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 import java.awt.BorderLayout;\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 showSeqFeatures = 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   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 115   protected ButtonGroup colours = new ButtonGroup();\r
 116   JMenuItem vamsasStore = new JMenuItem();\r
 117   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\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   JMenu addSequenceMenu = new JMenu();\r
 129   JMenuItem addFromFile = new JMenuItem();\r
 130   JMenuItem addFromText = new JMenuItem();\r
 131   JMenuItem addFromURL = new JMenuItem();\r
 132   JMenuItem exportAnnotations = new JMenuItem();\r
 133   JMenuItem exportFeatures = new JMenuItem();\r
 134   JMenuItem dbRefs = new JMenuItem();\r
 135   protected JPanel statusPanel = new JPanel();\r
 136   GridLayout gridLayout1 = new GridLayout();\r
 137   public GAlignFrame()\r
 138   {\r
 139 \r
 140 \r
 141     try\r
 142     {\r
 143       jbInit();\r
 144       setJMenuBar(alignFrameMenuBar);\r
 145 \r
 146       // dynamically fill save as menu with available formats\r
 147       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 148       {\r
 149         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 150                              elementAt(\r
 151                                  i));\r
 152         item.addActionListener(new java.awt.event.ActionListener()\r
 153         {\r
 154           public void actionPerformed(ActionEvent e)\r
 155           {\r
 156             outputText_actionPerformed(e);\r
 157           }\r
 158         });\r
 159 \r
 160         outputTextboxMenu.add(item);\r
 161       }\r
 162     }\r
 163     catch (Exception e)\r
 164     {\r
 165     }\r
 166 \r
 167 \r
 168     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 169     {\r
 170       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 171           getUserColourSchemes().keys();\r
 172 \r
 173       while (userColours.hasMoreElements())\r
 174       {\r
 175         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 176             nextElement().toString());\r
 177         radioItem.setName("USER_DEFINED");\r
 178         radioItem.addMouseListener(new MouseAdapter()\r
 179             {\r
 180               public void mousePressed(MouseEvent evt)\r
 181               {\r
 182                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 183                 {\r
 184                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 185 \r
 186                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 187                       "Remove from default list?",\r
 188                       "Remove user defined colour",\r
 189                       JOptionPane.YES_NO_OPTION);\r
 190                   if(option == JOptionPane.YES_OPTION)\r
 191                   {\r
 192                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 193                     colourMenu.remove(radioItem);\r
 194                   }\r
 195                   else\r
 196                     radioItem.addActionListener(new ActionListener()\r
 197                     {\r
 198                       public void actionPerformed(ActionEvent evt)\r
 199                       {\r
 200                         userDefinedColour_actionPerformed(evt);\r
 201                       }\r
 202                     });\r
 203                 }\r
 204               }\r
 205             });\r
 206         radioItem.addActionListener(new ActionListener()\r
 207         {\r
 208           public void actionPerformed(ActionEvent evt)\r
 209           {\r
 210             userDefinedColour_actionPerformed(evt);\r
 211           }\r
 212         });\r
 213         colourMenu.insert(radioItem, 15);\r
 214         colours.add(radioItem);\r
 215       }\r
 216     }\r
 217     colours.add(noColourmenuItem);\r
 218     colours.add(clustalColour);\r
 219     colours.add(zappoColour);\r
 220     colours.add(taylorColour);\r
 221     colours.add(hydrophobicityColour);\r
 222     colours.add(helixColour);\r
 223     colours.add(strandColour);\r
 224     colours.add(turnColour);\r
 225     colours.add(buriedColour);\r
 226     colours.add(userDefinedColour);\r
 227     colours.add(PIDColour);\r
 228     colours.add(BLOSUM62Colour);\r
 229     colours.add(nucleotideColour);\r
 230 \r
 231     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 232 \r
 233 \r
 234   }\r
 235 \r
 236   public void setColourSelected(String defaultColour)\r
 237   {\r
 238 \r
 239     if (defaultColour != null)\r
 240     {\r
 241       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 242 \r
 243       switch (index)\r
 244       {\r
 245         case ColourSchemeProperty.NONE:\r
 246               noColourmenuItem.setSelected(true);\r
 247               break;\r
 248         case ColourSchemeProperty.CLUSTAL:\r
 249           clustalColour.setSelected(true);\r
 250 \r
 251           break;\r
 252 \r
 253         case ColourSchemeProperty.BLOSUM:\r
 254           BLOSUM62Colour.setSelected(true);\r
 255 \r
 256           break;\r
 257 \r
 258         case ColourSchemeProperty.PID:\r
 259           PIDColour.setSelected(true);\r
 260 \r
 261           break;\r
 262 \r
 263         case ColourSchemeProperty.ZAPPO:\r
 264           zappoColour.setSelected(true);\r
 265 \r
 266           break;\r
 267 \r
 268         case ColourSchemeProperty.TAYLOR:\r
 269           taylorColour.setSelected(true);\r
 270           break;\r
 271 \r
