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