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   public GAlignFrame()\r
  83   {\r
  84     try\r
  85     {\r
  86       jbInit();\r
  87       setJMenuBar(alignFrameMenuBar);\r
  88 \r
  89       JMenuItem item;\r
  90       // dynamically fill save as menu with available formats\r
  91       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
  92         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
  93         saveAlignmentMenu.add( item );\r
  94         item.addActionListener(new java.awt.event.ActionListener()\r
  95         {\r
  96           public void actionPerformed(ActionEvent e)\r
  97           {\r
  98             saveAs_actionPerformed(e);\r
  99           }\r
 100         });\r
 101 \r
 102         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 103         item.addActionListener(new java.awt.event.ActionListener()\r
 104         {\r
 105           public void actionPerformed(ActionEvent e)\r
 106           {\r
 107             outputText_actionPerformed(e);\r
 108           }\r
 109         });\r
 110 \r
 111         outputTextboxMenu.add( item );\r
 112       }\r
 113 \r
 114     }\r
 115     catch(Exception e)\r
 116     {\r
 117       e.printStackTrace();\r
 118     }\r
 119 \r
 120     ButtonGroup colours = new ButtonGroup();\r
 121     colours.add(clustalColour);\r
 122     colours.add(zappoColour);\r
 123     colours.add(taylorColour);\r
 124     colours.add(hydrophobicityColour);\r
 125     colours.add(helixColour);\r
 126     colours.add(strandColour);\r
 127     colours.add(turnColour);\r
 128     colours.add(buriedColour);\r
 129     colours.add(conservationColour);\r
 130     colours.add(abovePIDColour);\r
 131     colours.add(userDefinedColour);\r
 132     colours.add(PIDColour);\r
 133     colours.add(BLOSUM62Colour);\r
 134   }\r
 135   private void jbInit() throws Exception\r
 136   {\r
 137     fileMenu.setMnemonic('F');\r
 138     fileMenu.setText("File");\r
 139     saveAlignmentMenu.setMnemonic('L');\r
 140     saveAlignmentMenu.setText("Save alignment to local file");\r
 141     saveAsPostscriptMenuItem.setMnemonic('P');\r
 142     saveAsPostscriptMenuItem.setText("Save alignment as postscript");\r
 143     saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 144     {\r
 145       public void actionPerformed(ActionEvent e)\r
 146       {\r
 147         saveAsPostscriptMenuItem_actionPerformed(e);\r
 148       }\r
 149     });\r
 150     closeMenuItem.setMnemonic('C');\r
 151     closeMenuItem.setText("Close");\r
 152     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 153     {\r
 154       public void actionPerformed(ActionEvent e)\r
 155       {\r
 156         closeMenuItem_actionPerformed(e);\r
 157       }\r
 158     });\r
 159     editMenu.setText("Edit");\r
 160     fontMenu.setText("Font");\r
 161     viewMenu.setText("View");\r
 162     colourMenu.setText("Colour");\r
 163     calculateMenu.setText("Calculate");\r
 164     alignMenu.setText("Web Service");\r
 165     groupsMenuItem.setEnabled(false);\r
 166     groupsMenuItem.setText("Groups");\r
 167     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 168     {\r
 169       public void actionPerformed(ActionEvent e)\r
 170       {\r
 171         groupsMenuItem_actionPerformed(e);\r
 172       }\r
 173     });\r
 174     groupEditingMenuItem.setEnabled(false);\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("Deselect all sequences");\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.setSelected(false);\r
 409     clustalColour.setText("Clustalx colours");\r
 410     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 411     {\r
 412       public void actionPerformed(ActionEvent e)\r
 413       {\r
 414         clustalColour_actionPerformed(e);\r
 415       }\r
 416     });\r
 417     zappoColour.setSelected(true);\r
 418     zappoColour.setText("Zappo colour scheme");\r
 419     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 420     {\r
 421       public void actionPerformed(ActionEvent e)\r
 422       {\r
 423         zappoColour_actionPerformed(e);\r
 424       }\r
 425     });\r
 426     taylorColour.setText("Taylor colour scheme");\r
 427     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 428     {\r