 272         case ColourSchemeProperty.HYDROPHOBIC:\r
 273           hydrophobicityColour.setSelected(true);\r
 274 \r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.HELIX:\r
 278           helixColour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.STRAND:\r
 283           strandColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.TURN:\r
 288           turnColour.setSelected(true);\r
 289 \r
 290           break;\r
 291 \r
 292         case ColourSchemeProperty.BURIED:\r
 293           buriedColour.setSelected(true);\r
 294 \r
 295           break;\r
 296 \r
 297         case ColourSchemeProperty.NUCLEOTIDE:\r
 298           nucleotideColour.setSelected(true);\r
 299 \r
 300           break;\r
 301 \r
 302         case ColourSchemeProperty.USER_DEFINED:\r
 303           userDefinedColour.setSelected(true);\r
 304 \r
 305           break;\r
 306       }\r
 307     }\r
 308 \r
 309   }\r
 310 \r
 311   private void jbInit()\r
 312       throws Exception\r
 313   {\r
 314     fileMenu.setMnemonic('F');\r
 315     fileMenu.setText("File");\r
 316     saveAlignmentMenu.setMnemonic('L');\r
 317     saveAlignmentMenu.setText("Save As");\r
 318     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 319         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 320     saveAlignmentMenu.addActionListener(new ActionListener()\r
 321     {\r
 322       public void actionPerformed(ActionEvent e)\r
 323       {\r
 324         saveAlignmentMenu_actionPerformed(e);\r
 325       }\r
 326     });\r
 327     closeMenuItem.setMnemonic('C');\r
 328     closeMenuItem.setText("Close");\r
 329     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 330     {\r
 331       public void actionPerformed(ActionEvent e)\r
 332       {\r
 333         closeMenuItem_actionPerformed(e);\r
 334       }\r
 335     });\r
 336     editMenu.setText("Edit");\r
 337     viewMenu.setText("View");\r
 338     colourMenu.setText("Colour");\r
 339     calculateMenu.setText("Calculate");\r
 340     webService.setText("Web Service");\r
 341     selectAllSequenceMenuItem.setText("Select all");\r
 342     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 343         java.awt.event.KeyEvent.VK_A,\r
 344         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 345     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 346                                                 ActionListener()\r
 347     {\r
 348       public void actionPerformed(ActionEvent e)\r
 349       {\r
 350         selectAllSequenceMenuItem_actionPerformed(e);\r
 351       }\r
 352     });\r
 353     deselectAllSequenceMenuItem.setText("Deselect All");\r
 354     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 355                                                getKeyStroke(\r
 356         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 357     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 358                                                   ActionListener()\r
 359     {\r
 360       public void actionPerformed(ActionEvent e)\r
 361       {\r
 362         deselectAllSequenceMenuItem_actionPerformed(e);\r
 363       }\r
 364     });\r
 365     invertSequenceMenuItem.setText("Invert Selection");\r
 366     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 367     {\r
 368       public void actionPerformed(ActionEvent e)\r
 369       {\r
 370         invertSequenceMenuItem_actionPerformed(e);\r
 371       }\r
 372     });\r
 373     remove2LeftMenuItem.setText("Remove Left");\r
 374     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 375     {\r
 376       public void actionPerformed(ActionEvent e)\r
 377       {\r
 378         remove2LeftMenuItem_actionPerformed(e);\r
 379       }\r
 380     });\r
 381     remove2RightMenuItem.setText("Remove Right");\r
 382     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 383     {\r
 384       public void actionPerformed(ActionEvent e)\r
 385       {\r
 386         remove2RightMenuItem_actionPerformed(e);\r
 387       }\r
 388     });\r
 389     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 390     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 391                                                  ActionListener()\r
 392     {\r
 393       public void actionPerformed(ActionEvent e)\r
 394       {\r
 395         removeGappedColumnMenuItem_actionPerformed(e);\r
 396       }\r
 397     });\r
 398     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 399     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 400     {\r
 401       public void actionPerformed(ActionEvent e)\r
 402       {\r
 403         removeAllGapsMenuItem_actionPerformed(e);\r
 404       }\r
 405     });\r
 406     viewBoxesMenuItem.setText("Boxes");\r
 407     viewBoxesMenuItem.setState(true);\r
 408     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 409     {\r
 410       public void actionPerformed(ActionEvent e)\r
 411       {\r
 412         viewBoxesMenuItem_actionPerformed(e);\r
 413       }\r
 414     });\r
 415     viewTextMenuItem.setText("Text");\r
 416     viewTextMenuItem.setState(true);\r
 417     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 418     {\r
 419       public void actionPerformed(ActionEvent e)\r
 420       {\r
 421         viewTextMenuItem_actionPerformed(e);\r
 422       }\r
 423     });\r
 424     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 425     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 426     {\r
 427       public void actionPerformed(ActionEvent e)\r
 428       {\r
 429         sortPairwiseMenuItem_actionPerformed(e);\r
 430       }\r
