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