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