 431     });\r
 432     sortIDMenuItem.setText("by ID");\r
 433     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 434     {\r
 435       public void actionPerformed(ActionEvent e)\r
 436       {\r
 437         sortIDMenuItem_actionPerformed(e);\r
 438       }\r
 439     });\r
 440     sortGroupMenuItem.setText("by Group");\r
 441     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 442     {\r
 443       public void actionPerformed(ActionEvent e)\r
 444       {\r
 445         sortGroupMenuItem_actionPerformed(e);\r
 446       }\r
 447     });\r
 448     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 449     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 450                                                ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         removeRedundancyMenuItem_actionPerformed(e);\r
 455       }\r
 456     });\r
 457     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 458     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 459                                                 ActionListener()\r
 460     {\r
 461       public void actionPerformed(ActionEvent e)\r
 462       {\r
 463         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 464       }\r
 465     });\r
 466     PCAMenuItem.setText("Principal Component Analysis");\r
 467     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 468     {\r
 469       public void actionPerformed(ActionEvent e)\r
 470       {\r
 471         PCAMenuItem_actionPerformed(e);\r
 472       }\r
 473     });\r
 474     averageDistanceTreeMenuItem.setText(\r
 475         "Average Distance Using % Identity");\r
 476     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 477                                                   ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         averageDistanceTreeMenuItem_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 485     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         neighbourTreeMenuItem_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     this.getContentPane().setLayout(borderLayout1);\r
 493     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 494     statusBar.setBackground(Color.white);\r
 495     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 496     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 497     statusBar.setText("Status bar");\r
 498     outputTextboxMenu.setMnemonic('T');\r
 499     outputTextboxMenu.setText("Output to Textbox");\r
 500     clustalColour.setText("Clustalx");\r
 501 \r
 502     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         clustalColour_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     zappoColour.setText("Zappo");\r
 510     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         zappoColour_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     taylorColour.setText("Taylor");\r
 518     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         taylorColour_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     hydrophobicityColour.setText("Hydrophobicity");\r
 526     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 527     {\r
 528       public void actionPerformed(ActionEvent e)\r
 529       {\r
 530         hydrophobicityColour_actionPerformed(e);\r
 531       }\r
 532     });\r
 533     helixColour.setText("Helix Propensity");\r
 534     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 535     {\r
 536       public void actionPerformed(ActionEvent e)\r
 537       {\r
 538         helixColour_actionPerformed(e);\r
 539       }\r
 540     });\r
 541     strandColour.setText("Strand Propensity");\r
 542     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 543     {\r
 544       public void actionPerformed(ActionEvent e)\r
 545       {\r
 546         strandColour_actionPerformed(e);\r
 547       }\r
 548     });\r
 549     turnColour.setText("Turn Propensity");\r
 550     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 551     {\r
 552       public void actionPerformed(ActionEvent e)\r
 553       {\r
 554         turnColour_actionPerformed(e);\r
 555       }\r
 556     });\r
 557     buriedColour.setText("Buried Index");\r
 558     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 559     {\r
 560       public void actionPerformed(ActionEvent e)\r
 561       {\r
 562         buriedColour_actionPerformed(e);\r
 563       }\r
 564     });\r
 565     userDefinedColour.setText("User Defined...");\r
 566     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 567     {\r
 568       public void actionPerformed(ActionEvent e)\r
 569       {\r
 570         userDefinedColour_actionPerformed(e);\r
 571       }\r
 572     });\r
 573     PIDColour.setText("Percentage Identity");\r
 574     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         PIDColour_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 582     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 583     {\r
 584       public void actionPerformed(ActionEvent e)\r
 585       {\r
 586         BLOSUM62Colour_actionPerformed(e);\r
 587       }\r
 588     });\r
 589     avDistanceTreeBlosumMenuItem.setText(\r
 590         "Average Distance Using BLOSUM62");\r
 591     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 592         ActionListener()\r
 593     {\r
 594       public void actionPerformed(ActionEvent e)\r
 595       {\r
 596         avTreeBlosumMenuItem_actionPerformed(e);\r
 597       }\r
 598     });\r
 599     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 600     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 601     {\r
