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 fontMenu = new JMenu();\r
  22   protected JMenu viewMenu = new JMenu();\r
  23   protected JMenu colourMenu = new JMenu();\r
  24   protected JMenu calculateMenu = new JMenu();\r
  25   protected JMenu alignMenu = new JMenu();\r
  26   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  27   protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\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 deleteSelectedMenuItem = new JMenuItem();\r
  32   protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
  33   protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
  34   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  35   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  36   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  37   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  38   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  39   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  40   protected JMenuItem fontNameMenuItem = new JMenuItem();\r
  41   protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
  42   protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
  43   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  44   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  45   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  46   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  47   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  48   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  50   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  51   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  52   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  53   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  54   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  55   BorderLayout borderLayout1 = new BorderLayout();\r
  56   public JLabel statusBar = new JLabel();\r
  57   protected JMenu saveAlignmentMenu = new JMenu();\r
  58   protected JMenu outputTextboxMenu = new JMenu();\r
  59   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  71   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  72   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  73   protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  75   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  76   JMenuItem htmlMenuItem = new JMenuItem();\r
  77   JMenuItem schemeKeyMenuItem = new JMenuItem();\r
  78   JMenuItem overviewMenuItem = new JMenuItem();\r
  79   protected JMenuItem undoMenuItem = new JMenuItem();\r
  80   protected JMenuItem redoMenuItem = new JMenuItem();\r
  81   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  82   JMenuItem noColourmenuItem = new JMenuItem();\r
  83   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  84   JMenuItem pdbTest = new JMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   public GAlignFrame()\r
  87   {\r
  88     try\r
  89     {\r
  90       jbInit();\r
  91       setJMenuBar(alignFrameMenuBar);\r
  92 \r
  93       JMenuItem item;\r
  94       // dynamically fill save as menu with available formats\r
  95       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
  96         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
  97         saveAlignmentMenu.add( item );\r
  98         item.addActionListener(new java.awt.event.ActionListener()\r
  99         {\r
 100           public void actionPerformed(ActionEvent e)\r
 101           {\r
 102             saveAs_actionPerformed(e);\r
 103           }\r
 104         });\r
 105 \r
 106         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 107         item.addActionListener(new java.awt.event.ActionListener()\r
 108         {\r
 109           public void actionPerformed(ActionEvent e)\r
 110           {\r
 111             outputText_actionPerformed(e);\r
 112           }\r
 113         });\r
 114 \r
 115         outputTextboxMenu.add( item );\r
 116       }\r
 117 \r
 118     }\r
 119     catch(Exception e)\r
 120     {\r
 121       e.printStackTrace();\r
 122     }\r
 123 \r
 124     ButtonGroup colours = new ButtonGroup();\r
 125     colours.add(clustalColour);\r
 126     colours.add(zappoColour);\r
 127     colours.add(taylorColour);\r
 128     colours.add(hydrophobicityColour);\r
 129     colours.add(helixColour);\r
 130     colours.add(strandColour);\r
 131     colours.add(turnColour);\r
 132     colours.add(buriedColour);\r
 133     colours.add(abovePIDColour);\r
 134     colours.add(userDefinedColour);\r
 135     colours.add(PIDColour);\r
 136     colours.add(BLOSUM62Colour);\r
 137   }\r
 138   private void jbInit() throws Exception\r
 139   {\r
 140     fileMenu.setMnemonic('F');\r
 141     fileMenu.setText("File");\r
 142     saveAlignmentMenu.setMnemonic('L');\r
 143     saveAlignmentMenu.setText("Save alignment to local file");\r
 144     closeMenuItem.setMnemonic('C');\r
 145     closeMenuItem.setText("Close");\r
 146     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 147     {\r
