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   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   public GAlignFrame()\r
  89   {\r
  90     try\r
  91     {\r
  92       jbInit();\r
  93       setJMenuBar(alignFrameMenuBar);\r
  94 \r
  95       JMenuItem item;\r
  96       // dynamically fill save as menu with available formats\r
  97       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
  98         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
  99         saveAlignmentMenu.add( item );\r
 100         item.addActionListener(new java.awt.event.ActionListener()\r
 101         {\r
 102           public void actionPerformed(ActionEvent e)\r
 103           {\r
 104             saveAs_actionPerformed(e);\r
 105           }\r
 106         });\r
 107 \r
 108         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 109         item.addActionListener(new java.awt.event.ActionListener()\r
 110         {\r
 111           public void actionPerformed(ActionEvent e)\r
 112           {\r
 113             outputText_actionPerformed(e);\r
 114           }\r
 115         });\r
 116 \r
 117         outputTextboxMenu.add( item );\r
 118       }\r
 119 \r
 120     }\r
 121     catch(Exception e)\r
 122     {\r
 123       e.printStackTrace();\r
 124     }\r
 125 \r
 126     ButtonGroup colours = new ButtonGroup();\r
 127     colours.add(clustalColour);\r
 128     colours.add(zappoColour);\r
 129     colours.add(taylorColour);\r
 130     colours.add(hydrophobicityColour);\r
 131     colours.add(helixColour);\r
 132     colours.add(strandColour);\r
 133     colours.add(turnColour);\r
 134     colours.add(buriedColour);\r
 135     colours.add(abovePIDColour);\r
 136     colours.add(userDefinedColour);\r
 137     colours.add(PIDColour);\r
 138     colours.add(BLOSUM62Colour);\r
 139   }\r
 140   private void jbInit() throws Exception\r
 141   {\r
 142     fileMenu.setMnemonic('F');\r
 143     fileMenu.setText("File");\r
 144     saveAlignmentMenu.setMnemonic('L');\r
 145     saveAlignmentMenu.setText("Save alignment to local file");\r
 146     closeMenuItem.setMnemonic('C');\r
 147     closeMenuItem.setText("Close");\r
 148     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 149     {\r
 150       public void actionPerformed(ActionEvent e)\r
 151       {\r
 152         closeMenuItem_actionPerformed(e);\r
 153       }\r
 154     });\r
 155     editMenu.setText("Edit");\r
 156     fontMenu.setText("Font");\r
 157     viewMenu.setText("View");\r
 158     colourMenu.setText("Colour");\r
 159     calculateMenu.setText("Calculate");\r
 160     alignMenu.setText("Web Service");\r
 161     groupsMenuItem.setText("Groups");\r
 162     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 163     {\r
 164       public void actionPerformed(ActionEvent e)\r
 165       {\r
 166         groupsMenuItem_actionPerformed(e);\r
 167       }\r
 168     });\r
 169     groupEditingMenuItem.setText("Group editing mode");\r
 170     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 171     {\r
 172       public void actionPerformed(ActionEvent e)\r
 173       {\r
 174         groupEditingMenuItem_actionPerformed(e);\r
 175       }\r
 176     });\r
 177     selectAllSequenceMenuItem.setText("Select all sequences");\r
 178     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 179     {\r
 180       public void actionPerformed(ActionEvent e)\r
 181       {\r
 182         selectAllSequenceMenuItem_actionPerformed(e);\r
 183       }\r
 184     });\r
 185     deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
 186     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         deselectAllSequenceMenuItem_actionPerformed(e);\r
 191       }\r
 192     });\r
 193     invertSequenceMenuItem.setText("Invert sequence selection");\r
 194     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 195     {\r
 196       public void actionPerformed(ActionEvent e)\r
 197       {\r
 198         invertSequenceMenuItem_actionPerformed(e);\r
 199       }\r
 200     });\r
 201     deleteSelectedMenuItem.setText("Delete selected sequences");\r
 202     deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 203     {\r
 204       public void actionPerformed(ActionEvent e)\r
 205       {\r
 206         deleteSelectedMenuItem_actionPerformed(e);\r
 207       }\r
 208     });\r
 209     moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
 210     moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 211     {\r
 212       public void actionPerformed(ActionEvent e)\r
 213       {\r
