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