src/jalview/jbgui/GAlignFrame.java

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