 148       public void actionPerformed(ActionEvent e)\r
 149       {\r
 150         closeMenuItem_actionPerformed(e);\r
 151       }\r
 152     });\r
 153     editMenu.setText("Edit");\r
 154     fontMenu.setText("Font");\r
 155     viewMenu.setText("View");\r
 156     colourMenu.setText("Colour");\r
 157     calculateMenu.setText("Calculate");\r
 158     alignMenu.setText("Web Service");\r
 159     groupsMenuItem.setText("Groups");\r
 160     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 161     {\r
 162       public void actionPerformed(ActionEvent e)\r
 163       {\r
 164         groupsMenuItem_actionPerformed(e);\r
 165       }\r
 166     });\r
 167     groupEditingMenuItem.setText("Group editing mode");\r
 168     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 169     {\r
 170       public void actionPerformed(ActionEvent e)\r
 171       {\r
 172         groupEditingMenuItem_actionPerformed(e);\r
 173       }\r
 174     });\r
 175     selectAllSequenceMenuItem.setText("Select all sequences");\r
 176     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 177     {\r
 178       public void actionPerformed(ActionEvent e)\r
 179       {\r
 180         selectAllSequenceMenuItem_actionPerformed(e);\r
 181       }\r
 182     });\r
 183     deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
 184     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 185     {\r
 186       public void actionPerformed(ActionEvent e)\r
 187       {\r
 188         deselectAllSequenceMenuItem_actionPerformed(e);\r
 189       }\r
 190     });\r
 191     invertSequenceMenuItem.setText("Invert sequence selection");\r
 192     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 193     {\r
 194       public void actionPerformed(ActionEvent e)\r
 195       {\r
 196         invertSequenceMenuItem_actionPerformed(e);\r
 197       }\r
 198     });\r
 199     deleteSelectedMenuItem.setText("Delete selected sequences");\r
 200     deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 201     {\r
 202       public void actionPerformed(ActionEvent e)\r
 203       {\r
 204         deleteSelectedMenuItem_actionPerformed(e);\r
 205       }\r
 206     });\r
 207     moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
 208     moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 209     {\r
 210       public void actionPerformed(ActionEvent e)\r
 211       {\r
 212         moveSelectedMenuItem_actionPerformed(e);\r
 213       }\r
 214     });\r
 215     copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
 216     copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         copySelectedMenuItem_actionPerformed(e);\r
 221       }\r
 222     });\r
 223     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 224     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 225     {\r
 226       public void actionPerformed(ActionEvent e)\r
 227       {\r
 228         deselectAllColumnsMenuItem_actionPerformed(e);\r
 229       }\r
 230     });\r
 231     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 232     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 233     {\r
 234       public void actionPerformed(ActionEvent e)\r
 235       {\r
 236         remove2LeftMenuItem_actionPerformed(e);\r
 237       }\r
 238     });\r
 239     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 240     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 241     {\r
 242       public void actionPerformed(ActionEvent e)\r
 243       {\r
 244         remove2RightMenuItem_actionPerformed(e);\r
 245       }\r
 246     });\r
 247     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 248     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 249     {\r
 250       public void actionPerformed(ActionEvent e)\r
 251       {\r
 252         removeGappedColumnMenuItem_actionPerformed(e);\r
 253       }\r
 254     });\r
 255     removeAllGapsMenuItem.setText("Remove all gaps");\r
 256     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 257     {\r
 258       public void actionPerformed(ActionEvent e)\r
 259       {\r
 260         removeAllGapsMenuItem_actionPerformed(e);\r
 261       }\r
 262     });\r
 263     setGapCharMenuItem.setText("Set gap character to \"-\"");\r
 264     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 265     {\r
 266       public void actionPerformed(ActionEvent e)\r
 267       {\r
 268         setGapCharMenuItem_actionPerformed(e);\r
 269       }\r
 270     });\r
 271     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 272     {\r
 273       public void actionPerformed(ActionEvent e)\r
 274       {\r
 275         fontNameMenuItem_actionPerformed(e);\r
 276       }\r
 277     });\r
 278     fontSizeMenuItem.setText("10");\r
 279     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 280     {\r
 281       public void actionPerformed(ActionEvent e)\r
 282       {\r
 283         fontSizeMenuItem_actionPerformed(e);\r
 284       }\r
 285     });\r
