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