src/jalview/jbgui/GAlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 package jalview.jbgui;\r
  10 \r
  11 import javax.swing.*;\r
  12 import java.awt.event.*;\r
  13 import java.awt.*;\r
  14 \r
  15 import jalview.gui.Preferences;\r
  16 import jalview.schemes.ColourSchemeProperty;\r
  17 import javax.swing.event.AncestorListener;\r
  18 import javax.swing.event.AncestorEvent;\r
  19 \r
  20 public class GAlignFrame extends JInternalFrame\r
  21 {\r
  22   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  23   protected JMenu fileMenu = new JMenu();\r
  24   protected JMenuItem closeMenuItem = new JMenuItem();\r
  25   protected JMenu editMenu = new JMenu();\r
  26   protected JMenu viewMenu = new JMenu();\r
  27   protected JMenu colourMenu = new JMenu();\r
  28   protected JMenu calculateMenu = new JMenu();\r
  29   protected JMenu webService = new JMenu();\r
  30   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  31   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  32   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  33   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  34   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  35   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  36   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  37   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  38   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  39   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  40   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  41   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  42   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  43   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  44   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  45   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  46   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  47   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  48   BorderLayout borderLayout1 = new BorderLayout();\r
  49   public JLabel statusBar = new JLabel();\r
  50   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  51   protected JMenu outputTextboxMenu = new JMenu();\r
  52   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  53   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  54   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  55   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  58   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  59   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  63   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  64   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  65   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  66   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  67   JMenuItem htmlMenuItem = new JMenuItem();\r
  68   JMenuItem overviewMenuItem = new JMenuItem();\r
  69   protected JMenuItem undoMenuItem = new JMenuItem();\r
  70   protected JMenuItem redoMenuItem = new JMenuItem();\r
  71   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  72   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  73   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  74   JMenuItem printMenuItem = new JMenuItem();\r
  75   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  76   JMenuItem findMenuItem = new JMenuItem();\r
  77   JMenu searchMenu = new JMenu();\r
  78   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  79   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  80   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  81   JMenuItem deleteGroups = new JMenuItem();\r
  82   JMenuItem delete = new JMenuItem();\r
  83   JMenuItem copy = new JMenuItem();\r
  84   JMenuItem cut = new JMenuItem();\r
  85   JMenu jMenu1 = new JMenu();\r
  86   JMenuItem pasteNew = new JMenuItem();\r
  87   JMenuItem pasteThis = new JMenuItem();\r
  88   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  89   JMenuItem createPNG = new JMenuItem();\r
  90   protected JMenuItem font = new JMenuItem();\r
  91   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
  92   JMenuItem epsFile = new JMenuItem();\r
  93   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
  94   JMenuItem jpred = new JMenuItem();\r
  95   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
  96   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
  97   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
  98   JMenuItem modifyPID = new JMenuItem();\r
  99   JMenuItem modifyConservation = new JMenuItem();\r
 100   protected JMenu sortByTreeMenu = new JMenu();\r
 101   protected JMenu sort = new JMenu();\r
 102   JMenu calculate = new JMenu();\r
 103   JMenuItem msaAlignMenuItem = new JMenuItem();\r
 104   JMenu jMenu2 = new JMenu();\r
 105   JMenuItem padGapsMenuitem = new JMenuItem();\r
 106   JMenuItem ClustalRealign = new JMenuItem();\r
 107   public GAlignFrame()\r
 108   {\r
 109     ButtonGroup colours = new ButtonGroup();\r
 110     colours.add(noColourmenuItem);\r
 111     colours.add(clustalColour);\r
