479     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 480     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 481     {\r
 482       public void actionPerformed(ActionEvent e)\r
 483       {\r
 484         neighbourTreeMenuItem_actionPerformed(e);\r
 485       }\r
 486     });\r
 487     this.getContentPane().setLayout(borderLayout1);\r
 488     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 489     statusBar.setBackground(Color.white);\r
 490     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 491     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 492     statusBar.setText("Status bar");\r
 493     outputTextboxMenu.setMnemonic('T');\r
 494     outputTextboxMenu.setText("Output to Textbox");\r
 495     clustalColour.setText("Clustalx");\r
 496 \r
 497     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         clustalColour_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     zappoColour.setText("Zappo");\r
 505     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         zappoColour_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     taylorColour.setText("Taylor");\r
 513     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 514     {\r
 515       public void actionPerformed(ActionEvent e)\r
 516       {\r
 517         taylorColour_actionPerformed(e);\r
 518       }\r
 519     });\r
 520     hydrophobicityColour.setText("Hydrophobicity");\r
 521     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         hydrophobicityColour_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     helixColour.setText("Helix Propensity");\r
 529     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         helixColour_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     strandColour.setText("Strand Propensity");\r
 537     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         strandColour_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     turnColour.setText("Turn Propensity");\r
 545     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         turnColour_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     buriedColour.setText("Buried Index");\r
 553     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         buriedColour_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     userDefinedColour.setText("User Defined...");\r
 561     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         userDefinedColour_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     PIDColour.setText("Percentage Identity");\r
 569     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         PIDColour_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 577     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 578     {\r
 579       public void actionPerformed(ActionEvent e)\r
 580       {\r
 581         BLOSUM62Colour_actionPerformed(e);\r
 582       }\r
 583     });\r
 584     avDistanceTreeBlosumMenuItem.setText(\r
 585         "Average Distance Using BLOSUM62");\r
 586     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 587         ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent e)\r
 590       {\r
 591         avTreeBlosumMenuItem_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 595     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 596     {\r
 597       public void actionPerformed(ActionEvent e)\r
 598       {\r
 599         njTreeBlosumMenuItem_actionPerformed(e);\r
 600       }\r
 601     });\r
 602     annotationPanelMenuItem.setActionCommand("");\r
 603     annotationPanelMenuItem.setText("Show Annotations");\r
 604     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 605     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 606     {\r
 607       public void actionPerformed(ActionEvent e)\r
 608       {\r
 609         annotationPanelMenuItem_actionPerformed(e);\r
 610       }\r
 611     });\r
 612     colourTextMenuItem.setText("Colour Text");\r
 613     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 614     {\r
 615       public void actionPerformed(ActionEvent e)\r
 616       {\r
 617         colourTextMenuItem_actionPerformed(e);\r
 618       }\r
 619     });\r
 620     htmlMenuItem.setText("HTML");\r
 621     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 622     {\r
 623       public void actionPerformed(ActionEvent e)\r
 624       {\r
