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 import javax.swing.event.*;\r
  15 \r
  16 \r
  17 public class GAlignFrame extends JInternalFrame\r
  18 {\r
  19   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  20   protected JMenu fileMenu = new JMenu();\r
  21   protected JMenuItem saveAsPostscriptMenuItem = new JMenuItem();\r
  22   protected JMenuItem closeMenuItem = new JMenuItem();\r
  23   protected JMenu editMenu = new JMenu();\r
  24   protected JMenu fontMenu = new JMenu();\r
  25   protected JMenu viewMenu = new JMenu();\r
  26   protected JMenu colourMenu = new JMenu();\r
  27   protected JMenu calculateMenu = new JMenu();\r
  28   protected JMenu alignMenu = new JMenu();\r
  29   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  30   protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
  31   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  32   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  33   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  34   protected JMenuItem deleteSelectedMenuItem = new JMenuItem();\r
  35   protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
  36   protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
  37   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  38   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  39   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  40   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  41   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  42   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  43   protected JMenuItem fontNameMenuItem = new JMenuItem();\r
  44   protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
  45   protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
  46   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  47   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  48   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  49   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  50   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  51   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  54   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  57   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  58   BorderLayout borderLayout1 = new BorderLayout();\r
  59   public JLabel statusBar = new JLabel();\r
  60   protected JMenu saveAlignmentMenu = new JMenu();\r
  61   protected JMenu outputTextboxMenu = new JMenu();\r
  62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem conservationColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  75   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  76   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  77   JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
  78   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  79   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  80   JMenuItem htmlMenuItem = new JMenuItem();\r
  81   JMenuItem schemeKeyMenuItem = new JMenuItem();\r
  82   JMenuItem overviewMenuItem = new JMenuItem();\r
  83   public GAlignFrame()\r
  84   {\r
  85     try\r
  86     {\r
  87       jbInit();\r
  88       setJMenuBar(alignFrameMenuBar);\r
  89 \r
  90       JMenuItem item;\r
  91       // dynamically fill save as menu with available formats\r
  92       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
  93         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
  94         saveAlignmentMenu.add( item );\r
  95         item.addActionListener(new java.awt.event.ActionListener()\r
  96         {\r
  97           public void actionPerformed(ActionEvent e)\r
  98           {\r
  99             saveAs_actionPerformed(e);\r
 100           }\r
 101         });\r
 102 \r
 103         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 104         item.addActionListener(new java.awt.event.ActionListener()\r
 105         {\r
 106           public void actionPerformed(ActionEvent e)\r
 107           {\r
 108             outputText_actionPerformed(e);\r
 109           }\r
 110         });\r
 111 \r
 112         outputTextboxMenu.add( item );\r
 113       }\r
 114 \r
 115     }\r
 116     catch(Exception e)\r
 117     {\r
 118       e.printStackTrace();\r
 119     }\r
 120 \r
 121     ButtonGroup colours = new ButtonGroup();\r
 122     colours.add(clustalColour);\r
 123     colours.add(zappoColour);\r
 124     colours.add(taylorColour);\r
 125     colours.add(hydrophobicityColour);\r
 126     colours.add(helixColour);\r
 127     colours.add(strandColour);\r
 128     colours.add(turnColour);\r
 129     colours.add(buriedColour);\r
 130     colours.add(conservationColour);\r
 131     colours.add(abovePIDColour);\r
 132     colours.add(userDefinedColour);\r
 133     colours.add(PIDColour);\r
 134     colours.add(BLOSUM62Colour);\r
 135   }\r
 136   private void jbInit() throws Exception\r