 112     colours.add(zappoColour);\r
 113     colours.add(taylorColour);\r
 114     colours.add(hydrophobicityColour);\r
 115     colours.add(helixColour);\r
 116     colours.add(strandColour);\r
 117     colours.add(turnColour);\r
 118     colours.add(buriedColour);\r
 119     colours.add(userDefinedColour);\r
 120     colours.add(PIDColour);\r
 121     colours.add(BLOSUM62Colour);\r
 122     colours.add(nucleotideColour);\r
 123 \r
 124    noColourmenuItem.setSelected(true);\r
 125    String defaultColour = Preferences.defaultColour;\r
 126    if(defaultColour!=null)\r
 127    {\r
 128    int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 129    switch(index)\r
 130    {\r
 131      case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;\r
 132      case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;\r
 133      case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;\r
 134      case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;\r
 135      case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;\r
 136      case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;\r
 137      case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;\r
 138      case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;\r
 139      case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;\r
 140      case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;\r
 141      case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;\r
 142    }\r
 143    }\r
 144 \r
 145 \r
 146     try\r
 147     {\r
 148       jbInit();\r
 149       setJMenuBar(alignFrameMenuBar);\r
 150 \r
 151       JMenuItem item;\r
 152       // dynamically fill save as menu with available formats\r
 153       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
 154         item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
 155         item.addActionListener(new java.awt.event.ActionListener()\r
 156         {\r
 157           public void actionPerformed(ActionEvent e)\r
 158           {\r
 159             outputText_actionPerformed(e);\r
 160           }\r
 161         });\r
 162 \r
 163         outputTextboxMenu.add( item );\r
 164       }\r
 165 \r
 166     }\r
 167     catch(Exception e)\r
 168     {\r
 169       e.printStackTrace();\r
 170     }\r
 171 \r
 172   }\r
 173   private void jbInit() throws Exception\r
 174   {\r
 175     fileMenu.setMnemonic('F');\r
 176     fileMenu.setText("File");\r
 177     saveAlignmentMenu.setMnemonic('L');\r
 178     saveAlignmentMenu.setText("Save As");\r
 179     saveAlignmentMenu.addActionListener(new ActionListener()\r
 180     {\r
 181       public void actionPerformed(ActionEvent e)\r
 182       {\r
 183         saveAlignmentMenu_actionPerformed(e);\r
 184       }\r
 185     });\r
 186     closeMenuItem.setMnemonic('C');\r
 187     closeMenuItem.setText("Close");\r
 188     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 189     {\r
 190       public void actionPerformed(ActionEvent e)\r
 191       {\r
 192         closeMenuItem_actionPerformed(e);\r
 193       }\r
 194     });\r
 195     editMenu.setText("Edit");\r
 196     viewMenu.setText("View");\r
 197     colourMenu.setText("Colour");\r
 198     calculateMenu.setText("Calculate");\r
 199     webService.setText("Web Service");\r
 200     selectAllSequenceMenuItem.setText("Select all");\r
 201     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 202         java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 203     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 204     {\r
 205       public void actionPerformed(ActionEvent e)\r
 206       {\r
 207         selectAllSequenceMenuItem_actionPerformed(e);\r
 208       }\r
 209     });\r
 210     deselectAllSequenceMenuItem.setText("Deselect All");\r
 211     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 212                                                getKeyStroke(java.awt.event.\r
 213         KeyEvent.VK_ESCAPE, 0, false));\r
 214     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 215     {\r
 216       public void actionPerformed(ActionEvent e)\r
 217       {\r
 218         deselectAllSequenceMenuItem_actionPerformed(e);\r
 219       }\r
 220     });\r
 221     invertSequenceMenuItem.setText("Invert Selection");\r
 222     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 223     {\r
 224       public void actionPerformed(ActionEvent e)\r
 225       {\r
 226         invertSequenceMenuItem_actionPerformed(e);\r
 227       }\r
 228     });\r
 229     remove2LeftMenuItem.setText("Remove Left");\r
 230     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 231     {\r
 232       public void actionPerformed(ActionEvent e)\r
 233       {\r
 234         remove2LeftMenuItem_actionPerformed(e);\r
 235       }\r
 236     });\r
 237     remove2RightMenuItem.setText("Remove Right");\r
 238     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 239     {\r
 240       public void actionPerformed(ActionEvent e)\r
 241       {\r
 242         remove2RightMenuItem_actionPerformed(e);\r
 243       }\r
 244     });\r