 214         moveSelectedMenuItem_actionPerformed(e);\r
 215       }\r
 216     });\r
 217     copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
 218     copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 219     {\r
 220       public void actionPerformed(ActionEvent e)\r
 221       {\r
 222         copySelectedMenuItem_actionPerformed(e);\r
 223       }\r
 224     });\r
 225     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 226     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 227     {\r
 228       public void actionPerformed(ActionEvent e)\r
 229       {\r
 230         deselectAllColumnsMenuItem_actionPerformed(e);\r
 231       }\r
 232     });\r
 233     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 234     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 235     {\r
 236       public void actionPerformed(ActionEvent e)\r
 237       {\r
 238         remove2LeftMenuItem_actionPerformed(e);\r
 239       }\r
 240     });\r
 241     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 242     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 243     {\r
 244       public void actionPerformed(ActionEvent e)\r
 245       {\r
 246         remove2RightMenuItem_actionPerformed(e);\r
 247       }\r
 248     });\r
 249     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 250     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 251     {\r
 252       public void actionPerformed(ActionEvent e)\r
 253       {\r
 254         removeGappedColumnMenuItem_actionPerformed(e);\r
 255       }\r
 256     });\r
 257     removeAllGapsMenuItem.setText("Remove all gaps");\r
 258     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 259     {\r
 260       public void actionPerformed(ActionEvent e)\r
 261       {\r
 262         removeAllGapsMenuItem_actionPerformed(e);\r
 263       }\r
 264     });\r
 265     setGapCharMenuItem.setText("Set gap character to \"-\"");\r
 266     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 267     {\r
 268       public void actionPerformed(ActionEvent e)\r
 269       {\r
 270         setGapCharMenuItem_actionPerformed(e);\r
 271       }\r
 272     });\r
 273     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 274     {\r
 275       public void actionPerformed(ActionEvent e)\r
 276       {\r
 277         fontNameMenuItem_actionPerformed(e);\r
 278       }\r
 279     });\r
 280     fontSizeMenuItem.setText("10");\r
 281     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 282     {\r
 283       public void actionPerformed(ActionEvent e)\r
 284       {\r
 285         fontSizeMenuItem_actionPerformed(e);\r
 286       }\r
 287     });\r
 288     fontStyleMenuItem.setText("Plain");\r
 289     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 290     {\r
 291       public void actionPerformed(ActionEvent e)\r
 292       {\r
 293         fontStyleMenuItem_actionPerformed(e);\r
 294       }\r
 295     });\r
 296     viewBoxesMenuItem.setText("Boxes");\r
 297     viewBoxesMenuItem.setState(true);\r
 298     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 299     {\r
 300       public void actionPerformed(ActionEvent e)\r
 301       {\r
 302         viewBoxesMenuItem_actionPerformed(e);\r
 303       }\r
 304     });\r
 305     viewTextMenuItem.setText("Text");\r
 306     viewTextMenuItem.setState(true);\r
 307     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 308     {\r
 309       public void actionPerformed(ActionEvent e)\r
 310       {\r
 311         viewTextMenuItem_actionPerformed(e);\r
 312       }\r
 313     });\r
 314     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 315     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         sortPairwiseMenuItem_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     sortIDMenuItem.setText("Sort by ID");\r
 323     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 324     {\r
 325       public void actionPerformed(ActionEvent e)\r
 326       {\r
 327         sortIDMenuItem_actionPerformed(e);\r
 328       }\r
 329     });\r
 330     sortGroupMenuItem.setText("Sort by group");\r
 331     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 332     {\r
 333       public void actionPerformed(ActionEvent e)\r
 334       {\r
 335         sortGroupMenuItem_actionPerformed(e);\r
 336       }\r
 337     });\r
 338     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 339     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 340     {\r
 341       public void actionPerformed(ActionEvent e)\r
 342       {\r
 343         sortTreeOrderMenuItem_actionPerformed(e);\r