 429       public void actionPerformed(ActionEvent e)\r
 430       {\r
 431         taylorColour_actionPerformed(e);\r
 432       }\r
 433     });\r
 434     hydrophobicityColour.setText("By hydrophobicity");\r
 435     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         hydrophobicityColour_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     helixColour.setText("Helix propensity");\r
 443     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 444     {\r
 445       public void actionPerformed(ActionEvent e)\r
 446       {\r
 447         helixColour_actionPerformed(e);\r
 448       }\r
 449     });\r
 450     strandColour.setText("Strand propensity");\r
 451     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 452     {\r
 453       public void actionPerformed(ActionEvent e)\r
 454       {\r
 455         strandColour_actionPerformed(e);\r
 456       }\r
 457     });\r
 458     turnColour.setText("Turn propensity");\r
 459     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 460     {\r
 461       public void actionPerformed(ActionEvent e)\r
 462       {\r
 463         turnColour_actionPerformed(e);\r
 464       }\r
 465     });\r
 466     buriedColour.setText("Buried index");\r
 467     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 468     {\r
 469       public void actionPerformed(ActionEvent e)\r
 470       {\r
 471         buriedColour_actionPerformed(e);\r
 472       }\r
 473     });\r
 474     conservationColour.setEnabled(false);\r
 475     conservationColour.setText("By conservation");\r
 476     conservationColour.addActionListener(new java.awt.event.ActionListener()\r
 477     {\r
 478       public void actionPerformed(ActionEvent e)\r
 479       {\r
 480         conservationColour_actionPerformed(e);\r
 481       }\r
 482     });\r
 483     abovePIDColour.setEnabled(false);\r
 484     abovePIDColour.setText("Above PID threshold only");\r
 485     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         abovePIDColour_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     userDefinedColour.setText("User defined colours");\r
 493     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         userDefinedColour_actionPerformed(e);\r
 498       }\r
 499     });\r
 500     PIDColour.setEnabled(false);\r
 501     PIDColour.setText("By PID");\r
 502     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         PIDColour_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 510     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         BLOSUM62Colour_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 518     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         avTreeBlosumMenuItem_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 526     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 527     {\r
 528       public void actionPerformed(ActionEvent e)\r
 529       {\r
 530         njTreeBlosumMenuItem_actionPerformed(e);\r
 531       }\r
 532     });\r
 533     conservationColourIncMenuItem.setEnabled(false);\r
 534     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 535     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 536     {\r
 537       public void actionPerformed(ActionEvent e)\r
 538       {\r
 539         conservationColourIncMenuItem_actionPerformed(e);\r
 540       }\r
 541     });\r
 542     consensusGraphMenuItem.setActionCommand("");\r
 543     consensusGraphMenuItem.setText("Consensus graph");\r
 544     consensusGraphMenuItem.setState(true);\r
 545     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         consensusGraphMenuItem_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     colourTextMenuItem.setText("Colour text");\r
 553     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         colourTextMenuItem_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     htmlMenuItem.setText("Output as HTML");\r
 561     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         htmlMenuItem_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 569     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         schemeKeyMenuItem_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     alignFrameMenuBar.add(fileMenu);\r
 577     alignFrameMenuBar.add(editMenu);\r