 245     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 246     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 247     {\r
 248       public void actionPerformed(ActionEvent e)\r
 249       {\r
 250         removeGappedColumnMenuItem_actionPerformed(e);\r
 251       }\r
 252     });\r
 253     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 254     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 255     {\r
 256       public void actionPerformed(ActionEvent e)\r
 257       {\r
 258         removeAllGapsMenuItem_actionPerformed(e);\r
 259       }\r
 260     });\r
 261     viewBoxesMenuItem.setText("Boxes");\r
 262     viewBoxesMenuItem.setState(true);\r
 263     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 264     {\r
 265       public void actionPerformed(ActionEvent e)\r
 266       {\r
 267         viewBoxesMenuItem_actionPerformed(e);\r
 268       }\r
 269     });\r
 270     viewTextMenuItem.setText("Text");\r
 271     viewTextMenuItem.setState(true);\r
 272     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 273     {\r
 274       public void actionPerformed(ActionEvent e)\r
 275       {\r
 276         viewTextMenuItem_actionPerformed(e);\r
 277       }\r
 278     });\r
 279     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 280     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 281     {\r
 282       public void actionPerformed(ActionEvent e)\r
 283       {\r
 284         sortPairwiseMenuItem_actionPerformed(e);\r
 285       }\r
 286     });\r
 287     sortIDMenuItem.setText("by ID");\r
 288     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 289     {\r
 290       public void actionPerformed(ActionEvent e)\r
 291       {\r
 292         sortIDMenuItem_actionPerformed(e);\r
 293       }\r
 294     });\r
 295     sortGroupMenuItem.setText("by Group");\r
 296     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 297     {\r
 298       public void actionPerformed(ActionEvent e)\r
 299       {\r
 300         sortGroupMenuItem_actionPerformed(e);\r
 301       }\r
 302     });\r
 303     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 304     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 305     {\r
 306       public void actionPerformed(ActionEvent e)\r
 307       {\r
 308         removeRedundancyMenuItem_actionPerformed(e);\r
 309       }\r
 310     });\r
 311     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 312     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 313     {\r
 314       public void actionPerformed(ActionEvent e)\r
 315       {\r
 316         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 317       }\r
 318     });\r
 319     PCAMenuItem.setText("Principal Component Analysis...");\r
 320     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 321     {\r
 322       public void actionPerformed(ActionEvent e)\r
 323       {\r
 324         PCAMenuItem_actionPerformed(e);\r
 325       }\r
 326     });\r
 327     averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");\r
 328     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 329     {\r
 330       public void actionPerformed(ActionEvent e)\r
 331       {\r
 332         averageDistanceTreeMenuItem_actionPerformed(e);\r
 333       }\r
 334     });\r
 335     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
 336     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 337     {\r
 338       public void actionPerformed(ActionEvent e)\r
 339       {\r
 340         neighbourTreeMenuItem_actionPerformed(e);\r
 341       }\r
 342     });\r
 343     clustalAlignMenuItem.setText("Clustal Alignment...");\r
 344     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 345     {\r
 346       public void actionPerformed(ActionEvent e)\r
 347       {\r
 348         clustalAlignMenuItem_actionPerformed(e);\r
 349       }\r
 350     });\r
 351     this.getContentPane().setLayout(borderLayout1);\r
 352     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 353     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
 354     {\r
 355       public void ancestorAdded(AncestorEvent event)\r
 356       {\r
 357         alignFrameMenuBar_ancestorAdded(event);\r
 358       }\r
 359 \r
 360       public void ancestorRemoved(AncestorEvent event)\r
 361       {\r
 362       }\r
 363 \r
 364       public void ancestorMoved(AncestorEvent event)\r
 365       {\r
 366       }\r
 367     });\r
 368     statusBar.setBackground(Color.white);\r
 369     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 370     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 371     statusBar.setText("Status bar");\r
 372     outputTextboxMenu.setMnemonic('T');\r
 373     outputTextboxMenu.setText("Output to Textbox");\r
 374     clustalColour.setText("Clustalx");\r
 375 \r
 376     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 377     {\r
 378       public void actionPerformed(ActionEvent e)\r
 379       {\r
 380         clustalColour_actionPerformed(e);\r
 381       }\r
 382     });\r
 383     zappoColour.setText("Zappo");\r