 625         htmlMenuItem_actionPerformed(e);\r
 626       }\r
 627     });\r
 628     overviewMenuItem.setText("Overview Window");\r
 629     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 630     {\r
 631       public void actionPerformed(ActionEvent e)\r
 632       {\r
 633         overviewMenuItem_actionPerformed(e);\r
 634       }\r
 635     });\r
 636     undoMenuItem.setEnabled(false);\r
 637     undoMenuItem.setMnemonic('Z');\r
 638     undoMenuItem.setText("Undo");\r
 639     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 640         java.awt.event.KeyEvent.VK_Z,\r
 641         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 642     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 643     {\r
 644       public void actionPerformed(ActionEvent e)\r
 645       {\r
 646         undoMenuItem_actionPerformed(e);\r
 647       }\r
 648     });\r
 649     redoMenuItem.setEnabled(false);\r
 650     redoMenuItem.setMnemonic('0');\r
 651     redoMenuItem.setText("Redo");\r
 652     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 653     {\r
 654       public void actionPerformed(ActionEvent e)\r
 655       {\r
 656         redoMenuItem_actionPerformed(e);\r
 657       }\r
 658     });\r
 659     conservationMenuItem.setText("By Conservation");\r
 660     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 661     {\r
 662       public void actionPerformed(ActionEvent e)\r
 663       {\r
 664         conservationMenuItem_actionPerformed(e);\r
 665       }\r
 666     });\r
 667     noColourmenuItem.setText("None");\r
 668     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 669     {\r
 670       public void actionPerformed(ActionEvent e)\r
 671       {\r
 672         noColourmenuItem_actionPerformed(e);\r
 673       }\r
 674     });\r
 675     wrapMenuItem.setText("Wrap");\r
 676     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 677     {\r
 678       public void actionPerformed(ActionEvent e)\r
 679       {\r
 680         wrapMenuItem_actionPerformed(e);\r
 681       }\r
 682     });\r
 683     printMenuItem.setText("Print");\r
 684     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 685     {\r
 686       public void actionPerformed(ActionEvent e)\r
 687       {\r
 688         printMenuItem_actionPerformed(e);\r
 689       }\r
 690     });\r
 691     renderGapsMenuItem.setText("Show Gaps");\r
 692     renderGapsMenuItem.setState(true);\r
 693     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 694     {\r
 695       public void actionPerformed(ActionEvent e)\r
 696       {\r
 697         renderGapsMenuItem_actionPerformed(e);\r
 698       }\r
 699     });\r
 700     findMenuItem.setText("Find...");\r
 701     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 702         java.awt.event.KeyEvent.VK_F,\r
 703         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 704     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 705     {\r
 706       public void actionPerformed(ActionEvent e)\r
 707       {\r
 708         findMenuItem_actionPerformed(e);\r
 709       }\r
 710     });\r
 711     searchMenu.setText("Search");\r
 712 \r
 713     abovePIDThreshold.setText("Above Identity Threshold");\r
 714     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 715     {\r
 716       public void actionPerformed(ActionEvent e)\r
 717       {\r
 718         abovePIDThreshold_actionPerformed(e);\r
 719       }\r
 720     });\r
 721     showSeqFeatures.setText("Show Sequence Features");\r
 722     showSeqFeatures.addActionListener(new ActionListener()\r
 723     {\r
 724       public void actionPerformed(ActionEvent actionEvent)\r
 725       {\r
 726         showSeqFeatures_actionPerformed(actionEvent);\r
 727       }\r
 728     });\r
 729     nucleotideColour.setText("Nucleotide");\r
 730     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 731     {\r
 732       public void actionPerformed(ActionEvent e)\r
 733       {\r
 734         nucleotideColour_actionPerformed(e);\r
 735       }\r
 736     });\r
 737     deleteGroups.setText("Undefine groups");\r
 738     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 739     {\r
 740       public void actionPerformed(ActionEvent e)\r
 741       {\r
 742         deleteGroups_actionPerformed(e);\r
 743       }\r
 744     });\r
 745     copy.setText("Copy");\r
