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