 602       public void actionPerformed(ActionEvent e)\r
 603       {\r
 604         njTreeBlosumMenuItem_actionPerformed(e);\r
 605       }\r
 606     });\r
 607     annotationPanelMenuItem.setActionCommand("");\r
 608     annotationPanelMenuItem.setText("Show Annotations");\r
 609     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 610     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 611     {\r
 612       public void actionPerformed(ActionEvent e)\r
 613       {\r
 614         annotationPanelMenuItem_actionPerformed(e);\r
 615       }\r
 616     });\r
 617     colourTextMenuItem.setText("Colour Text");\r
 618     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 619     {\r
 620       public void actionPerformed(ActionEvent e)\r
 621       {\r
 622         colourTextMenuItem_actionPerformed(e);\r
 623       }\r
 624     });\r
 625     htmlMenuItem.setText("HTML");\r
 626     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         htmlMenuItem_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     overviewMenuItem.setText("Overview Window");\r
 634     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         overviewMenuItem_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     undoMenuItem.setEnabled(false);\r
 642     undoMenuItem.setMnemonic('Z');\r
 643     undoMenuItem.setText("Undo");\r
 644     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 645         java.awt.event.KeyEvent.VK_Z,\r
 646         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 647     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 648     {\r
 649       public void actionPerformed(ActionEvent e)\r
 650       {\r
 651         undoMenuItem_actionPerformed(e);\r
 652       }\r
 653     });\r
 654     redoMenuItem.setEnabled(false);\r
 655     redoMenuItem.setMnemonic('0');\r
 656     redoMenuItem.setText("Redo");\r
 657     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 658     {\r
 659       public void actionPerformed(ActionEvent e)\r
 660       {\r
 661         redoMenuItem_actionPerformed(e);\r
 662       }\r
 663     });\r
 664     conservationMenuItem.setText("By Conservation");\r
 665     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 666     {\r
 667       public void actionPerformed(ActionEvent e)\r
 668       {\r
 669         conservationMenuItem_actionPerformed(e);\r
 670       }\r
 671     });\r
 672     noColourmenuItem.setText("None");\r
 673     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 674     {\r
 675       public void actionPerformed(ActionEvent e)\r
 676       {\r
 677         noColourmenuItem_actionPerformed(e);\r
 678       }\r
 679     });\r
 680     wrapMenuItem.setText("Wrap");\r
 681     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 682     {\r
 683       public void actionPerformed(ActionEvent e)\r
 684       {\r
 685         wrapMenuItem_actionPerformed(e);\r
 686       }\r
 687     });\r
 688     printMenuItem.setText("Print");\r
 689     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 690     {\r
 691       public void actionPerformed(ActionEvent e)\r
 692       {\r
 693         printMenuItem_actionPerformed(e);\r
 694       }\r
 695     });\r
 696     renderGapsMenuItem.setText("Show Gaps");\r
 697     renderGapsMenuItem.setState(true);\r
 698     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 699     {\r
 700       public void actionPerformed(ActionEvent e)\r
 701       {\r
 702         renderGapsMenuItem_actionPerformed(e);\r
 703       }\r
 704     });\r
 705     findMenuItem.setText("Find...");\r
 706     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 707         java.awt.event.KeyEvent.VK_F,\r
 708         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 709     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 710     {\r
 711       public void actionPerformed(ActionEvent e)\r
 712       {\r
 713         findMenuItem_actionPerformed(e);\r
 714       }\r
 715     });\r
 716     searchMenu.setText("Search");\r
 717 \r
 718     abovePIDThreshold.setText("Above Identity Threshold");\r
 719     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 720     {\r
 721       public void actionPerformed(ActionEvent e)\r
 722       {\r
 723         abovePIDThreshold_actionPerformed(e);\r
 724       }\r
 725     });\r
 726     showSeqFeatures.setText("Show Sequence Features");\r
 727     showSeqFeatures.addActionListener(new ActionListener()\r
 728     {\r
 729       public void actionPerformed(ActionEvent actionEvent)\r
 730       {\r
 731         showSeqFeatures_actionPerformed(actionEvent);\r
 732       }\r
 733     });\r
 734     nucleotideColour.setText("Nucleotide");\r
 735     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 736     {\r
 737       public void actionPerformed(ActionEvent e)\r
 738       {\r
 739         nucleotideColour_actionPerformed(e);\r
 740       }\r
 741     });\r
 742     deleteGroups.setText("Undefine groups");\r
 743     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 744     {\r
 745       public void actionPerformed(ActionEvent e)\r
 746       {\r
 747         deleteGroups_actionPerformed(e);\r
 748       }\r
 749     });\r
 750     copy.setText("Copy");\r
 751     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 752         java.awt.event.KeyEvent.VK_C,\r
 753         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 754     copy.setMnemonic(KeyEvent.VK_C);\r
 755 \r
 756     copy.addActionListener(new java.awt.event.ActionListener()\r
 757     {\r
 758       public void actionPerformed(ActionEvent e)\r