 746     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 747         java.awt.event.KeyEvent.VK_C,\r
 748         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 749     copy.setMnemonic(KeyEvent.VK_C);\r
 750 \r
 751     copy.addActionListener(new java.awt.event.ActionListener()\r
 752     {\r
 753       public void actionPerformed(ActionEvent e)\r
 754       {\r
 755         copy_actionPerformed(e);\r
 756       }\r
 757     });\r
 758     cut.setText("Cut");\r
 759     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 760         java.awt.event.KeyEvent.VK_X,\r
 761         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 762     cut.setMnemonic(KeyEvent.VK_X);\r
 763     cut.addActionListener(new java.awt.event.ActionListener()\r
 764     {\r
 765       public void actionPerformed(ActionEvent e)\r
 766       {\r
 767         cut_actionPerformed(e);\r
 768       }\r
 769     });\r
 770     delete.setText("Delete");\r
 771     delete.addActionListener(new java.awt.event.ActionListener()\r
 772     {\r
 773       public void actionPerformed(ActionEvent e)\r
 774       {\r
 775         delete_actionPerformed(e);\r
 776       }\r
 777     });\r
 778     jMenu1.setMnemonic('V');\r
 779     jMenu1.setText("Paste");\r
 780     pasteNew.setText("To New Alignment");\r
 781     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 782         java.awt.event.KeyEvent.VK_V,\r
 783         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 784     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 785     {\r
 786       public void actionPerformed(ActionEvent e)\r
 787       {\r
 788         pasteNew_actionPerformed(e);\r
 789       }\r
 790     });\r
 791     pasteThis.setText("Add To This Alignment");\r
 792     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 793     {\r
 794       public void actionPerformed(ActionEvent e)\r
 795       {\r
 796         pasteThis_actionPerformed(e);\r
 797       }\r
 798     });\r
 799     applyToAllGroups.setText("Apply Colour To All Groups");\r
 800     applyToAllGroups.setState(true);\r
 801     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 802     {\r
 803       public void actionPerformed(ActionEvent e)\r
 804       {\r
 805         applyToAllGroups_actionPerformed(e);\r
 806       }\r
 807     });\r
 808     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 809     {\r
 810       public void actionPerformed(ActionEvent e)\r
 811       {\r
 812         createPNG(null);\r
 813       }\r
 814     });\r
 815     createPNG.setActionCommand("Save As PNG Image");\r
 816     createPNG.setText("PNG");\r
 817     font.setText("Font...");\r
 818     font.addActionListener(new java.awt.event.ActionListener()\r
 819     {\r
 820       public void actionPerformed(ActionEvent e)\r
 821       {\r
 822         font_actionPerformed(e);\r
 823       }\r
 824     });\r
 825 \r
 826     seqLimits.setText("Show Sequence Limits");\r
 827     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 828     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 829     {\r
 830       public void actionPerformed(ActionEvent e)\r
 831       {\r
 832         seqLimit_actionPerformed(e);\r
 833       }\r
 834     });\r
 835     epsFile.setText("EPS");\r
 836     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 837     {\r
 838       public void actionPerformed(ActionEvent e)\r
 839       {\r
 840         createEPS(null);\r
 841       }\r
 842     });\r
 843     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 844     LoadtreeMenuItem.setText("Load Associated Tree");\r
 845     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 846     {\r
 847       public void actionPerformed(ActionEvent e)\r
 848       {\r
 849         LoadtreeMenuItem_actionPerformed(e);\r
 850       }\r
 851     });\r
 852     scaleAbove.setVisible(false);\r
 853     scaleAbove.setText("Scale Above");\r
 854     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 855     {\r
 856       public void actionPerformed(ActionEvent e)\r
 857       {\r
 858         scaleAbove_actionPerformed(e);\r
 859       }\r
 860     });\r
 861     scaleLeft.setVisible(false);\r
 862     scaleLeft.setSelected(true);\r
 863     scaleLeft.setText("Scale Left");\r
 864     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 865     {\r
 866       public void actionPerformed(ActionEvent e)\r