 384     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 385     {\r
 386       public void actionPerformed(ActionEvent e)\r
 387       {\r
 388         zappoColour_actionPerformed(e);\r
 389       }\r
 390     });\r
 391     taylorColour.setText("Taylor");\r
 392     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 393     {\r
 394       public void actionPerformed(ActionEvent e)\r
 395       {\r
 396         taylorColour_actionPerformed(e);\r
 397       }\r
 398     });\r
 399     hydrophobicityColour.setText("Hydrophobicity");\r
 400     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 401     {\r
 402       public void actionPerformed(ActionEvent e)\r
 403       {\r
 404         hydrophobicityColour_actionPerformed(e);\r
 405       }\r
 406     });\r
 407     helixColour.setText("Helix Propensity");\r
 408     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 409     {\r
 410       public void actionPerformed(ActionEvent e)\r
 411       {\r
 412         helixColour_actionPerformed(e);\r
 413       }\r
 414     });\r
 415     strandColour.setText("Strand Propensity");\r
 416     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 417     {\r
 418       public void actionPerformed(ActionEvent e)\r
 419       {\r
 420         strandColour_actionPerformed(e);\r
 421       }\r
 422     });\r
 423     turnColour.setText("Turn Propensity");\r
 424     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 425     {\r
 426       public void actionPerformed(ActionEvent e)\r
 427       {\r
 428         turnColour_actionPerformed(e);\r
 429       }\r
 430     });\r
 431     buriedColour.setText("Buried Index");\r
 432     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 433     {\r
 434       public void actionPerformed(ActionEvent e)\r
 435       {\r
 436         buriedColour_actionPerformed(e);\r
 437       }\r
 438     });\r
 439     userDefinedColour.setText("User Defined...");\r
 440     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 441     {\r
 442       public void actionPerformed(ActionEvent e)\r
 443       {\r
 444         userDefinedColour_actionPerformed(e);\r
 445       }\r
 446     });\r
 447     PIDColour.setText("Percentage Identity");\r
 448     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 449     {\r
 450       public void actionPerformed(ActionEvent e)\r
 451       {\r
 452         PIDColour_actionPerformed(e);\r
 453       }\r
 454     });\r
 455     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 456     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 457     {\r
 458       public void actionPerformed(ActionEvent e)\r
 459       {\r
 460         BLOSUM62Colour_actionPerformed(e);\r
 461       }\r
 462     });\r
 463     avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62...");\r
 464     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 465     {\r
 466       public void actionPerformed(ActionEvent e)\r
 467       {\r
 468         avTreeBlosumMenuItem_actionPerformed(e);\r
 469       }\r
 470     });\r
 471     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
 472     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         njTreeBlosumMenuItem_actionPerformed(e);\r
 477       }\r
 478     });\r
 479     annotationPanelMenuItem.setActionCommand("");\r
 480     annotationPanelMenuItem.setText("Show Annotations");\r
 481     annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );\r
 482     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         annotationPanelMenuItem_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     colourTextMenuItem.setText("Colour Text");\r
 490     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         colourTextMenuItem_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     htmlMenuItem.setText("HTML");\r
 498     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 499     {\r
 500       public void actionPerformed(ActionEvent e)\r
 501       {\r
 502         htmlMenuItem_actionPerformed(e);\r
 503       }\r
 504     });\r
 505     overviewMenuItem.setText("Overview Window...");\r
 506     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 507     {\r
 508       public void actionPerformed(ActionEvent e)\r
 509       {\r
 510         overviewMenuItem_actionPerformed(e);\r
 511       }\r
 512     });\r
 513     undoMenuItem.setEnabled(false);\r
 514     undoMenuItem.setMnemonic('Z');\r
 515     undoMenuItem.setText("Undo");\r
 516     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 517         event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 518     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         undoMenuItem_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     redoMenuItem.setEnabled(false);\r
 526     redoMenuItem.setMnemonic('0');\r
 527     redoMenuItem.setText("Redo");\r
 528     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 529     {\r
 530       public void actionPerformed(ActionEvent e)\r
 531       {\r
 532         redoMenuItem_actionPerformed(e);\r
 533       }\r
 534     });\r
 535     conservationMenuItem.setText("By Conservation");\r