 759       {\r
 760         copy_actionPerformed(e);\r
 761       }\r
 762     });\r
 763     cut.setText("Cut");\r
 764     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 765         java.awt.event.KeyEvent.VK_X,\r
 766         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 767     cut.setMnemonic(KeyEvent.VK_X);\r
 768     cut.addActionListener(new java.awt.event.ActionListener()\r
 769     {\r
 770       public void actionPerformed(ActionEvent e)\r
 771       {\r
 772         cut_actionPerformed(e);\r
 773       }\r
 774     });\r
 775     delete.setText("Delete");\r
 776     delete.addActionListener(new java.awt.event.ActionListener()\r
 777     {\r
 778       public void actionPerformed(ActionEvent e)\r
 779       {\r
 780         delete_actionPerformed(e);\r
 781       }\r
 782     });\r
 783     jMenu1.setMnemonic('V');\r
 784     jMenu1.setText("Paste");\r
 785     pasteNew.setText("To New Alignment");\r
 786     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 787         java.awt.event.KeyEvent.VK_V,\r
 788         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 789     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 790     {\r
 791       public void actionPerformed(ActionEvent e)\r
 792       {\r
 793         pasteNew_actionPerformed(e);\r
 794       }\r
 795     });\r
 796     pasteThis.setText("Add To This Alignment");\r
 797     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 798     {\r
 799       public void actionPerformed(ActionEvent e)\r
 800       {\r
 801         pasteThis_actionPerformed(e);\r
 802       }\r
 803     });\r
 804     applyToAllGroups.setText("Apply Colour To All Groups");\r
 805     applyToAllGroups.setState(true);\r
 806     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 807     {\r
 808       public void actionPerformed(ActionEvent e)\r
 809       {\r
 810         applyToAllGroups_actionPerformed(e);\r
 811       }\r
 812     });\r
 813     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 814     {\r
 815       public void actionPerformed(ActionEvent e)\r
 816       {\r
 817         createPNG(null);\r
 818       }\r
 819     });\r
 820     createPNG.setActionCommand("Save As PNG Image");\r
 821     createPNG.setText("PNG");\r
 822     font.setText("Font...");\r
 823     font.addActionListener(new java.awt.event.ActionListener()\r
 824     {\r
 825       public void actionPerformed(ActionEvent e)\r
 826       {\r
 827         font_actionPerformed(e);\r
 828       }\r
 829     });\r
 830 \r
 831     seqLimits.setText("Show Sequence Limits");\r
 832     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 833     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 834     {\r
 835       public void actionPerformed(ActionEvent e)\r
 836       {\r
 837         seqLimit_actionPerformed(e);\r
 838       }\r
 839     });\r
 840     epsFile.setText("EPS");\r
 841     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 842     {\r
 843       public void actionPerformed(ActionEvent e)\r
 844       {\r
 845         createEPS(null);\r
 846       }\r
 847     });\r
 848     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 849     LoadtreeMenuItem.setText("Load Associated Tree");\r
 850     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 851     {\r
 852       public void actionPerformed(ActionEvent e)\r
 853       {\r
 854         LoadtreeMenuItem_actionPerformed(e);\r
 855       }\r
 856     });\r
 857     scaleAbove.setVisible(false);\r
 858     scaleAbove.setText("Scale Above");\r
 859     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 860     {\r
 861       public void actionPerformed(ActionEvent e)\r
 862       {\r
 863         scaleAbove_actionPerformed(e);\r
 864       }\r
 865     });\r
 866     scaleLeft.setVisible(false);\r
 867     scaleLeft.setSelected(true);\r
 868     scaleLeft.setText("Scale Left");\r
 869     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 870     {\r
 871       public void actionPerformed(ActionEvent e)\r
 872       {\r
 873         scaleLeft_actionPerformed(e);\r
 874       }\r
 875     });\r
 876     scaleRight.setVisible(false);\r
 877     scaleRight.setSelected(true);\r
 878     scaleRight.setText("Scale Right");\r
 879     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 880     {\r
 881       public void actionPerformed(ActionEvent e)\r
 882       {\r
 883         scaleRight_actionPerformed(e);\r
 884       }\r
 885     });\r
 886     modifyPID.setText("Modify Identity Threshold...");\r
 887     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 888     {\r
 889       public void actionPerformed(ActionEvent e)\r
 890       {\r
 891         modifyPID_actionPerformed(e);\r
 892       }\r
 893     });\r
 894     modifyConservation.setText("Modify Conservation Threshold...");\r
 895     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 896     {\r
 897       public void actionPerformed(ActionEvent e)\r
 898       {\r
 899         modifyConservation_actionPerformed(e);\r
 900       }\r
 901     });\r
 902     sortByTreeMenu.setText("By Tree Order");\r
 903     sort.setText("Sort");\r
 904     calculate.setText("Calculate Tree");\r
 905 \r
 906     jMenu2.setText("Export");\r
 907     padGapsMenuitem.setText("Pad Gaps");\r
 908     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\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.setVisible(false);\r
 917     vamsasStore.setText("VAMSAS store");\r
 918     vamsasStore.addActionListener(new ActionListener()\r
 919     {\r
 920       public void actionPerformed(ActionEvent e)\r
