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