 578     alignFrameMenuBar.add(fontMenu);\r
 579     alignFrameMenuBar.add(viewMenu);\r
 580     alignFrameMenuBar.add(colourMenu);\r
 581     alignFrameMenuBar.add(calculateMenu);\r
 582     alignFrameMenuBar.add(alignMenu);\r
 583     fileMenu.add(saveAlignmentMenu);\r
 584     fileMenu.add(saveAsPostscriptMenuItem);\r
 585     fileMenu.add(outputTextboxMenu);\r
 586     fileMenu.add(htmlMenuItem);\r
 587     fileMenu.addSeparator();\r
 588     fileMenu.add(closeMenuItem);\r
 589     editMenu.add(groupsMenuItem);\r
 590     editMenu.add(groupEditingMenuItem);\r
 591     editMenu.addSeparator();\r
 592     editMenu.add(selectAllSequenceMenuItem);\r
 593     editMenu.add(deselectAllSequenceMenuItem);\r
 594     editMenu.add(invertSequenceMenuItem);\r
 595     editMenu.addSeparator();\r
 596     editMenu.add(deleteSelectedMenuItem);\r
 597     editMenu.add(moveSelectedMenuItem);\r
 598     editMenu.add(copySelectedMenuItem);\r
 599     editMenu.addSeparator();\r
 600     editMenu.add(deselectAllColumnsMenuItem);\r
 601     editMenu.add(remove2LeftMenuItem);\r
 602     editMenu.add(remove2RightMenuItem);\r
 603     editMenu.addSeparator();\r
 604     editMenu.add(removeGappedColumnMenuItem);\r
 605     editMenu.add(removeAllGapsMenuItem);\r
 606     editMenu.add(setGapCharMenuItem);\r
 607     fontMenu.add(fontNameMenuItem);\r
 608     fontMenu.add(fontSizeMenuItem);\r
 609     fontMenu.add(fontStyleMenuItem);\r
 610     fontMenu.addSeparator();\r
 611     fontMenu.add(colourTextMenuItem);\r
 612     viewMenu.add(viewBoxesMenuItem);\r
 613     viewMenu.add(viewTextMenuItem);\r
 614     viewMenu.add(consensusGraphMenuItem);\r
 615     colourMenu.add(clustalColour);\r
 616     colourMenu.add(zappoColour);\r
 617     colourMenu.add(taylorColour);\r
 618     colourMenu.add(hydrophobicityColour);\r
 619     colourMenu.add(helixColour);\r
 620     colourMenu.add(strandColour);\r
 621     colourMenu.add(turnColour);\r
 622     colourMenu.add(buriedColour);\r
 623     colourMenu.add(userDefinedColour);\r
 624     colourMenu.addSeparator();\r
 625     colourMenu.add(conservationColour);\r
 626     colourMenu.add(conservationColourIncMenuItem);\r
 627     colourMenu.addSeparator();\r
 628     colourMenu.add(abovePIDColour);\r
 629     colourMenu.add(PIDColour);\r
 630     colourMenu.add(BLOSUM62Colour);\r
 631     colourMenu.addSeparator();\r
 632     colourMenu.add(schemeKeyMenuItem);\r
 633     calculateMenu.add(sortPairwiseMenuItem);\r
 634     calculateMenu.add(sortIDMenuItem);\r
 635     calculateMenu.add(sortGroupMenuItem);\r
 636     calculateMenu.add(sortTreeOrderMenuItem);\r
 637     calculateMenu.add(removeRedundancyMenuItem);\r
 638     calculateMenu.addSeparator();\r
 639     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 640     calculateMenu.add(PCAMenuItem);\r
 641     calculateMenu.addSeparator();\r
 642     calculateMenu.add(averageDistanceTreeMenuItem);\r
 643     calculateMenu.add(neighbourTreeMenuItem);\r
 644     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 645     calculateMenu.add(njTreeBlosumMenuItem);\r
 646     alignMenu.add(clustalAlignMenuItem);\r
 647     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 648   }\r
 649 \r
 650   protected void saveAs_actionPerformed(ActionEvent e)\r
 651   {\r
 652 \r
 653   }\r
 654 \r
 655   protected void outputText_actionPerformed(ActionEvent e)\r
 656   {\r
 657 \r
 658   }\r
 659 \r
 660   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 661   {\r
 662 \r
 663   }\r
 664 \r
 665 \r
 666 \r
 667   protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)\r
 668   {\r
 669 \r
 670   }\r
 671 \r
 672 \r
 673   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 674   {\r
 675 \r
 676   }\r
 677 \r
 678   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 679   {\r
 680 \r
 681   }\r
 682 \r
 683   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 684   {\r
 685 \r
 686   }\r
 687 \r
 688   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 689   {\r
 690 \r
 691   }\r
 692 \r
 693   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 694   {\r
 695 \r
 696   }\r
 697 \r
 698   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 699   {\r
 700 \r
 701   }\r
 702 \r