 536     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 537     {\r
 538       public void actionPerformed(ActionEvent e)\r
 539       {\r
 540         conservationMenuItem_actionPerformed(e);\r
 541       }\r
 542     });\r
 543     noColourmenuItem.setText("None");\r
 544     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 545     {\r
 546       public void actionPerformed(ActionEvent e)\r
 547       {\r
 548         noColourmenuItem_actionPerformed(e);\r
 549       }\r
 550     });\r
 551     wrapMenuItem.setText("Wrap");\r
 552     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 553     {\r
 554       public void actionPerformed(ActionEvent e)\r
 555       {\r
 556         wrapMenuItem_actionPerformed(e);\r
 557       }\r
 558     });\r
 559     printMenuItem.setText("Print");\r
 560     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 561     {\r
 562       public void actionPerformed(ActionEvent e)\r
 563       {\r
 564         printMenuItem_actionPerformed(e);\r
 565       }\r
 566     });\r
 567     renderGapsMenuItem.setText("Show Gaps");\r
 568     renderGapsMenuItem.setState(true);\r
 569     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         renderGapsMenuItem_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     findMenuItem.setText("Find...");\r
 577     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 578         event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 579     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent e)\r
 582       {\r
 583         findMenuItem_actionPerformed(e);\r
 584       }\r
 585     });\r
 586     searchMenu.setText("Search");\r
 587 \r
 588     abovePIDThreshold.setText("Above Identity Threshold");\r
 589     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 590       public void actionPerformed(ActionEvent e) {\r
 591         abovePIDThreshold_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     sequenceFeatures.setText("Sequence Features");\r
 595     sequenceFeatures.addActionListener(new ActionListener()\r
 596     {\r
 597       public void actionPerformed(ActionEvent actionEvent)\r
 598       {\r
 599         sequenceFeatures_actionPerformed(actionEvent);\r
 600       }\r
 601     });\r
 602     nucleotideColour.setText("Nucleotide");\r
 603     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 604     {\r
 605       public void actionPerformed(ActionEvent e)\r
 606       {\r
 607         nucleotideColour_actionPerformed(e);\r
 608       }\r
 609     });\r
 610     deleteGroups.setText("Undefine groups");\r
 611     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 612     {\r
 613       public void actionPerformed(ActionEvent e)\r
 614       {\r
 615         deleteGroups_actionPerformed(e);\r
 616       }\r
 617     });\r
 618     copy.setText("Copy");\r
 619     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 620         KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 621     copy.setMnemonic(KeyEvent.VK_C);\r
 622 \r
 623     copy.addActionListener(new java.awt.event.ActionListener()\r
 624     {\r
 625       public void actionPerformed(ActionEvent e)\r
 626       {\r
 627         copy_actionPerformed(e);\r
 628       }\r
 629     });\r
 630     cut.setText("Cut");\r
 631     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 632         KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 633     cut.setMnemonic(KeyEvent.VK_X);\r
 634     cut.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         cut_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     delete.setText("Delete");\r
 642     delete.addActionListener(new java.awt.event.ActionListener()\r
 643     {\r
 644       public void actionPerformed(ActionEvent e)\r
 645       {\r
 646         delete_actionPerformed(e);\r
 647       }\r
 648     });\r
 649     jMenu1.setMnemonic('V');\r
 650     jMenu1.setText("Paste");\r
 651     pasteNew.setText("To New Alignment");\r
 652     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 653         KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 654     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 655     {\r
 656       public void actionPerformed(ActionEvent e)\r
 657       {\r
 658         pasteNew_actionPerformed(e);\r
 659       }\r
 660     });\r
 661     pasteThis.setText("Add To This Alignment");\r
 662     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 663     {\r
 664       public void actionPerformed(ActionEvent e)\r
 665       {\r
 666         pasteThis_actionPerformed(e);\r
 667       }\r
 668     });\r
 669     applyToAllGroups.setText("Apply Colour To All Groups");\r
 670     applyToAllGroups.setState(true);\r
 671     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 672     {\r
 673       public void actionPerformed(ActionEvent e)\r
 674       {\r
 675         applyToAllGroups_actionPerformed(e);\r
 676       }\r
 677     });\r
 678     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 679     {\r
 680       public void actionPerformed(ActionEvent e)\r
