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