 867       {\r
 868         scaleLeft_actionPerformed(e);\r
 869       }\r
 870     });\r
 871     scaleRight.setVisible(false);\r
 872     scaleRight.setSelected(true);\r
 873     scaleRight.setText("Scale Right");\r
 874     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 875     {\r
 876       public void actionPerformed(ActionEvent e)\r
 877       {\r
 878         scaleRight_actionPerformed(e);\r
 879       }\r
 880     });\r
 881     modifyPID.setText("Modify Identity Threshold...");\r
 882     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 883     {\r
 884       public void actionPerformed(ActionEvent e)\r
 885       {\r
 886         modifyPID_actionPerformed(e);\r
 887       }\r
 888     });\r
 889     modifyConservation.setText("Modify Conservation Threshold...");\r
 890     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 891     {\r
 892       public void actionPerformed(ActionEvent e)\r
 893       {\r
 894         modifyConservation_actionPerformed(e);\r
 895       }\r
 896     });\r
 897     sortByTreeMenu.setText("By Tree Order");\r
 898     sort.setText("Sort");\r
 899     calculate.setText("Calculate Tree");\r
 900 \r
 901     jMenu2.setText("Export");\r
 902     padGapsMenuitem.setText("Pad Gaps");\r
 903     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 904     padGapsMenuitem.addActionListener(new ActionListener()\r
 905     {\r
 906       public void actionPerformed(ActionEvent e)\r
 907       {\r
 908         padGapsMenuitem_actionPerformed(e);\r
 909       }\r
 910     });\r
 911     vamsasStore.setVisible(false);\r
 912     vamsasStore.setText("VAMSAS store");\r
 913     vamsasStore.addActionListener(new ActionListener()\r
 914     {\r
 915       public void actionPerformed(ActionEvent e)\r
 916       {\r
 917         vamsasStore_actionPerformed(e);\r
 918       }\r
 919     });\r
 920     showTranslation.setText("Translate cDNA");\r
 921     showTranslation.addActionListener(new ActionListener()\r
 922     {\r
 923       public void actionPerformed(ActionEvent e)\r
 924       {\r
 925         showTranslation_actionPerformed(e);\r
 926       }\r
 927     });\r
 928 \r
 929    /* tabbedPane.addChangeListener(new ChangeListener()\r
 930         {\r
 931           public void stateChanged(ChangeEvent ece)\r
 932           {\r
 933 \r
 934             tabSelected();\r
 935           }\r
 936         });*/\r
 937     featureSettings.setText("Feature Settings...");\r
 938     featureSettings.addActionListener(new ActionListener()\r
 939     {\r
 940       public void actionPerformed(ActionEvent e)\r
 941       {\r
 942         featureSettings_actionPerformed(e);\r
 943       }\r
 944     });\r
 945     fetchSequence.setText("Fetch Sequence(s)...");\r
 946     fetchSequence.addActionListener(new ActionListener()\r
 947     {\r
 948       public void actionPerformed(ActionEvent e)\r
 949       {\r
 950         fetchSequence_actionPerformed(e);\r
 951       }\r
 952     });\r
 953     smoothFont.setText("Smooth Fonts");\r
 954     smoothFont.addActionListener(new ActionListener()\r
 955     {\r
 956       public void actionPerformed(ActionEvent e)\r
 957       {\r
 958         smoothFont_actionPerformed(e);\r
 959       }\r
 960     });\r
 961     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 962     annotationColour.setText("By Annotation...");\r
 963     annotationColour.addActionListener(new ActionListener()\r
 964     {\r
 965       public void actionPerformed(ActionEvent e)\r
 966       {\r
 967         annotationColour_actionPerformed(e);\r
 968       }\r
 969     });\r
 970     fetchSeqFeatures.setText("Fetch Sequence Features");\r
 971     fetchSeqFeatures.addActionListener(new ActionListener()\r
 972     {\r
 973       public void actionPerformed(ActionEvent e)\r
 974       {\r
 975         fetchSeqFeatures_actionPerformed(e);\r
 976       }\r
 977     });\r
 978     associatedData.setText("Load Features / Annotations");\r
 979     associatedData.addActionListener(new ActionListener()\r
 980     {\r
 981       public void actionPerformed(ActionEvent e)\r
 982       {\r
 983         associatedData_actionPerformed(e);\r
 984       }\r
 985     });\r
 986     autoCalculate.setText("Autocalculate Consensus");\r
 987     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 988     autoCalculate.addActionListener(new ActionListener()\r