 137   {\r
 138     fileMenu.setMnemonic('F');\r
 139     fileMenu.setText("File");\r
 140     saveAlignmentMenu.setMnemonic('L');\r
 141     saveAlignmentMenu.setText("Save alignment to local file");\r
 142     saveAsPostscriptMenuItem.setMnemonic('P');\r
 143     saveAsPostscriptMenuItem.setText("Save alignment as postscript");\r
 144     saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 145     {\r
 146       public void actionPerformed(ActionEvent e)\r
 147       {\r
 148         saveAsPostscriptMenuItem_actionPerformed(e);\r
 149       }\r
 150     });\r
 151     closeMenuItem.setMnemonic('C');\r
 152     closeMenuItem.setText("Close");\r
 153     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 154     {\r
 155       public void actionPerformed(ActionEvent e)\r
 156       {\r
 157         closeMenuItem_actionPerformed(e);\r
 158       }\r
 159     });\r
 160     editMenu.setText("Edit");\r
 161     fontMenu.setText("Font");\r
 162     viewMenu.setText("View");\r
 163     colourMenu.setText("Colour");\r
 164     calculateMenu.setText("Calculate");\r
 165     alignMenu.setText("Web Service");\r
 166     groupsMenuItem.setEnabled(false);\r
 167     groupsMenuItem.setText("Groups");\r
 168     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 169     {\r
 170       public void actionPerformed(ActionEvent e)\r
 171       {\r
 172         groupsMenuItem_actionPerformed(e);\r
 173       }\r
 174     });\r
 175     groupEditingMenuItem.setEnabled(false);\r
 176     groupEditingMenuItem.setText("Group editing mode");\r
 177     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 178     {\r
 179       public void actionPerformed(ActionEvent e)\r
 180       {\r
 181         groupEditingMenuItem_actionPerformed(e);\r
 182       }\r
 183     });\r
 184     selectAllSequenceMenuItem.setText("Select all sequences");\r
 185     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 186     {\r
 187       public void actionPerformed(ActionEvent e)\r
 188       {\r
 189         selectAllSequenceMenuItem_actionPerformed(e);\r
 190       }\r
 191     });\r
 192     deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
 193     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 194     {\r
 195       public void actionPerformed(ActionEvent e)\r
 196       {\r
 197         deselectAllSequenceMenuItem_actionPerformed(e);\r
 198       }\r
 199     });\r
 200     invertSequenceMenuItem.setText("Invert sequence selection");\r
 201     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 202     {\r
 203       public void actionPerformed(ActionEvent e)\r
 204       {\r
 205         invertSequenceMenuItem_actionPerformed(e);\r
 206       }\r
 207     });\r
 208     deleteSelectedMenuItem.setText("Delete selected sequences");\r
 209     deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 210     {\r
 211       public void actionPerformed(ActionEvent e)\r
 212       {\r
 213         deleteSelectedMenuItem_actionPerformed(e);\r
 214       }\r
 215     });\r
 216     moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
 217     moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 218     {\r
 219       public void actionPerformed(ActionEvent e)\r
 220       {\r
 221         moveSelectedMenuItem_actionPerformed(e);\r
 222       }\r
 223     });\r
 224     copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
 225     copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 226     {\r
 227       public void actionPerformed(ActionEvent e)\r
 228       {\r
 229         copySelectedMenuItem_actionPerformed(e);\r
 230       }\r
 231     });\r
 232     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 233     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 234     {\r
 235       public void actionPerformed(ActionEvent e)\r
 236       {\r
 237         deselectAllColumnsMenuItem_actionPerformed(e);\r
 238       }\r
 239     });\r
 240     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 241     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 242     {\r
 243       public void actionPerformed(ActionEvent e)\r
 244       {\r
 245         remove2LeftMenuItem_actionPerformed(e);\r
 246       }\r
 247     });\r
 248     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 249     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 250     {\r
 251       public void actionPerformed(ActionEvent e)\r
 252       {\r
 253         remove2RightMenuItem_actionPerformed(e);\r
 254       }\r
 255     });\r
 256     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 257     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 258     {\r
 259       public void actionPerformed(ActionEvent e)\r
 260       {\r
 261         removeGappedColumnMenuItem_actionPerformed(e);\r
 262       }\r
 263     });\r
 264     removeAllGapsMenuItem.setText("Remove all gaps");\r