 286     fontStyleMenuItem.setText("Plain");\r
 287     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 288     {\r
 289       public void actionPerformed(ActionEvent e)\r
 290       {\r
 291         fontStyleMenuItem_actionPerformed(e);\r
 292       }\r
 293     });\r
 294     viewBoxesMenuItem.setText("Boxes");\r
 295     viewBoxesMenuItem.setState(true);\r
 296     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 297     {\r
 298       public void actionPerformed(ActionEvent e)\r
 299       {\r
 300         viewBoxesMenuItem_actionPerformed(e);\r
 301       }\r
 302     });\r
 303     viewTextMenuItem.setText("Text");\r
 304     viewTextMenuItem.setState(true);\r
 305     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 306     {\r
 307       public void actionPerformed(ActionEvent e)\r
 308       {\r
 309         viewTextMenuItem_actionPerformed(e);\r
 310       }\r
 311     });\r
 312     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 313     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 314     {\r
 315       public void actionPerformed(ActionEvent e)\r
 316       {\r
 317         sortPairwiseMenuItem_actionPerformed(e);\r
 318       }\r
 319     });\r
 320     sortIDMenuItem.setText("Sort by ID");\r
 321     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 322     {\r
 323       public void actionPerformed(ActionEvent e)\r
 324       {\r
 325         sortIDMenuItem_actionPerformed(e);\r
 326       }\r
 327     });\r
 328     sortGroupMenuItem.setText("Sort by group");\r
 329     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 330     {\r
 331       public void actionPerformed(ActionEvent e)\r
 332       {\r
 333         sortGroupMenuItem_actionPerformed(e);\r
 334       }\r
 335     });\r
 336     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 337     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 338     {\r
 339       public void actionPerformed(ActionEvent e)\r
 340       {\r
 341         sortTreeOrderMenuItem_actionPerformed(e);\r
 342       }\r
 343     });\r
 344     removeRedundancyMenuItem.setText("Remove redundancy");\r
 345     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 346     {\r
 347       public void actionPerformed(ActionEvent e)\r
 348       {\r
 349         removeRedundancyMenuItem_actionPerformed(e);\r
 350       }\r
 351     });\r
 352     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 353     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 354     {\r
 355       public void actionPerformed(ActionEvent e)\r
 356       {\r
 357         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 358       }\r
 359     });\r
 360     PCAMenuItem.setText("Principal component analysis");\r
 361     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 362     {\r
 363       public void actionPerformed(ActionEvent e)\r
 364       {\r
 365         PCAMenuItem_actionPerformed(e);\r
 366       }\r
 367     });\r
 368     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 369     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 370     {\r
 371       public void actionPerformed(ActionEvent e)\r
 372       {\r
 373         averageDistanceTreeMenuItem_actionPerformed(e);\r
 374       }\r
 375     });\r
 376     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 377     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 378     {\r
 379       public void actionPerformed(ActionEvent e)\r
 380       {\r
 381         neighbourTreeMenuItem_actionPerformed(e);\r
 382       }\r
 383     });\r
 384     clustalAlignMenuItem.setText("Clustal alignment");\r
 385     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 386     {\r
 387       public void actionPerformed(ActionEvent e)\r
 388       {\r
 389         clustalAlignMenuItem_actionPerformed(e);\r
 390       }\r
 391     });\r
 392     this.getContentPane().setLayout(borderLayout1);\r
 393     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 394     statusBar.setBackground(Color.white);\r
 395     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 396     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 397     statusBar.setText("Status bar");\r
 398     outputTextboxMenu.setMnemonic('T');\r
 399     outputTextboxMenu.setText("Output alignment via textbox");\r
 400     clustalColour.setEnabled(false);\r
 401     clustalColour.setSelected(false);\r
 402     clustalColour.setText("Clustalx colours");\r
 403     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         clustalColour_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     zappoColour.setSelected(true);\r
 411     zappoColour.setText("Zappo colour scheme");\r
 412     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 413     {\r
 414       public void actionPerformed(ActionEvent e)\r
 415       {\r
 416         zappoColour_actionPerformed(e);\r
 417       }\r
 418     });\r
 419     taylorColour.setText("Taylor colour scheme");\r
 420     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 421     {\r