 921       {\r
 922         vamsasStore_actionPerformed(e);\r
 923       }\r
 924     });\r
 925     showTranslation.setText("Translate cDNA");\r
 926     showTranslation.addActionListener(new ActionListener()\r
 927     {\r
 928       public void actionPerformed(ActionEvent e)\r
 929       {\r
 930         showTranslation_actionPerformed(e);\r
 931       }\r
 932     });\r
 933 \r
 934    /* tabbedPane.addChangeListener(new ChangeListener()\r
 935         {\r
 936           public void stateChanged(ChangeEvent ece)\r
 937           {\r
 938 \r
 939             tabSelected();\r
 940           }\r
 941         });*/\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     fetchSequence.setText("Fetch Sequence(s)...");\r
 951     fetchSequence.addActionListener(new ActionListener()\r
 952     {\r
 953       public void actionPerformed(ActionEvent e)\r
 954       {\r
 955         fetchSequence_actionPerformed(e);\r
 956       }\r
 957     });\r
 958     smoothFont.setText("Smooth Fonts");\r
 959     smoothFont.addActionListener(new ActionListener()\r
 960     {\r
 961       public void actionPerformed(ActionEvent e)\r
 962       {\r
 963         smoothFont_actionPerformed(e);\r
 964       }\r
 965     });\r
 966     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 967     annotationColour.setText("By Annotation...");\r
 968     annotationColour.addActionListener(new ActionListener()\r
 969     {\r
 970       public void actionPerformed(ActionEvent e)\r
 971       {\r
 972         annotationColour_actionPerformed(e);\r
 973       }\r
 974     });\r
 975     fetchSeqFeatures.setText("Fetch Sequence Features");\r
 976     fetchSeqFeatures.addActionListener(new ActionListener()\r
 977     {\r
 978       public void actionPerformed(ActionEvent e)\r
 979       {\r
 980         fetchSeqFeatures_actionPerformed(e);\r
 981       }\r
 982     });\r
 983     associatedData.setText("Load Features / Annotations");\r
 984     associatedData.addActionListener(new ActionListener()\r
 985     {\r
 986       public void actionPerformed(ActionEvent e)\r
 987       {\r
 988         associatedData_actionPerformed(e);\r
 989       }\r
 990     });\r
 991     autoCalculate.setText("Autocalculate Consensus");\r
 992     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 993     autoCalculate.addActionListener(new ActionListener()\r
 994     {\r
 995       public void actionPerformed(ActionEvent e)\r
 996       {\r
 997         autoCalculate_actionPerformed(e);\r
 998       }\r
 999     });\r
1000     addSequenceMenu.setText("Add Sequences");\r
1001     addFromFile.setText("From File");\r
1002     addFromFile.addActionListener(new ActionListener()\r
1003     {\r
1004       public void actionPerformed(ActionEvent e)\r
1005       {\r
1006         addFromFile_actionPerformed(e);\r
1007       }\r
1008     });\r
1009     addFromText.setText("From Textbox");\r
1010     addFromText.addActionListener(new ActionListener()\r
1011     {\r
1012       public void actionPerformed(ActionEvent e)\r
1013       {\r
1014         addFromText_actionPerformed(e);\r
1015       }\r
1016     });\r
1017     addFromURL.setText("From URL");\r
1018     addFromURL.addActionListener(new ActionListener()\r
1019     {\r
1020       public void actionPerformed(ActionEvent e)\r
1021       {\r
1022         addFromURL_actionPerformed(e);\r
1023       }\r
1024     });\r
1025     exportFeatures.setText("Export Features...");\r
1026     exportFeatures.addActionListener(new ActionListener()\r
1027     {\r
1028       public void actionPerformed(ActionEvent e)\r
1029       {\r
1030         exportFeatures_actionPerformed(e);\r
1031       }\r
1032     });\r
1033     exportAnnotations.setText("Export Annotations...");\r
1034     exportAnnotations.addActionListener(new ActionListener()\r
1035     {\r
1036       public void actionPerformed(ActionEvent e)\r
1037       {\r
1038         exportAnnotations_actionPerformed(e);\r
1039       }\r
1040     });\r
1041     dbRefs.setText("Fetch DB Refs");\r
1042     dbRefs.addActionListener(new ActionListener()\r
1043     {\r
1044       public void actionPerformed(ActionEvent e)\r
1045       {\r
1046         dbRefs_actionPerformed(e);\r
1047       }\r
1048     });\r
1049     statusPanel.setLayout(gridLayout1);\r
1050     alignFrameMenuBar.add(fileMenu);\r
1051     alignFrameMenuBar.add(editMenu);\r
1052     alignFrameMenuBar.add(searchMenu);\r
1053     alignFrameMenuBar.add(viewMenu);\r
1054     alignFrameMenuBar.add(colourMenu);\r
1055     alignFrameMenuBar.add(calculateMenu);\r
1056     alignFrameMenuBar.add(webService);\r
1057     fileMenu.add(addSequenceMenu);\r
1058     fileMenu.add(fetchSequence);\r
1059     fileMenu.addSeparator();\r
1060     fileMenu.add(vamsasStore);\r
1061     fileMenu.add(saveAlignmentMenu);\r
1062     fileMenu.add(jMenu2);\r
1063     fileMenu.add(outputTextboxMenu);\r
1064     fileMenu.add(printMenuItem);\r
1065     fileMenu.addSeparator();\r
1066     fileMenu.add(exportFeatures);\r
1067     fileMenu.add(exportAnnotations);\r
1068     fileMenu.add(LoadtreeMenuItem);\r
1069     fileMenu.add(associatedData);\r
1070     fileMenu.addSeparator();\r
1071     fileMenu.add(closeMenuItem);\r
1072     editMenu.add(undoMenuItem);\r
1073     editMenu.add(redoMenuItem);\r
1074     editMenu.add(cut);\r
1075     editMenu.add(copy);\r
1076     editMenu.add(jMenu1);\r
1077     editMenu.add(delete);\r
1078     editMenu.addSeparator();\r
1079     editMenu.add(selectAllSequenceMenuItem);\r
1080     editMenu.add(deselectAllSequenceMenuItem);\r
1081     editMenu.add(invertSequenceMenuItem);\r