 265     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 266     {\r
 267       public void actionPerformed(ActionEvent e)\r
 268       {\r
 269         removeAllGapsMenuItem_actionPerformed(e);\r
 270       }\r
 271     });\r
 272     setGapCharMenuItem.setText("Set gap character to \"-\"");\r
 273     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 274     {\r
 275       public void actionPerformed(ActionEvent e)\r
 276       {\r
 277         setGapCharMenuItem_actionPerformed(e);\r
 278       }\r
 279     });\r
 280     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 281     {\r
 282       public void actionPerformed(ActionEvent e)\r
 283       {\r
 284         fontNameMenuItem_actionPerformed(e);\r
 285       }\r
 286     });\r
 287     fontSizeMenuItem.setText("10");\r
 288     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 289     {\r
 290       public void actionPerformed(ActionEvent e)\r
 291       {\r
 292         fontSizeMenuItem_actionPerformed(e);\r
 293       }\r
 294     });\r
 295     fontStyleMenuItem.setText("Plain");\r
 296     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 297     {\r
 298       public void actionPerformed(ActionEvent e)\r
 299       {\r
 300         fontStyleMenuItem_actionPerformed(e);\r
 301       }\r
 302     });\r
 303     viewBoxesMenuItem.setText("Boxes");\r
 304     viewBoxesMenuItem.setState(true);\r
 305     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 306     {\r
 307       public void actionPerformed(ActionEvent e)\r
 308       {\r
 309         viewBoxesMenuItem_actionPerformed(e);\r
 310       }\r
 311     });\r
 312     viewTextMenuItem.setText("Text");\r
 313     viewTextMenuItem.setState(true);\r
 314     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 315     {\r
 316       public void actionPerformed(ActionEvent e)\r
 317       {\r
 318         viewTextMenuItem_actionPerformed(e);\r
 319       }\r
 320     });\r
 321     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 322     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 323     {\r
 324       public void actionPerformed(ActionEvent e)\r
 325       {\r
 326         sortPairwiseMenuItem_actionPerformed(e);\r
 327       }\r
 328     });\r
 329     sortIDMenuItem.setText("Sort by ID");\r
 330     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 331     {\r
 332       public void actionPerformed(ActionEvent e)\r
 333       {\r
 334         sortIDMenuItem_actionPerformed(e);\r
 335       }\r
 336     });\r
 337     sortGroupMenuItem.setText("Sort by group");\r
 338     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 339     {\r
 340       public void actionPerformed(ActionEvent e)\r
 341       {\r
 342         sortGroupMenuItem_actionPerformed(e);\r
 343       }\r
 344     });\r
 345     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 346     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 347     {\r
 348       public void actionPerformed(ActionEvent e)\r
 349       {\r
 350         sortTreeOrderMenuItem_actionPerformed(e);\r
 351       }\r
 352     });\r
 353     removeRedundancyMenuItem.setText("Remove redundancy");\r
 354     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 355     {\r
 356       public void actionPerformed(ActionEvent e)\r
 357       {\r
 358         removeRedundancyMenuItem_actionPerformed(e);\r
 359       }\r
 360     });\r
 361     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 362     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 363     {\r
 364       public void actionPerformed(ActionEvent e)\r
 365       {\r
 366         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 367       }\r
 368     });\r
 369     PCAMenuItem.setText("Principal component analysis");\r
 370     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 371     {\r
 372       public void actionPerformed(ActionEvent e)\r
 373       {\r
 374         PCAMenuItem_actionPerformed(e);\r
 375       }\r
 376     });\r
 377     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 378     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 379     {\r
 380       public void actionPerformed(ActionEvent e)\r
 381       {\r
 382         averageDistanceTreeMenuItem_actionPerformed(e);\r
 383       }\r
 384     });\r
 385     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 386     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 387     {\r
 388       public void actionPerformed(ActionEvent e)\r
 389       {\r
 390         neighbourTreeMenuItem_actionPerformed(e);\r
 391       }\r
 392     });\r
 393     clustalAlignMenuItem.setText("Clustal alignment");\r
 394     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         clustalAlignMenuItem_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     this.getContentPane().setLayout(borderLayout1);\r