 681       {\r
 682         createPNG_actionPerformed(e);\r
 683       }\r
 684     });\r
 685     createPNG.setActionCommand("Save As PNG Image");\r
 686     createPNG.setText("PNG");\r
 687     font.setText("Font...");\r
 688     font.addActionListener(new java.awt.event.ActionListener()\r
 689     {\r
 690       public void actionPerformed(ActionEvent e)\r
 691       {\r
 692         font_actionPerformed(e);\r
 693       }\r
 694     });\r
 695     fullSeqId.setText("Show Full Sequence ID");\r
 696     fullSeqId.setState(true);\r
 697     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
 698     {\r
 699       public void actionPerformed(ActionEvent e)\r
 700       {\r
 701         fullSeqId_actionPerformed(e);\r
 702       }\r
 703     });\r
 704     epsFile.setText("EPS");\r
 705     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 706     {\r
 707       public void actionPerformed(ActionEvent e)\r
 708       {\r
 709         epsFile_actionPerformed(e);\r
 710       }\r
 711     });\r
 712     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 713     LoadtreeMenuItem.setText("Load Assocated Tree");\r
 714     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 715       public void actionPerformed(ActionEvent e)\r
 716       {\r
 717         LoadtreeMenuItem_actionPerformed(e);\r
 718       }\r
 719     });\r
 720     jpred.setText("JPred...");\r
 721     jpred.addActionListener(new java.awt.event.ActionListener()\r
 722     {\r
 723       public void actionPerformed(ActionEvent e)\r
 724       {\r
 725         jpred_actionPerformed(e);\r
 726       }\r
 727     });\r
 728     scaleAbove.setVisible(false);\r
 729     scaleAbove.setText("Scale Above");\r
 730     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 731     {\r
 732       public void actionPerformed(ActionEvent e)\r
 733       {\r
 734         scaleAbove_actionPerformed(e);\r
 735       }\r
 736     });\r
 737     scaleLeft.setVisible(false);\r
 738     scaleLeft.setSelected(true);\r
 739     scaleLeft.setText("Scale Left");\r
 740     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 741     {\r
 742       public void actionPerformed(ActionEvent e)\r
 743       {\r
 744         scaleLeft_actionPerformed(e);\r
 745       }\r
 746     });\r
 747     scaleRight.setVisible(false);\r
 748     scaleRight.setSelected(true);\r
 749     scaleRight.setText("Scale Right");\r
 750     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 751     {\r
 752       public void actionPerformed(ActionEvent e)\r
 753       {\r
 754         scaleRight_actionPerformed(e);\r
 755       }\r
 756     });\r
 757     modifyPID.setText("Modify Identity Threshold...");\r
 758     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 759     {\r
 760       public void actionPerformed(ActionEvent e)\r
 761       {\r
 762         modifyPID_actionPerformed(e);\r
 763       }\r
 764     });\r
 765     modifyConservation.setText("Modify Conservation Threshold...");\r
 766     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 767     {\r
 768       public void actionPerformed(ActionEvent e)\r
 769       {\r
 770         modifyConservation_actionPerformed(e);\r
 771       }\r
 772     });\r
 773     sortByTreeMenu.setText("By Tree Order");\r
 774     sort.setText("Sort");\r
 775     calculate.setText("Calculate Tree");\r
 776     msaAlignMenuItem.setText("Muscle Alignment...");\r
 777     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 778       public void actionPerformed(ActionEvent e) {\r
 779         msaAlignMenuItem_actionPerformed(e);\r
 780       }\r
 781     });\r
 782     jMenu2.setText("Export");\r
 783     padGapsMenuitem.setText("Pad Gaps");\r
 784     padGapsMenuitem.addActionListener(new ActionListener()\r
 785     {\r
 786       public void actionPerformed(ActionEvent e)\r
 787       {\r
 788         padGapsMenuitem_actionPerformed(e);\r
 789       }\r
 790     });\r
 791     ClustalRealign.setText("Clustal Realign...");\r
 792     ClustalRealign.addActionListener(new ActionListener()\r
 793     {\r
 794       public void actionPerformed(ActionEvent e)\r
 795       {\r
 796         ClustalRealign_actionPerformed(e);\r
 797       }\r
 798     });\r
 799     alignFrameMenuBar.add(fileMenu);\r
 800     alignFrameMenuBar.add(editMenu);\r
 801     alignFrameMenuBar.add(searchMenu);\r
 802     alignFrameMenuBar.add(viewMenu);\r
 803     alignFrameMenuBar.add(colourMenu);\r
 804     alignFrameMenuBar.add(calculateMenu);\r
 805     fileMenu.add(saveAlignmentMenu);\r
 806     fileMenu.add(jMenu2);\r
 807     fileMenu.add(outputTextboxMenu);\r
 808     fileMenu.add(printMenuItem);\r
 809     fileMenu.addSeparator();\r
 810     fileMenu.add(LoadtreeMenuItem);\r
 811     fileMenu.addSeparator();\r
 812     fileMenu.add(closeMenuItem);\r
 813     editMenu.add(undoMenuItem);\r
 814     editMenu.add(redoMenuItem);\r
 815     editMenu.add(cut);\r
 816     editMenu.add(copy);\r
 817     editMenu.add(jMenu1);\r
 818     editMenu.add(delete);\r
 819     editMenu.addSeparator();\r
 820     editMenu.add(selectAllSequenceMenuItem);\r