1082     editMenu.add(deleteGroups);\r
1083     editMenu.addSeparator();\r
1084     editMenu.add(remove2LeftMenuItem);\r
1085     editMenu.add(remove2RightMenuItem);\r
1086     editMenu.add(removeGappedColumnMenuItem);\r
1087     editMenu.add(removeAllGapsMenuItem);\r
1088     editMenu.add(removeRedundancyMenuItem);\r
1089     editMenu.addSeparator();\r
1090     editMenu.add(padGapsMenuitem);\r
1091     searchMenu.add(findMenuItem);\r
1092     viewMenu.add(font);\r
1093     viewMenu.add(smoothFont);\r
1094     viewMenu.addSeparator();\r
1095     viewMenu.add(wrapMenuItem);\r
1096     viewMenu.add(seqLimits);\r
1097     viewMenu.add(scaleAbove);\r
1098     viewMenu.add(scaleLeft);\r
1099     viewMenu.add(scaleRight);\r
1100     viewMenu.add(viewBoxesMenuItem);\r
1101     viewMenu.add(viewTextMenuItem);\r
1102     viewMenu.add(colourTextMenuItem);\r
1103     viewMenu.add(renderGapsMenuItem);\r
1104     viewMenu.add(annotationPanelMenuItem);\r
1105     viewMenu.addSeparator();\r
1106     viewMenu.add(dbRefs);\r
1107     viewMenu.add(fetchSeqFeatures);\r
1108     viewMenu.add(showSeqFeatures);\r
1109     viewMenu.add(featureSettings);\r
1110     viewMenu.addSeparator();\r
1111     viewMenu.add(overviewMenuItem);\r
1112     colourMenu.add(applyToAllGroups);\r
1113     colourMenu.addSeparator();\r
1114     colourMenu.add(noColourmenuItem);\r
1115     colourMenu.add(clustalColour);\r
1116     colourMenu.add(BLOSUM62Colour);\r
1117     colourMenu.add(PIDColour);\r
1118     colourMenu.add(zappoColour);\r
1119     colourMenu.add(taylorColour);\r
1120     colourMenu.add(hydrophobicityColour);\r
1121     colourMenu.add(helixColour);\r
1122     colourMenu.add(strandColour);\r
1123     colourMenu.add(turnColour);\r
1124     colourMenu.add(buriedColour);\r
1125     colourMenu.add(nucleotideColour);\r
1126     colourMenu.add(userDefinedColour);\r
1127     colourMenu.addSeparator();\r
1128     colourMenu.add(conservationMenuItem);\r
1129     colourMenu.add(modifyConservation);\r
1130     colourMenu.add(abovePIDThreshold);\r
1131     colourMenu.add(modifyPID);\r
1132     colourMenu.add(annotationColour);\r
1133     calculateMenu.add(sort);\r
1134     calculateMenu.add(calculate);\r
1135     calculateMenu.addSeparator();\r
1136     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1137     calculateMenu.add(PCAMenuItem);\r
1138     calculateMenu.addSeparator();\r
1139     calculateMenu.add(showTranslation);\r
1140     calculateMenu.add(autoCalculate);\r
1141     webServiceNoServices=new JMenuItem("<No Services>");\r
1142     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1143     jMenu1.add(pasteThis);\r
1144     sort.add(sortIDMenuItem);\r
1145     sort.add(sortGroupMenuItem);\r
1146     sort.add(sortPairwiseMenuItem);\r
1147     calculate.add(averageDistanceTreeMenuItem);\r
1148     calculate.add(neighbourTreeMenuItem);\r
1149     calculate.add(avDistanceTreeBlosumMenuItem);\r
1150     calculate.add(njTreeBlosumMenuItem);\r
1151     jMenu2.add(htmlMenuItem);\r
1152     jMenu2.add(epsFile);\r
1153     jMenu2.add(createPNG);\r
1154     addSequenceMenu.add(addFromFile);\r
1155     addSequenceMenu.add(addFromText);\r
1156     addSequenceMenu.add(addFromURL);\r
1157     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1158     statusPanel.add(statusBar, null);\r
1159   }\r
1160 \r
1161   protected void outputText_actionPerformed(ActionEvent e)\r
1162   {\r
1163   }\r
1164 \r
1165   public void addFromFile_actionPerformed(ActionEvent e)\r
1166   {\r
1167 \r
1168   }\r
1169 \r
1170   public void addFromText_actionPerformed(ActionEvent e)\r
1171   {\r
1172 \r
1173   }\r
1174 \r
1175   public void addFromURL_actionPerformed(ActionEvent e)\r
1176   {\r
1177 \r
1178   }\r
1179 \r
1180   public void exportFeatures_actionPerformed(ActionEvent e)\r
1181   {\r
1182 \r
1183   }\r
1184 \r
1185   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1186   {\r
1187 \r
1188   }\r
1189 \r
1190   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1191   {\r
1192   }\r
1193 \r
1194   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1195   {\r
1196   }\r
1197 \r
1198   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1199   {\r
1200   }\r
1201 \r
1202   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1203   {\r
1204   }\r
1205 \r
1206   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1207   {\r
1208   }\r
1209 \r
1210   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1211   {\r
1212   }\r
1213 \r
1214   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1215   {\r
1216   }\r
1217 \r
1218   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1219   {\r
1220   }\r
1221 \r
1222   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1223   {\r
1224   }\r
1225 \r
1226   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1227   {\r
1228   }\r
1229 \r
1230   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1231   {\r
1232   }\r
1233 \r
1234   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1235   {\r
1236   }\r
1237 \r
1238   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1239   {\r
1240   }\r
1241 \r
1242   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1243   {\r
1244   }\r
1245 \r
1246   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1247   {\r
1248   }\r
1249 \r
1250   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1251   {\r
1252   }\r
1253 \r
1254   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1255   {\r
1256   }\r
1257 \r
1258   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1259   {\r
1260   }\r
1261 \r
1262   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1263   {\r