 402     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 403     statusBar.setBackground(Color.white);\r
 404     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 405     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 406     statusBar.setText("Status bar");\r
 407     outputTextboxMenu.setMnemonic('T');\r
 408     outputTextboxMenu.setText("Output alignment via textbox");\r
 409     clustalColour.setSelected(false);\r
 410     clustalColour.setText("Clustalx colours");\r
 411     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 412     {\r
 413       public void actionPerformed(ActionEvent e)\r
 414       {\r
 415         clustalColour_actionPerformed(e);\r
 416       }\r
 417     });\r
 418     zappoColour.setSelected(true);\r
 419     zappoColour.setText("Zappo colour scheme");\r
 420     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 421     {\r
 422       public void actionPerformed(ActionEvent e)\r
 423       {\r
 424         zappoColour_actionPerformed(e);\r
 425       }\r
 426     });\r
 427     taylorColour.setText("Taylor colour scheme");\r
 428     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         taylorColour_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     hydrophobicityColour.setText("By hydrophobicity");\r
 436     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 437     {\r
 438       public void actionPerformed(ActionEvent e)\r
 439       {\r
 440         hydrophobicityColour_actionPerformed(e);\r
 441       }\r
 442     });\r
 443     helixColour.setText("Helix propensity");\r
 444     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         helixColour_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     strandColour.setText("Strand propensity");\r
 452     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 453     {\r
 454       public void actionPerformed(ActionEvent e)\r
 455       {\r
 456         strandColour_actionPerformed(e);\r
 457       }\r
 458     });\r
 459     turnColour.setText("Turn propensity");\r
 460     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 461     {\r
 462       public void actionPerformed(ActionEvent e)\r
 463       {\r
 464         turnColour_actionPerformed(e);\r
 465       }\r
 466     });\r
 467     buriedColour.setText("Buried index");\r
 468     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 469     {\r
 470       public void actionPerformed(ActionEvent e)\r
 471       {\r
 472         buriedColour_actionPerformed(e);\r
 473       }\r
 474     });\r
 475     conservationColour.setEnabled(false);\r
 476     conservationColour.setText("By conservation");\r
 477     conservationColour.addActionListener(new java.awt.event.ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         conservationColour_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     abovePIDColour.setEnabled(false);\r
 485     abovePIDColour.setText("Above PID threshold only");\r
 486     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         abovePIDColour_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     userDefinedColour.setText("User defined colours");\r
 494     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         userDefinedColour_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     PIDColour.setEnabled(false);\r
 502     PIDColour.setText("By PID");\r
 503     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 504     {\r
 505       public void actionPerformed(ActionEvent e)\r
 506       {\r
 507         PIDColour_actionPerformed(e);\r
 508       }\r
 509     });\r
 510     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 511     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 512     {\r
 513       public void actionPerformed(ActionEvent e)\r
 514       {\r
 515         BLOSUM62Colour_actionPerformed(e);\r
 516       }\r
 517     });\r
 518     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 519     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 520     {\r
 521       public void actionPerformed(ActionEvent e)\r
 522       {\r
 523         avTreeBlosumMenuItem_actionPerformed(e);\r
 524       }\r
 525     });\r
 526     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 527     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 528     {\r
 529       public void actionPerformed(ActionEvent e)\r
 530       {\r
 531         njTreeBlosumMenuItem_actionPerformed(e);\r
 532       }\r
 533     });\r
 534     conservationColourIncMenuItem.setEnabled(false);\r
 535     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 536     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 537     {\r
 538       public void actionPerformed(ActionEvent e)\r
 539       {\r
 540         conservationColourIncMenuItem_actionPerformed(e);\r
 541       }\r
 542     });\r
 543     consensusGraphMenuItem.setActionCommand("");\r