 422       public void actionPerformed(ActionEvent e)\r
 423       {\r
 424         taylorColour_actionPerformed(e);\r
 425       }\r
 426     });\r
 427     hydrophobicityColour.setText("By hydrophobicity");\r
 428     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         hydrophobicityColour_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     helixColour.setText("Helix propensity");\r
 436     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 437     {\r
 438       public void actionPerformed(ActionEvent e)\r
 439       {\r
 440         helixColour_actionPerformed(e);\r
 441       }\r
 442     });\r
 443     strandColour.setText("Strand propensity");\r
 444     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         strandColour_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     turnColour.setText("Turn propensity");\r
 452     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 453     {\r
 454       public void actionPerformed(ActionEvent e)\r
 455       {\r
 456         turnColour_actionPerformed(e);\r
 457       }\r
 458     });\r
 459     buriedColour.setText("Buried index");\r
 460     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 461     {\r
 462       public void actionPerformed(ActionEvent e)\r
 463       {\r
 464         buriedColour_actionPerformed(e);\r
 465       }\r
 466     });\r
 467     abovePIDColour.setEnabled(false);\r
 468     abovePIDColour.setText("Above PID threshold only");\r
 469     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         abovePIDColour_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     userDefinedColour.setText("User defined colours");\r
 477     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         userDefinedColour_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     PIDColour.setEnabled(false);\r
 485     PIDColour.setText("By PID");\r
 486     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         PIDColour_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 494     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         BLOSUM62Colour_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 502     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         avTreeBlosumMenuItem_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 510     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         njTreeBlosumMenuItem_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     conservationColourIncMenuItem.setEnabled(false);\r
 518     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 519     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 520     {\r
 521       public void actionPerformed(ActionEvent e)\r
 522       {\r
 523         conservationColourIncMenuItem_actionPerformed(e);\r
 524       }\r
 525     });\r
 526     consensusGraphMenuItem.setActionCommand("");\r
 527     consensusGraphMenuItem.setText("Consensus graph");\r
 528     consensusGraphMenuItem.setState(true);\r
 529     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         consensusGraphMenuItem_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     colourTextMenuItem.setText("Colour text");\r
 537     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         colourTextMenuItem_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     htmlMenuItem.setText("Output as HTML");\r
 545     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         htmlMenuItem_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 553     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         schemeKeyMenuItem_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     overviewMenuItem.setText("Overview window");\r
 561     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         overviewMenuItem_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     undoMenuItem.setEnabled(false);\r
 569     undoMenuItem.setMnemonic('Z');\r
 570     undoMenuItem.setText("Undo");\r
 571     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 572     {\r
 573       public void actionPerformed(ActionEvent e)\r
 574       {\r
 575         undoMenuItem_actionPerformed(e);\r
 576       }\r
 577     });\r
 578     redoMenuItem.setEnabled(false);\r
 579     redoMenuItem.setMnemonic('0');\r
 580     redoMenuItem.setText("Redo");\r
 581     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 582     {\r
 583       public void actionPerformed(ActionEvent e)\r
 584       {\r
 585         redoMenuItem_actionPerformed(e);\r
 586       }\r
 587     });\r
 588     conservationMenuItem.setText("By conservation");\r
 589     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 590     {\r
 591       public void actionPerformed(ActionEvent e)\r
 592       {\r
 593         conservationMenuItem_actionPerformed(e);\r
 594       }\r
 595     });\r
 596     noColourmenuItem.setText("None");\r
 597     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 598     {\r
 599       public void actionPerformed(ActionEvent e)\r
 600       {\r