 344       }\r
 345     });\r
 346     removeRedundancyMenuItem.setText("Remove redundancy");\r
 347     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 348     {\r
 349       public void actionPerformed(ActionEvent e)\r
 350       {\r
 351         removeRedundancyMenuItem_actionPerformed(e);\r
 352       }\r
 353     });\r
 354     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 355     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 356     {\r
 357       public void actionPerformed(ActionEvent e)\r
 358       {\r
 359         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 360       }\r
 361     });\r
 362     PCAMenuItem.setText("Principal component analysis");\r
 363     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 364     {\r
 365       public void actionPerformed(ActionEvent e)\r
 366       {\r
 367         PCAMenuItem_actionPerformed(e);\r
 368       }\r
 369     });\r
 370     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 371     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 372     {\r
 373       public void actionPerformed(ActionEvent e)\r
 374       {\r
 375         averageDistanceTreeMenuItem_actionPerformed(e);\r
 376       }\r
 377     });\r
 378     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 379     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         neighbourTreeMenuItem_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     clustalAlignMenuItem.setText("Clustal alignment");\r
 387     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         clustalAlignMenuItem_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     this.getContentPane().setLayout(borderLayout1);\r
 395     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 396     statusBar.setBackground(Color.white);\r
 397     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 398     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 399     statusBar.setText("Status bar");\r
 400     outputTextboxMenu.setMnemonic('T');\r
 401     outputTextboxMenu.setText("Output alignment via textbox");\r
 402     clustalColour.setEnabled(false);\r
 403     clustalColour.setSelected(false);\r
 404     clustalColour.setText("Clustalx colours");\r
 405     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 406     {\r
 407       public void actionPerformed(ActionEvent e)\r
 408       {\r
 409         clustalColour_actionPerformed(e);\r
 410       }\r
 411     });\r
 412     zappoColour.setSelected(true);\r
 413     zappoColour.setText("Zappo colour scheme");\r
 414     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 415     {\r
 416       public void actionPerformed(ActionEvent e)\r
 417       {\r
 418         zappoColour_actionPerformed(e);\r
 419       }\r
 420     });\r
 421     taylorColour.setText("Taylor colour scheme");\r
 422     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 423     {\r
 424       public void actionPerformed(ActionEvent e)\r
 425       {\r
 426         taylorColour_actionPerformed(e);\r
 427       }\r
 428     });\r
 429     hydrophobicityColour.setText("By hydrophobicity");\r
 430     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 431     {\r
 432       public void actionPerformed(ActionEvent e)\r
 433       {\r
 434         hydrophobicityColour_actionPerformed(e);\r
 435       }\r
 436     });\r
 437     helixColour.setText("Helix propensity");\r
 438     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 439     {\r
 440       public void actionPerformed(ActionEvent e)\r
 441       {\r
 442         helixColour_actionPerformed(e);\r
 443       }\r
 444     });\r
 445     strandColour.setText("Strand propensity");\r
 446     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 447     {\r
 448       public void actionPerformed(ActionEvent e)\r
 449       {\r
 450         strandColour_actionPerformed(e);\r
 451       }\r
 452     });\r
 453     turnColour.setText("Turn propensity");\r
 454     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 455     {\r
 456       public void actionPerformed(ActionEvent e)\r
 457       {\r
 458         turnColour_actionPerformed(e);\r
 459       }\r
 460     });\r
 461     buriedColour.setText("Buried index");\r
 462     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         buriedColour_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     abovePIDColour.setEnabled(false);\r
 470     abovePIDColour.setText("Above PID threshold only");\r
 471     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 472     {\r
 473       public void actionPerformed(ActionEvent e)\r