 544     consensusGraphMenuItem.setText("Consensus graph");\r
 545     consensusGraphMenuItem.setState(true);\r
 546     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         consensusGraphMenuItem_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     colourTextMenuItem.setText("Colour text");\r
 554     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         colourTextMenuItem_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     htmlMenuItem.setText("Output as HTML");\r
 562     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 563     {\r
 564       public void actionPerformed(ActionEvent e)\r
 565       {\r
 566         htmlMenuItem_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 570     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent e)\r
 573       {\r
 574         schemeKeyMenuItem_actionPerformed(e);\r
 575       }\r
 576     });\r
 577     overviewMenuItem.setText("Overview window");\r
 578     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent e)\r
 581       {\r
 582         overviewMenuItem_actionPerformed(e);\r
 583       }\r
 584     });\r
 585     alignFrameMenuBar.add(fileMenu);\r
 586     alignFrameMenuBar.add(editMenu);\r
 587     alignFrameMenuBar.add(fontMenu);\r
 588     alignFrameMenuBar.add(viewMenu);\r
 589     alignFrameMenuBar.add(colourMenu);\r
 590     alignFrameMenuBar.add(calculateMenu);\r
 591     alignFrameMenuBar.add(alignMenu);\r
 592     fileMenu.add(saveAlignmentMenu);\r
 593     fileMenu.add(saveAsPostscriptMenuItem);\r
 594     fileMenu.add(outputTextboxMenu);\r
 595     fileMenu.add(htmlMenuItem);\r
 596     fileMenu.addSeparator();\r
 597     fileMenu.add(closeMenuItem);\r
 598     editMenu.add(groupsMenuItem);\r
 599     editMenu.add(groupEditingMenuItem);\r
 600     editMenu.addSeparator();\r
 601     editMenu.add(selectAllSequenceMenuItem);\r
 602     editMenu.add(deselectAllSequenceMenuItem);\r
 603     editMenu.add(invertSequenceMenuItem);\r
 604     editMenu.addSeparator();\r
 605     editMenu.add(copySelectedMenuItem);\r
 606     editMenu.add(moveSelectedMenuItem);\r
 607     editMenu.add(deleteSelectedMenuItem);\r
 608     editMenu.addSeparator();\r
 609     editMenu.add(deselectAllColumnsMenuItem);\r
 610     editMenu.add(remove2LeftMenuItem);\r
 611     editMenu.add(remove2RightMenuItem);\r
 612     editMenu.addSeparator();\r
 613     editMenu.add(removeGappedColumnMenuItem);\r
 614     editMenu.add(removeAllGapsMenuItem);\r
 615     editMenu.add(setGapCharMenuItem);\r
 616     fontMenu.add(fontNameMenuItem);\r
 617     fontMenu.add(fontSizeMenuItem);\r
 618     fontMenu.add(fontStyleMenuItem);\r
 619     fontMenu.addSeparator();\r
 620     fontMenu.add(colourTextMenuItem);\r
 621     viewMenu.add(viewBoxesMenuItem);\r
 622     viewMenu.add(viewTextMenuItem);\r
 623     viewMenu.add(consensusGraphMenuItem);\r
 624     viewMenu.add(overviewMenuItem);\r
 625     colourMenu.add(clustalColour);\r
 626     colourMenu.add(zappoColour);\r
 627     colourMenu.add(taylorColour);\r
 628     colourMenu.add(hydrophobicityColour);\r
 629     colourMenu.add(helixColour);\r
 630     colourMenu.add(strandColour);\r
 631     colourMenu.add(turnColour);\r
 632     colourMenu.add(buriedColour);\r
 633     colourMenu.add(userDefinedColour);\r
 634     colourMenu.addSeparator();\r
 635     colourMenu.add(conservationColour);\r
 636     colourMenu.add(conservationColourIncMenuItem);\r
 637     colourMenu.addSeparator();\r
 638     colourMenu.add(abovePIDColour);\r
 639     colourMenu.add(PIDColour);\r
 640     colourMenu.add(BLOSUM62Colour);\r
 641     colourMenu.addSeparator();\r
 642     colourMenu.add(schemeKeyMenuItem);\r
 643     calculateMenu.add(sortPairwiseMenuItem);\r
 644     calculateMenu.add(sortIDMenuItem);\r
 645     calculateMenu.add(sortGroupMenuItem);\r
 646     calculateMenu.add(sortTreeOrderMenuItem);\r
 647     calculateMenu.add(removeRedundancyMenuItem);\r
 648     calculateMenu.addSeparator();\r
 649     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 650     calculateMenu.add(PCAMenuItem);\r
 651     calculateMenu.addSeparator();\r
 652     calculateMenu.add(averageDistanceTreeMenuItem);\r
 653     calculateMenu.add(neighbourTreeMenuItem);\r
 654     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 655     calculateMenu.add(njTreeBlosumMenuItem);\r
 656     alignMenu.add(clustalAlignMenuItem);\r
 657     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 658   }\r
 659 \r
 660   protected void saveAs_actionPerformed(ActionEvent e)\r
 661   {\r
 662 \r
 663   }\r
 664 \r
 665   protected void outputText_actionPerformed(ActionEvent e)\r
 666   {\r
 667 \r
 668   }\r
 669 \r
 670   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 671   {\r
 672 \r
 673   }\r
 674 \r
 675 \r
 676 \r
 677   protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
