src/jalview/jbgui/GAlignFrame.java

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