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