 678   {\r
 679 \r
 680   }\r
 681 \r
 682 \r
 683   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 684   {\r
 685 \r
 686   }\r
 687 \r
 688   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 689   {\r
 690 \r
 691   }\r
 692 \r
 693   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 694   {\r
 695 \r
 696   }\r
 697 \r
 698   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 699   {\r
 700 \r
 701   }\r
 702 \r
 703   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 704   {\r
 705 \r
 706   }\r
 707 \r
 708   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 709   {\r
 710 \r
 711   }\r
 712 \r
 713   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 714   {\r
 715 \r
 716   }\r
 717 \r
 718   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 719   {\r
 720 \r
 721   }\r
 722 \r
 723   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 724   {\r
 725 \r
 726   }\r
 727 \r
 728   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730 \r
 731   }\r
 732 \r
 733   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 734   {\r
 735 \r
 736   }\r
 737 \r
 738   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 739   {\r
 740 \r
 741   }\r
 742 \r
 743   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 744   {\r
 745 \r
 746   }\r
 747 \r
 748   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 749   {\r
 750 \r
 751   }\r
 752 \r
 753   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 754   {\r
 755 \r
 756   }\r
 757 \r
 758 \r
 759   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 760   {\r
 761 \r
 762   }\r
 763 \r
 764   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766 \r
 767   }\r
 768 \r
 769   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771 \r
 772   }\r
 773 \r
 774   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781 \r
 782   }\r
 783 \r
 784 \r
 785   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 786   {\r
 787 \r
 788   }\r
 789 \r
 790 \r
 791 \r
 792   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 793   {\r
 794 \r
 795   }\r
 796 \r
 797   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 798   {\r
 799 \r
 800   }\r
 801 \r
 802   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804 \r
 805   }\r
 806 \r
 807   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 808   {\r
 809 \r
 810   }\r
 811 \r
 812   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 813   {\r
 814 \r
 815   }\r
 816 \r
 817   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 818   {\r
 819 \r
 820   }\r
 821 \r
 822   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 823   {\r
 824 \r
 825   }\r
 826 \r
 827   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 828   {\r
 829 \r
 830   }\r
 831 \r
 832   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 833   {\r
 834 \r
 835   }\r
 836 \r
 837   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 838   {\r
 839 \r
 840   }\r
 841 \r
 842   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844 \r
 845   }\r
 846 \r
 847 \r
 848   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 849   {\r
 850 \r
 851   }\r
 852 \r
 853   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 854   {\r
 855 \r
 856   }\r
 857 \r
 858 \r
 859 \r
 860   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865 \r
 866 \r
 867 \r
 868   protected void clustalColour_actionPerformed(ActionEvent e)\r
 869   {\r
 870 \r
 871   }\r
 872 \r
 873   protected void zappoColour_actionPerformed(ActionEvent e)\r
 874   {\r
 875 \r
 876   }\r
 877 \r
 878   protected void taylorColour_actionPerformed(ActionEvent e)\r
 879   {\r
 880 \r
 881   }\r
 882 \r
 883 \r
 884   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 885   {\r
 886 \r
 887   }\r
 888 \r
 889   protected void helixColour_actionPerformed(ActionEvent e)\r
 890   {\r
 891 \r
 892   }\r
 893 \r
 894   protected void strandColour_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void turnColour_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904   protected void buriedColour_actionPerformed(ActionEvent e)\r
 905   {\r
 906 \r
 907   }\r
 908 \r
 909   protected void conservationColour_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912   }\r
 913 \r
 914   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 915  {\r
 916 \r
 917  }\r
 918 \r
 919 \r
 920   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 921   {\r
 922 \r
 923   }\r
 924 \r
 925 \r
 926   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 927   {\r
 928 \r
 929   }\r
 930 \r
 931   protected void PIDColour_actionPerformed(ActionEvent e)\r
 932   {\r
 933 \r
 934   }\r
 935 \r
 936   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 937   {\r
 938 \r
 939   }\r
 940 \r
 941   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 942   {\r
 943 \r
 944   }\r
 945 \r
 946 }\r