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