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