1264   }\r
1265 \r
1266   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1267   {\r
1268   }\r
1269 \r
1270   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1271   {\r
1272   }\r
1273 \r
1274   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1275   {\r
1276   }\r
1277 \r
1278   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1279   {\r
1280   }\r
1281 \r
1282   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1283   {\r
1284   }\r
1285 \r
1286   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1287   {\r
1288   }\r
1289 \r
1290   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1291   {\r
1292   }\r
1293 \r
1294   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1295   {\r
1296   }\r
1297 \r
1298   protected void clustalColour_actionPerformed(ActionEvent e)\r
1299   {\r
1300   }\r
1301 \r
1302   protected void zappoColour_actionPerformed(ActionEvent e)\r
1303   {\r
1304   }\r
1305 \r
1306   protected void taylorColour_actionPerformed(ActionEvent e)\r
1307   {\r
1308   }\r
1309 \r
1310   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1311   {\r
1312   }\r
1313 \r
1314   protected void helixColour_actionPerformed(ActionEvent e)\r
1315   {\r
1316   }\r
1317 \r
1318   protected void strandColour_actionPerformed(ActionEvent e)\r
1319   {\r
1320   }\r
1321 \r
1322   protected void turnColour_actionPerformed(ActionEvent e)\r
1323   {\r
1324   }\r
1325 \r
1326   protected void buriedColour_actionPerformed(ActionEvent e)\r
1327   {\r
1328   }\r
1329 \r
1330   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1331   {\r
1332   }\r
1333 \r
1334   protected void PIDColour_actionPerformed(ActionEvent e)\r
1335   {\r
1336   }\r
1337 \r
1338   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1339   {\r
1340   }\r
1341 \r
1342   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1343   {\r
1344   }\r
1345 \r
1346   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1347   {\r
1348   }\r
1349 \r
1350   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1351   {\r
1352   }\r
1353 \r
1354   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1355   {\r
1356   }\r
1357 \r
1358   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1359   {\r
1360   }\r
1361 \r
1362   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1363   {\r
1364   }\r
1365 \r
1366   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1367   {\r
1368   }\r
1369 \r
1370   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1371   {\r
1372   }\r
1373 \r
1374   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1375   {\r
1376   }\r
1377 \r
1378   protected void copy_actionPerformed(ActionEvent e)\r
1379   {\r
1380   }\r
1381 \r
1382   protected void cut_actionPerformed(ActionEvent e)\r
1383   {\r
1384   }\r
1385 \r
1386   protected void delete_actionPerformed(ActionEvent e)\r
1387   {\r
1388   }\r
1389 \r
1390   protected void pasteNew_actionPerformed(ActionEvent e)\r
1391   {\r
1392   }\r
1393 \r
1394   protected void pasteThis_actionPerformed(ActionEvent e)\r
1395   {\r
1396   }\r
1397 \r
1398   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1399   {\r
1400   }\r
1401 \r
1402   public void createPNG(java.io.File f)\r
1403   {\r
1404   }\r
1405 \r
1406   protected void font_actionPerformed(ActionEvent e)\r
1407   {\r
1408   }\r
1409 \r
1410   protected void seqLimit_actionPerformed(ActionEvent e)\r
1411   {\r
1412   }\r
1413 \r
1414   public void seqDBRef_actionPerformed(ActionEvent e)\r
1415   {\r
1416 \r
1417   }\r
1418 \r
1419 \r
1420   public void createEPS(java.io.File f)\r
1421   {\r
1422   }\r
1423 \r
1424   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1425   {\r
1426   }\r
1427 \r
1428   protected void jpred_actionPerformed(ActionEvent e)\r
1429   {\r
1430   }\r
1431 \r
1432   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1433   {\r
1434   }\r
1435 \r
1436   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1437   {\r
1438   }\r
1439 \r
1440   protected void scaleRight_actionPerformed(ActionEvent e)\r
1441   {\r
1442   }\r
1443 \r
1444   protected void modifyPID_actionPerformed(ActionEvent e)\r
1445   {\r
1446   }\r
1447 \r
1448   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1449   {\r
1450   }\r
1451 \r
1452 \r
1453 \r
1454   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1455   {\r
1456   }\r
1457 \r
1458   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1459   {\r
1460   }\r
1461 \r
1462 \r
1463   public void vamsasStore_actionPerformed(ActionEvent e)\r
1464   {\r
1465 \r
1466   }\r
1467 \r
1468   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1469   {\r
1470 \r
1471   }\r
1472 \r
1473   public void showTranslation_actionPerformed(ActionEvent e)\r
1474   {\r
1475 \r
1476   }\r
1477 \r
1478   public void featureSettings_actionPerformed(ActionEvent e)\r
1479   {\r
1480 \r
1481   }\r
1482 \r
1483   public void fetchSequence_actionPerformed(ActionEvent e)\r
1484   {\r
1485 \r
1486   }\r
1487 \r
1488   public void smoothFont_actionPerformed(ActionEvent e)\r
1489   {\r
1490 \r
1491   }\r
1492 \r
1493   public void annotationColour_actionPerformed(ActionEvent e)\r
1494   {\r
1495 \r
1496   }\r
1497 \r
1498   public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
1499   {\r
1500 \r
1501   }\r
1502 \r
1503   public void associatedData_actionPerformed(ActionEvent e)\r
1504   {\r
1505 \r
1506   }\r
1507 \r
1508   public void autoCalculate_actionPerformed(ActionEvent e)\r
1509   {\r
1510 \r
1511   }\r
1512 \r
1513   public void dbRefs_actionPerformed(ActionEvent e)\r
1514   {\r
1515 \r
1516   }\r
1517 }\r