 989     {\r
 990       public void actionPerformed(ActionEvent e)\r
 991       {\r
 992         autoCalculate_actionPerformed(e);\r
 993       }\r
 994     });\r
 995     addSequenceMenu.setText("Add Sequences");\r
 996     addFromFile.setText("From File");\r
 997     addFromFile.addActionListener(new ActionListener()\r
 998     {\r
 999       public void actionPerformed(ActionEvent e)\r
1000       {\r
1001         addFromFile_actionPerformed(e);\r
1002       }\r
1003     });\r
1004     addFromText.setText("From Textbox");\r
1005     addFromText.addActionListener(new ActionListener()\r
1006     {\r
1007       public void actionPerformed(ActionEvent e)\r
1008       {\r
1009         addFromText_actionPerformed(e);\r
1010       }\r
1011     });\r
1012     addFromURL.setText("From URL");\r
1013     addFromURL.addActionListener(new ActionListener()\r
1014     {\r
1015       public void actionPerformed(ActionEvent e)\r
1016       {\r
1017         addFromURL_actionPerformed(e);\r
1018       }\r
1019     });\r
1020     alignFrameMenuBar.add(fileMenu);\r
1021     alignFrameMenuBar.add(editMenu);\r
1022     alignFrameMenuBar.add(searchMenu);\r
1023     alignFrameMenuBar.add(viewMenu);\r
1024     alignFrameMenuBar.add(colourMenu);\r
1025     alignFrameMenuBar.add(calculateMenu);\r
1026     alignFrameMenuBar.add(webService);\r
1027     fileMenu.add(addSequenceMenu);\r
1028     fileMenu.add(fetchSequence);\r
1029     fileMenu.addSeparator();\r
1030     fileMenu.add(vamsasStore);\r
1031     fileMenu.add(saveAlignmentMenu);\r
1032     fileMenu.add(jMenu2);\r
1033     fileMenu.add(outputTextboxMenu);\r
1034     fileMenu.add(printMenuItem);\r
1035     fileMenu.addSeparator();\r
1036     fileMenu.add(LoadtreeMenuItem);\r
1037     fileMenu.add(associatedData);\r
1038     fileMenu.addSeparator();\r
1039     fileMenu.add(closeMenuItem);\r
1040     editMenu.add(undoMenuItem);\r
1041     editMenu.add(redoMenuItem);\r
1042     editMenu.add(cut);\r
1043     editMenu.add(copy);\r
1044     editMenu.add(jMenu1);\r
1045     editMenu.add(delete);\r
1046     editMenu.addSeparator();\r
1047     editMenu.add(selectAllSequenceMenuItem);\r
1048     editMenu.add(deselectAllSequenceMenuItem);\r
1049     editMenu.add(invertSequenceMenuItem);\r
1050     editMenu.add(deleteGroups);\r
1051     editMenu.addSeparator();\r
1052     editMenu.add(remove2LeftMenuItem);\r
1053     editMenu.add(remove2RightMenuItem);\r
1054     editMenu.add(removeGappedColumnMenuItem);\r
1055     editMenu.add(removeAllGapsMenuItem);\r
1056     editMenu.add(removeRedundancyMenuItem);\r
1057     editMenu.addSeparator();\r
1058     editMenu.add(padGapsMenuitem);\r
1059     searchMenu.add(findMenuItem);\r
1060     viewMenu.add(font);\r
1061     viewMenu.add(smoothFont);\r
1062     viewMenu.addSeparator();\r
1063     viewMenu.add(wrapMenuItem);\r
1064     viewMenu.add(seqLimits);\r
1065     viewMenu.add(scaleAbove);\r
1066     viewMenu.add(scaleLeft);\r
1067     viewMenu.add(scaleRight);\r
1068     viewMenu.add(viewBoxesMenuItem);\r
1069     viewMenu.add(viewTextMenuItem);\r
1070     viewMenu.add(colourTextMenuItem);\r
1071     viewMenu.add(renderGapsMenuItem);\r
1072     viewMenu.add(annotationPanelMenuItem);\r
1073     viewMenu.addSeparator();\r
1074     viewMenu.add(fetchSeqFeatures);\r
1075     viewMenu.add(showSeqFeatures);\r
1076     viewMenu.add(featureSettings);\r
1077     viewMenu.addSeparator();\r
1078     viewMenu.add(overviewMenuItem);\r
1079     colourMenu.add(applyToAllGroups);\r
1080     colourMenu.addSeparator();\r
1081     colourMenu.add(noColourmenuItem);\r
1082     colourMenu.add(clustalColour);\r
1083     colourMenu.add(BLOSUM62Colour);\r
1084     colourMenu.add(PIDColour);\r
1085     colourMenu.add(zappoColour);\r
1086     colourMenu.add(taylorColour);\r
1087     colourMenu.add(hydrophobicityColour);\r
1088     colourMenu.add(helixColour);\r
1089     colourMenu.add(strandColour);\r
1090     colourMenu.add(turnColour);\r
1091     colourMenu.add(buriedColour);\r
1092     colourMenu.add(nucleotideColour);\r
1093     colourMenu.add(userDefinedColour);\r
1094     colourMenu.addSeparator();\r
1095     colourMenu.add(conservationMenuItem);\r
1096     colourMenu.add(modifyConservation);\r
1097     colourMenu.add(abovePIDThreshold);\r
1098     colourMenu.add(modifyPID);\r
1099     colourMenu.add(annotationColour);\r
1100     calculateMenu.add(sort);\r
