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