 601         noColourmenuItem_actionPerformed(e);\r
 602       }\r
 603     });\r
 604     wrapMenuItem.setEnabled(false);\r
 605     wrapMenuItem.setText("Wrap alignment");\r
 606     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 607     {\r
 608       public void actionPerformed(ActionEvent e)\r
 609       {\r
 610         wrapMenuItem_actionPerformed(e);\r
 611       }\r
 612     });\r
 613     pdbTest.setText("PDB Test Viewer");\r
 614     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 615     {\r
 616       public void actionPerformed(ActionEvent e)\r
 617       {\r
 618         pdbTest_actionPerformed(e);\r
 619       }\r
 620     });\r
 621     printMenuItem.setText("Print");\r
 622     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 623     {\r
 624       public void actionPerformed(ActionEvent e)\r
 625       {\r
 626         printMenuItem_actionPerformed(e);\r
 627       }\r
 628     });\r
 629     alignFrameMenuBar.add(fileMenu);\r
 630     alignFrameMenuBar.add(editMenu);\r
 631     alignFrameMenuBar.add(fontMenu);\r
 632     alignFrameMenuBar.add(viewMenu);\r
 633     alignFrameMenuBar.add(colourMenu);\r
 634     alignFrameMenuBar.add(calculateMenu);\r
 635     alignFrameMenuBar.add(alignMenu);\r
 636     fileMenu.add(saveAlignmentMenu);\r
 637     fileMenu.add(outputTextboxMenu);\r
 638     fileMenu.add(htmlMenuItem);\r
 639     fileMenu.add(printMenuItem);\r
 640     fileMenu.addSeparator();\r
 641     fileMenu.add(closeMenuItem);\r
 642     editMenu.add(undoMenuItem);\r
 643     editMenu.add(redoMenuItem);\r
 644     editMenu.addSeparator();\r
 645     editMenu.add(groupsMenuItem);\r
 646     editMenu.add(groupEditingMenuItem);\r
 647     editMenu.addSeparator();\r
 648     editMenu.add(selectAllSequenceMenuItem);\r
 649     editMenu.add(deselectAllSequenceMenuItem);\r
 650     editMenu.add(invertSequenceMenuItem);\r
 651     editMenu.addSeparator();\r
 652     editMenu.add(copySelectedMenuItem);\r
 653     editMenu.add(moveSelectedMenuItem);\r
 654     editMenu.add(deleteSelectedMenuItem);\r
 655     editMenu.addSeparator();\r
 656     editMenu.add(deselectAllColumnsMenuItem);\r
 657     editMenu.add(remove2LeftMenuItem);\r
 658     editMenu.add(remove2RightMenuItem);\r
 659     editMenu.addSeparator();\r
 660     editMenu.add(removeGappedColumnMenuItem);\r
 661     editMenu.add(removeAllGapsMenuItem);\r
 662     editMenu.add(setGapCharMenuItem);\r
 663     fontMenu.add(fontNameMenuItem);\r
 664     fontMenu.add(fontSizeMenuItem);\r
 665     fontMenu.add(fontStyleMenuItem);\r
 666     viewMenu.add(wrapMenuItem);\r
 667     viewMenu.add(viewBoxesMenuItem);\r
 668     viewMenu.add(viewTextMenuItem);\r
 669     viewMenu.add(colourTextMenuItem);\r
 670     viewMenu.add(consensusGraphMenuItem);\r
 671     viewMenu.add(overviewMenuItem);\r
 672     colourMenu.add(noColourmenuItem);\r
 673     colourMenu.add(clustalColour);\r
 674     colourMenu.add(zappoColour);\r
 675     colourMenu.add(taylorColour);\r
 676     colourMenu.add(hydrophobicityColour);\r
 677     colourMenu.add(helixColour);\r
 678     colourMenu.add(strandColour);\r
 679     colourMenu.add(turnColour);\r
 680     colourMenu.add(buriedColour);\r
 681     colourMenu.add(userDefinedColour);\r
 682     colourMenu.addSeparator();\r
 683     colourMenu.add(conservationMenuItem);\r
 684     colourMenu.add(conservationColourIncMenuItem);\r
 685     colourMenu.addSeparator();\r
 686     colourMenu.add(abovePIDColour);\r
 687     colourMenu.add(PIDColour);\r
 688     colourMenu.add(BLOSUM62Colour);\r
 689     colourMenu.addSeparator();\r
 690     colourMenu.add(schemeKeyMenuItem);\r
 691     calculateMenu.add(sortPairwiseMenuItem);\r
 692     calculateMenu.add(sortIDMenuItem);\r
 693     calculateMenu.add(sortGroupMenuItem);\r
 694     calculateMenu.add(sortTreeOrderMenuItem);\r
 695     calculateMenu.add(removeRedundancyMenuItem);\r
 696     calculateMenu.addSeparator();\r
 697     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 698     calculateMenu.add(PCAMenuItem);\r
 699     calculateMenu.addSeparator();\r
 700     calculateMenu.add(averageDistanceTreeMenuItem);\r
 701     calculateMenu.add(neighbourTreeMenuItem);\r
 702     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 703     calculateMenu.add(njTreeBlosumMenuItem);\r
 704     alignMenu.add(clustalAlignMenuItem);\r
 705     alignMenu.add(pdbTest);\r
 706     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 707   }\r
 708 \r
 709   protected void saveAs_actionPerformed(ActionEvent e)\r
 710   {\r
 711 \r
 712   }\r
 713 \r
 714   protected void outputText_actionPerformed(ActionEvent e)\r
 715   {\r
 716 \r
 717   }\r
 718 \r
 719   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 720   {\r
 721 \r
 722   }\r
 723 \r
 724 \r
 725 \r
 726 \r
 727 \r
 728   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730 \r
 731   }\r
 732 \r
 733   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 734   {\r
 735 \r
 736   }\r
 737 \r
 738   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 739   {\r