1101     calculateMenu.add(calculate);\r
1102     calculateMenu.addSeparator();\r
1103     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1104     calculateMenu.add(PCAMenuItem);\r
1105     calculateMenu.addSeparator();\r
1106     calculateMenu.add(showTranslation);\r
1107     calculateMenu.add(autoCalculate);\r
1108     webServiceNoServices=new JMenuItem("<No Services>");\r
1109     webService.add(webServiceNoServices);\r
1110     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
1111     jMenu1.add(pasteNew);\r
1112     jMenu1.add(pasteThis);\r
1113     sort.add(sortIDMenuItem);\r
1114     sort.add(sortGroupMenuItem);\r
1115     sort.add(sortPairwiseMenuItem);\r
1116     calculate.add(averageDistanceTreeMenuItem);\r
1117     calculate.add(neighbourTreeMenuItem);\r
1118     calculate.add(avDistanceTreeBlosumMenuItem);\r
1119     calculate.add(njTreeBlosumMenuItem);\r
1120     jMenu2.add(htmlMenuItem);\r
1121     jMenu2.add(epsFile);\r
1122     jMenu2.add(createPNG);\r
1123     addSequenceMenu.add(addFromFile);\r
1124     addSequenceMenu.add(addFromText);\r
1125     addSequenceMenu.add(addFromURL);\r
1126   }\r
1127 \r
1128   protected void outputText_actionPerformed(ActionEvent e)\r
1129   {\r
1130   }\r
1131 \r
1132   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1133   {\r
1134   }\r
1135 \r
1136   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1137   {\r
1138   }\r
1139 \r
1140   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1141   {\r
1142   }\r
1143 \r
1144   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1145   {\r
1146   }\r
1147 \r
1148   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1149   {\r
1150   }\r
1151 \r
1152   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1153   {\r
1154   }\r
1155 \r
1156   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1157   {\r
1158   }\r
1159 \r
1160   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1161   {\r
1162   }\r
1163 \r
1164   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1165   {\r
1166   }\r
1167 \r
1168   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1169   {\r
1170   }\r
1171 \r
1172   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1173   {\r
1174   }\r
1175 \r
1176   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1177   {\r
1178   }\r
1179 \r
1180   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1181   {\r
1182   }\r
1183 \r
1184   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1185   {\r
1186   }\r
1187 \r
1188   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1189   {\r
1190   }\r
1191 \r
1192   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1193   {\r
1194   }\r
1195 \r
1196   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1197   {\r
1198   }\r
1199 \r
1200   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1201   {\r
1202   }\r
1203 \r
1204   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1205   {\r
1206   }\r
1207 \r
1208   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1209   {\r
1210   }\r
1211 \r
1212   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1213   {\r
1214   }\r
1215 \r
1216   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1217   {\r
1218   }\r
1219 \r
1220   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1221   {\r
1222   }\r
1223 \r
1224   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1225   {\r
1226   }\r
1227 \r
1228   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1229   {\r
1230   }\r
1231 \r
1232   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1233   {\r
1234   }\r
1235 \r
1236   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1237   {\r
1238   }\r
1239 \r
1240   protected void clustalColour_actionPerformed(ActionEvent e)\r
1241   {\r
1242   }\r
1243 \r
1244   protected void zappoColour_actionPerformed(ActionEvent e)\r
1245   {\r
1246   }\r
1247 \r
1248   protected void taylorColour_actionPerformed(ActionEvent e)\r
1249   {\r
1250   }\r
1251 \r
1252   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1253   {\r
1254   }\r
1255 \r
1256   protected void helixColour_actionPerformed(ActionEvent e)\r
1257   {\r
1258   }\r
1259 \r
1260   protected void strandColour_actionPerformed(ActionEvent e)\r
1261   {\r
1262   }\r
1263 \r
1264   protected void turnColour_actionPerformed(ActionEvent e)\r
1265   {\r
1266   }\r
1267 \r
