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