 703   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 704   {\r
 705 \r
 706   }\r
 707 \r
 708   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 709   {\r
 710 \r
 711   }\r
 712 \r
 713   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 714   {\r
 715 \r
 716   }\r
 717 \r
 718   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 719   {\r
 720 \r
 721   }\r
 722 \r
 723   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 724   {\r
 725 \r
 726   }\r
 727 \r
 728   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730 \r
 731   }\r
 732 \r
 733   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 734   {\r
 735 \r
 736   }\r
 737 \r
 738   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 739   {\r
 740 \r
 741   }\r
 742 \r
 743   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 744   {\r
 745 \r
 746   }\r
 747 \r
 748 \r
 749   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 750   {\r
 751 \r
 752   }\r
 753 \r
 754   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 755   {\r
 756 \r
 757   }\r
 758 \r
 759   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 760   {\r
 761 \r
 762   }\r
 763 \r
 764   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766 \r
 767   }\r
 768 \r
 769   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771 \r
 772   }\r
 773 \r
 774   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779 \r
 780 \r
 781   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 782   {\r
 783 \r
 784   }\r
 785 \r
 786 \r
 787 \r
 788 \r
 789 \r
 790 \r
 791   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793 \r
 794   }\r
 795 \r
 796   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798 \r
 799   }\r
 800 \r
 801   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 802   {\r
 803 \r
 804   }\r
 805 \r
 806   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 807   {\r
 808 \r
 809   }\r
 810 \r
 811   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 812   {\r
 813 \r
 814   }\r
 815 \r
 816   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 817   {\r
 818 \r
 819   }\r
 820 \r
 821   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 822   {\r
 823 \r
 824   }\r
 825 \r
 826   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 827   {\r
 828 \r
 829   }\r
 830 \r
 831   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 832   {\r
 833 \r
 834   }\r
 835 \r
 836 \r
 837   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 838   {\r
 839 \r
 840   }\r
 841 \r
 842   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844 \r
 845   }\r
 846 \r
 847 \r
 848 \r
 849   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 850   {\r
 851 \r
 852   }\r
 853 \r
 854 \r
 855 \r
 856 \r
 857   protected void clustalColour_actionPerformed(ActionEvent e)\r
 858   {\r
 859 \r
 860   }\r
 861 \r
 862   protected void zappoColour_actionPerformed(ActionEvent e)\r
 863   {\r
 864 \r
 865   }\r
 866 \r
 867   protected void taylorColour_actionPerformed(ActionEvent e)\r
 868   {\r
 869 \r
 870   }\r
 871 \r
 872 \r
 873   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 874   {\r
 875 \r
 876   }\r
 877 \r
 878   protected void helixColour_actionPerformed(ActionEvent e)\r
 879   {\r
 880 \r
 881   }\r
 882 \r
 883   protected void strandColour_actionPerformed(ActionEvent e)\r
 884   {\r
 885 \r
 886   }\r
 887 \r
 888   protected void turnColour_actionPerformed(ActionEvent e)\r
 889   {\r
 890 \r
 891   }\r
 892 \r
 893   protected void buriedColour_actionPerformed(ActionEvent e)\r
 894   {\r
 895 \r
 896   }\r
 897 \r
 898   protected void conservationColour_actionPerformed(ActionEvent e)\r
 899   {\r
 900 \r
 901   }\r
 902 \r
 903   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 904  {\r
 905 \r
 906  }\r
 907 \r
 908 \r
 909   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912   }\r
 913 \r
 914 \r
 915   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 916   {\r
 917 \r
 918   }\r
 919 \r
 920   protected void PIDColour_actionPerformed(ActionEvent e)\r
 921   {\r
 922 \r
 923   }\r
 924 \r
 925   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 926   {\r
 927 \r
 928   }\r
 929 \r
 930   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932 \r
 933   }\r
 934 \r
 935 }\r