 821     editMenu.add(deselectAllSequenceMenuItem);\r
 822     editMenu.add(invertSequenceMenuItem);\r
 823     editMenu.add(deleteGroups);\r
 824     editMenu.addSeparator();\r
 825     editMenu.add(remove2LeftMenuItem);\r
 826     editMenu.add(remove2RightMenuItem);\r
 827     editMenu.add(removeGappedColumnMenuItem);\r
 828     editMenu.add(removeAllGapsMenuItem);\r
 829     editMenu.add(removeRedundancyMenuItem);\r
 830     editMenu.addSeparator();\r
 831     editMenu.add(padGapsMenuitem);\r
 832     searchMenu.add(findMenuItem);\r
 833     viewMenu.add(font);\r
 834     viewMenu.addSeparator();\r
 835     viewMenu.add(wrapMenuItem);\r
 836     viewMenu.add(fullSeqId);\r
 837     viewMenu.add(scaleAbove);\r
 838     viewMenu.add(scaleLeft);\r
 839     viewMenu.add(scaleRight);\r
 840     viewMenu.add(viewBoxesMenuItem);\r
 841     viewMenu.add(viewTextMenuItem);\r
 842     viewMenu.add(colourTextMenuItem);\r
 843     viewMenu.add(renderGapsMenuItem);\r
 844     viewMenu.add(annotationPanelMenuItem);\r
 845     viewMenu.add(sequenceFeatures);\r
 846     viewMenu.addSeparator();\r
 847     viewMenu.add(overviewMenuItem);\r
 848     colourMenu.add(applyToAllGroups);\r
 849     colourMenu.addSeparator();\r
 850     colourMenu.add(noColourmenuItem);\r
 851     colourMenu.add(clustalColour);\r
 852     colourMenu.add(BLOSUM62Colour);\r
 853     colourMenu.add(PIDColour);\r
 854     colourMenu.add(zappoColour);\r
 855     colourMenu.add(taylorColour);\r
 856     colourMenu.add(hydrophobicityColour);\r
 857     colourMenu.add(helixColour);\r
 858     colourMenu.add(strandColour);\r
 859     colourMenu.add(turnColour);\r
 860     colourMenu.add(buriedColour);\r
 861     colourMenu.add(nucleotideColour);\r
 862     colourMenu.add(userDefinedColour);\r
 863     colourMenu.addSeparator();\r
 864     colourMenu.add(conservationMenuItem);\r
 865     colourMenu.add(modifyConservation);\r
 866     colourMenu.add(abovePIDThreshold);\r
 867     colourMenu.add(modifyPID);\r
 868     calculateMenu.add(sort);\r
 869     calculateMenu.add(calculate);\r
 870     calculateMenu.addSeparator();\r
 871     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 872     calculateMenu.add(PCAMenuItem);\r
 873     calculateMenu.addSeparator();\r
 874     calculateMenu.add(webService);\r
 875     webService.add(clustalAlignMenuItem);\r
 876     webService.add(msaAlignMenuItem);\r
 877     webService.add(jpred);\r
 878     webService.add(ClustalRealign);\r
 879     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 880     jMenu1.add(pasteNew);\r
 881     jMenu1.add(pasteThis);\r
 882     sort.add(sortIDMenuItem);\r
 883     sort.add(sortGroupMenuItem);\r
 884     sort.add(sortPairwiseMenuItem);\r
 885     calculate.add(averageDistanceTreeMenuItem);\r
 886     calculate.add(neighbourTreeMenuItem);\r
 887     calculate.add(avDistanceTreeBlosumMenuItem);\r
 888     calculate.add(njTreeBlosumMenuItem);\r
 889     jMenu2.add(htmlMenuItem);\r
 890     jMenu2.add(epsFile);\r
 891     jMenu2.add(createPNG);\r
 892   }\r
 893 \r
 894   protected void outputText_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904 \r
 905   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 906   {\r
 907 \r
 908   }\r
 909 \r
 910   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913   }\r
 914 \r
 915   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917 \r
 918   }\r
 919 \r
 920 \r
 921   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 922   {\r
 923 \r
 924   }\r
 925 \r
 926   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928 \r
 929   }\r
 930 \r
 931   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933 \r
 934   }\r
 935 \r
 936   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 937   {\r
 938 \r
 939   }\r
 940 \r
 941   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 942   {\r
 943 \r
 944   }\r
 945 \r
 946   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 947   {\r
 948 \r
 949   }\r
 950 \r
 951   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 952   {\r
 953 \r
 954   }\r
 955 \r
 956 \r
 957   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 958   {\r
 959 \r
 960   }\r
 961 \r
 962 \r
 963   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 964   {\r
 965 \r
 966   }\r
 967 \r
 968   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 969   {\r
 970 \r
 971   }\r
 972 \r
 973 \r
 974   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 975   {\r
 976 \r
 977   }\r
 978 \r
 979   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 980   {\r
 981 \r
 982   }\r
 983 \r
 984   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 985   {\r
 986 \r
 987   }\r
 988 \r
 989   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 990   {\r
 991 \r
 992   }\r
 993 \r
 994   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 995   {\r
 996 \r
 997   }\r
 998 \r
 999   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1000   {\r
1001 \r
1002   }\r
1003 \r
1004 \r
1005   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1006   {\r
1007 \r
1008   }\r
