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