1268   protected void buriedColour_actionPerformed(ActionEvent e)\r
1269   {\r
1270   }\r
1271 \r
1272   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1273   {\r
1274   }\r
1275 \r
1276   protected void PIDColour_actionPerformed(ActionEvent e)\r
1277   {\r
1278   }\r
1279 \r
1280   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1281   {\r
1282   }\r
1283 \r
1284   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1285   {\r
1286   }\r
1287 \r
1288   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1289   {\r
1290   }\r
1291 \r
1292   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1293   {\r
1294   }\r
1295 \r
1296   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1297   {\r
1298   }\r
1299 \r
1300   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1301   {\r
1302   }\r
1303 \r
1304   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1305   {\r
1306   }\r
1307 \r
1308   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1309   {\r
1310   }\r
1311 \r
1312   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1313   {\r
1314   }\r
1315 \r
1316   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1317   {\r
1318   }\r
1319 \r
1320   protected void copy_actionPerformed(ActionEvent e)\r
1321   {\r
1322   }\r
1323 \r
1324   protected void cut_actionPerformed(ActionEvent e)\r
1325   {\r
1326   }\r
1327 \r
1328   protected void delete_actionPerformed(ActionEvent e)\r
1329   {\r
1330   }\r
1331 \r
1332   protected void pasteNew_actionPerformed(ActionEvent e)\r
1333   {\r
1334   }\r
1335 \r
1336   protected void pasteThis_actionPerformed(ActionEvent e)\r
1337   {\r
1338   }\r
1339 \r
1340   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1341   {\r
1342   }\r
1343 \r
1344   public void createPNG(java.io.File f)\r
1345   {\r
1346   }\r
1347 \r
1348   protected void font_actionPerformed(ActionEvent e)\r
1349   {\r
1350   }\r
1351 \r
1352   protected void seqLimit_actionPerformed(ActionEvent e)\r
1353   {\r
1354   }\r
1355 \r
1356   public void seqDBRef_actionPerformed(ActionEvent e)\r
1357   {\r
1358 \r
1359   }\r
1360 \r
1361 \r
1362   public void createEPS(java.io.File f)\r
1363   {\r
1364   }\r
1365 \r
1366   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1367   {\r
1368   }\r
1369 \r
1370   protected void jpred_actionPerformed(ActionEvent e)\r
1371   {\r
1372   }\r
1373 \r
1374   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1375   {\r
1376   }\r
1377 \r
1378   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1379   {\r
1380   }\r
1381 \r
1382   protected void scaleRight_actionPerformed(ActionEvent e)\r
1383   {\r
1384   }\r
1385 \r
1386   protected void modifyPID_actionPerformed(ActionEvent e)\r
1387   {\r
1388   }\r
1389 \r
1390   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1391   {\r
1392   }\r
1393 \r
1394 \r
1395 \r
1396   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1397   {\r
1398   }\r
1399 \r
1400   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1401   {\r
1402   }\r
1403 \r
1404 \r
1405   public void vamsasStore_actionPerformed(ActionEvent e)\r
1406   {\r
1407 \r
1408   }\r
1409 \r
1410   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1411   {\r
1412 \r
1413   }\r
1414 \r
1415   public void showTranslation_actionPerformed(ActionEvent e)\r
1416   {\r
1417 \r
1418   }\r
1419 \r
1420   public void featureSettings_actionPerformed(ActionEvent e)\r
1421   {\r
1422 \r
1423   }\r
1424 \r
1425   public void fetchSequence_actionPerformed(ActionEvent e)\r
1426   {\r
1427 \r
1428   }\r
1429 \r
1430   public void smoothFont_actionPerformed(ActionEvent e)\r
1431   {\r
1432 \r
1433   }\r
1434 \r
1435   public void annotationColour_actionPerformed(ActionEvent e)\r
1436   {\r
1437 \r
1438   }\r
1439 \r
1440   public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
1441   {\r
1442 \r
1443   }\r
1444 \r
1445   public void associatedData_actionPerformed(ActionEvent e)\r
1446   {\r
1447 \r
1448   }\r
1449 \r
1450   public void autoCalculate_actionPerformed(ActionEvent e)\r
1451   {\r
1452 \r
1453   }\r
1454 \r
1455   public void addFromFile_actionPerformed(ActionEvent e)\r
1456   {\r
1457 \r
1458   }\r
1459 \r
1460   public void addFromText_actionPerformed(ActionEvent e)\r
1461   {\r
1462 \r
1463   }\r
1464 \r
1465   public void addFromURL_actionPerformed(ActionEvent e)\r
1466   {\r
1467 \r
1468   }\r
1469 }\r