1009 \r
1010   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1011   {\r
1012 \r
1013   }\r
1014 \r
1015   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1016   {\r
1017 \r
1018   }\r
1019 \r
1020   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1021   {\r
1022 \r
1023   }\r
1024 \r
1025   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1026   {\r
1027 \r
1028   }\r
1029 \r
1030 \r
1031   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1032   {\r
1033 \r
1034   }\r
1035 \r
1036   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038 \r
1039   }\r
1040 \r
1041 \r
1042 \r
1043   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1044   {\r
1045 \r
1046   }\r
1047 \r
1048 \r
1049 \r
1050 \r
1051   protected void clustalColour_actionPerformed(ActionEvent e)\r
1052   {\r
1053 \r
1054   }\r
1055 \r
1056   protected void zappoColour_actionPerformed(ActionEvent e)\r
1057   {\r
1058 \r
1059   }\r
1060 \r
1061   protected void taylorColour_actionPerformed(ActionEvent e)\r
1062   {\r
1063 \r
1064   }\r
1065 \r
1066 \r
1067   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1068   {\r
1069 \r
1070   }\r
1071 \r
1072   protected void helixColour_actionPerformed(ActionEvent e)\r
1073   {\r
1074 \r
1075   }\r
1076 \r
1077   protected void strandColour_actionPerformed(ActionEvent e)\r
1078   {\r
1079 \r
1080   }\r
1081 \r
1082   protected void turnColour_actionPerformed(ActionEvent e)\r
1083   {\r
1084 \r
1085   }\r
1086 \r
1087   protected void buriedColour_actionPerformed(ActionEvent e)\r
1088   {\r
1089 \r
1090   }\r
1091 \r
1092 \r
1093 \r
1094   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1095   {\r
1096 \r
1097   }\r
1098 \r
1099   protected void PIDColour_actionPerformed(ActionEvent e)\r
1100   {\r
1101 \r
1102   }\r
1103 \r
1104   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1105   {\r
1106 \r
1107   }\r
1108 \r
1109 \r
1110   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1111   {\r
1112 \r
1113   }\r
1114 \r
1115   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1116   {\r
1117 \r
1118   }\r
1119 \r
1120 \r
1121   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1122   {\r
1123 \r
1124   }\r
1125 \r
1126   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1127   {\r
1128 \r
1129   }\r
1130 \r
1131   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1132   {\r
1133 \r
1134   }\r
1135 \r
1136 \r
1137   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1138 \r
1139   }\r
1140 \r
1141   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1142   {\r
1143 \r
1144   }\r
1145 \r
1146   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1147   {\r
1148 \r
1149   }\r
1150 \r
1151   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1152   {\r
1153 \r
1154   }\r
1155 \r
1156  protected void copy_actionPerformed(ActionEvent e)\r
1157   {\r
1158 \r
1159   }\r
1160 \r
1161 \r
1162   protected void cut_actionPerformed(ActionEvent e)\r
1163   {\r
1164 \r
1165   }\r
1166 \r
1167   protected void delete_actionPerformed(ActionEvent e)\r
1168   {\r
1169 \r
1170   }\r
1171 \r
1172   protected void pasteNew_actionPerformed(ActionEvent e)\r
1173   {\r
1174 \r
1175   }\r
1176 \r
1177   protected void pasteThis_actionPerformed(ActionEvent e)\r
1178   {\r
1179 \r
1180   }\r
1181 \r
1182   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1183   {\r
1184 \r
1185   }\r
1186 \r
1187   protected void createPNG_actionPerformed(ActionEvent e)\r
1188   {\r
1189 \r
1190   }\r
1191 \r
1192   protected void font_actionPerformed(ActionEvent e)\r
1193   {\r
1194 \r
1195   }\r
1196 \r
1197   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1198   {\r
1199 \r
1200   }\r
1201 \r
1202   protected void epsFile_actionPerformed(ActionEvent e)\r
1203   {\r
1204 \r
1205   }\r
1206 \r
1207   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1208 \r
1209   }\r
1210 \r
1211   protected void jpred_actionPerformed(ActionEvent e)\r
1212   {\r
1213 \r
1214   }\r
1215 \r
1216   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1217   {\r
1218 \r
1219   }\r
1220 \r
1221   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1222   {\r
1223 \r
1224   }\r
1225 \r
1226   protected void scaleRight_actionPerformed(ActionEvent e)\r
1227   {\r
1228 \r
1229   }\r
1230 \r
1231   protected void modifyPID_actionPerformed(ActionEvent e)\r
1232   {\r
1233 \r
1234   }\r
1235 \r
1236   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1237   {\r
1238 \r
1239   }\r
1240 \r
1241   protected void preferences_actionPerformed(ActionEvent e)\r
1242   {\r
1243 \r
1244   }\r
1245 \r
1246   protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
1247 \r
1248   }\r
1249 \r
1250   protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
1251   {\r
1252 \r
1253   }\r
1254 \r
1255   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1256   {\r
1257 \r
1258   }\r
1259 \r
1260   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1261   {\r
1262 \r
1263   }\r
1264 \r
1265   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
1266   {\r
1267 \r
1268   }\r
1269 \r
1270 }\r