 740 \r
 741   }\r
 742 \r
 743 \r
 744   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 745   {\r
 746 \r
 747   }\r
 748 \r
 749   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 750   {\r
 751 \r
 752   }\r
 753 \r
 754   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 755   {\r
 756 \r
 757   }\r
 758 \r
 759   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 760   {\r
 761 \r
 762   }\r
 763 \r
 764   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766 \r
 767   }\r
 768 \r
 769   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771 \r
 772   }\r
 773 \r
 774   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781 \r
 782   }\r
 783 \r
 784   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786 \r
 787   }\r
 788 \r
 789   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 790   {\r
 791 \r
 792   }\r
 793 \r
 794   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 795   {\r
 796 \r
 797   }\r
 798 \r
 799   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 800   {\r
 801 \r
 802   }\r
 803 \r
 804   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 805   {\r
 806 \r
 807   }\r
 808 \r
 809   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 810   {\r
 811 \r
 812   }\r
 813 \r
 814 \r
 815   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 816   {\r
 817 \r
 818   }\r
 819 \r
 820   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 821   {\r
 822 \r
 823   }\r
 824 \r
 825   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 826   {\r
 827 \r
 828   }\r
 829 \r
 830   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 831   {\r
 832 \r
 833   }\r
 834 \r
 835 \r
 836   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 837   {\r
 838 \r
 839   }\r
 840 \r
 841   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 842   {\r
 843 \r
 844   }\r
 845 \r
 846 \r
 847   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849 \r
 850   }\r
 851 \r
 852 \r
 853 \r
 854   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 855   {\r
 856 \r
 857   }\r
 858 \r
 859   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 860   {\r
 861 \r
 862   }\r
 863 \r
 864   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 865   {\r
 866 \r
 867   }\r
 868 \r
 869   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871 \r
 872   }\r
 873 \r
 874   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 875   {\r
 876 \r
 877   }\r
 878 \r
 879   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 880   {\r
 881 \r
 882   }\r
 883 \r
 884   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886 \r
 887   }\r
 888 \r
 889   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 890   {\r
 891 \r
 892   }\r
 893 \r
 894   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 905   {\r
 906 \r
 907   }\r
 908 \r
 909 \r
 910   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913   }\r
 914 \r
 915   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917 \r
 918   }\r
 919 \r
 920 \r
 921 \r
 922   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 923   {\r
 924 \r
 925   }\r
 926 \r
 927 \r
 928 \r
 929 \r
 930   protected void clustalColour_actionPerformed(ActionEvent e)\r
 931   {\r
 932 \r
 933   }\r
 934 \r
 935   protected void zappoColour_actionPerformed(ActionEvent e)\r
 936   {\r
 937 \r
 938   }\r
 939 \r
 940   protected void taylorColour_actionPerformed(ActionEvent e)\r
 941   {\r
 942 \r
 943   }\r
 944 \r
 945 \r
 946   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 947   {\r
 948 \r
 949   }\r
 950 \r
 951   protected void helixColour_actionPerformed(ActionEvent e)\r
 952   {\r
 953 \r
 954   }\r
 955 \r
 956   protected void strandColour_actionPerformed(ActionEvent e)\r
 957   {\r
 958 \r
 959   }\r
 960 \r
 961   protected void turnColour_actionPerformed(ActionEvent e)\r
 962   {\r
 963 \r
 964   }\r
 965 \r
 966   protected void buriedColour_actionPerformed(ActionEvent e)\r
 967   {\r
 968 \r
 969   }\r
 970 \r
 971 \r
 972   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 973  {\r
 974 \r
 975  }\r
 976 \r
 977 \r
 978   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 979   {\r
 980 \r
 981   }\r
 982 \r
 983 \r
 984   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 985   {\r
 986 \r
 987   }\r
 988 \r
 989   protected void PIDColour_actionPerformed(ActionEvent e)\r
 990   {\r
 991 \r
 992   }\r
 993 \r
 994   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 995   {\r
 996 \r
 997   }\r
 998 \r
 999   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
1000   {\r
1001 \r
1002   }\r
1003 \r
1004   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1005   {\r
1006 \r
1007   }\r
1008 \r
1009   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1010   {\r
1011 \r
1012   }\r
1013 \r
1014   protected void pdbTest_actionPerformed(ActionEvent e)\r
1015   {\r
1016 \r
1017   }\r
1018 \r
1019   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1020   {\r
1021 \r
1022   }\r
1023 \r
1024 }\r