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