 474       {\r
 475         abovePIDColour_actionPerformed(e);\r
 476       }\r
 477     });\r
 478     userDefinedColour.setText("User defined colours");\r
 479     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 480     {\r
 481       public void actionPerformed(ActionEvent e)\r
 482       {\r
 483         userDefinedColour_actionPerformed(e);\r
 484       }\r
 485     });\r
 486     PIDColour.setEnabled(false);\r
 487     PIDColour.setText("By PID");\r
 488     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 489     {\r
 490       public void actionPerformed(ActionEvent e)\r
 491       {\r
 492         PIDColour_actionPerformed(e);\r
 493       }\r
 494     });\r
 495     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 496     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 497     {\r
 498       public void actionPerformed(ActionEvent e)\r
 499       {\r
 500         BLOSUM62Colour_actionPerformed(e);\r
 501       }\r
 502     });\r
 503     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 504     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 505     {\r
 506       public void actionPerformed(ActionEvent e)\r
 507       {\r
 508         avTreeBlosumMenuItem_actionPerformed(e);\r
 509       }\r
 510     });\r
 511     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 512     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 513     {\r
 514       public void actionPerformed(ActionEvent e)\r
 515       {\r
 516         njTreeBlosumMenuItem_actionPerformed(e);\r
 517       }\r
 518     });\r
 519     conservationColourIncMenuItem.setEnabled(false);\r
 520     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 521     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         conservationColourIncMenuItem_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     consensusGraphMenuItem.setActionCommand("");\r
 529     consensusGraphMenuItem.setText("Consensus graph");\r
 530     consensusGraphMenuItem.setState(true);\r
 531     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 532     {\r
 533       public void actionPerformed(ActionEvent e)\r
 534       {\r
 535         consensusGraphMenuItem_actionPerformed(e);\r
 536       }\r
 537     });\r
 538     colourTextMenuItem.setText("Colour text");\r
 539     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 540     {\r
 541       public void actionPerformed(ActionEvent e)\r
 542       {\r
 543         colourTextMenuItem_actionPerformed(e);\r
 544       }\r
 545     });\r
 546     htmlMenuItem.setText("Output as HTML");\r
 547     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 548     {\r
 549       public void actionPerformed(ActionEvent e)\r
 550       {\r
 551         htmlMenuItem_actionPerformed(e);\r
 552       }\r
 553     });\r
 554     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 555     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 556     {\r
 557       public void actionPerformed(ActionEvent e)\r
 558       {\r
 559         schemeKeyMenuItem_actionPerformed(e);\r
 560       }\r
 561     });\r
 562     overviewMenuItem.setText("Overview window");\r
 563     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 564     {\r
 565       public void actionPerformed(ActionEvent e)\r
 566       {\r
 567         overviewMenuItem_actionPerformed(e);\r
 568       }\r
 569     });\r
 570     undoMenuItem.setEnabled(false);\r
 571     undoMenuItem.setMnemonic('Z');\r
 572     undoMenuItem.setText("Undo");\r
 573     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 574     {\r
 575       public void actionPerformed(ActionEvent e)\r
 576       {\r
 577         undoMenuItem_actionPerformed(e);\r
 578       }\r
 579     });\r
 580     redoMenuItem.setEnabled(false);\r
 581     redoMenuItem.setMnemonic('0');\r
 582     redoMenuItem.setText("Redo");\r
 583     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 584     {\r
 585       public void actionPerformed(ActionEvent e)\r
 586       {\r
 587         redoMenuItem_actionPerformed(e);\r
 588       }\r
 589     });\r
 590     conservationMenuItem.setText("By conservation");\r
 591     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 592     {\r
 593       public void actionPerformed(ActionEvent e)\r
 594       {\r
 595         conservationMenuItem_actionPerformed(e);\r
 596       }\r
 597     });\r
 598     noColourmenuItem.setText("None");\r
 599     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 600     {\r
 601       public void actionPerformed(ActionEvent e)\r
 602       {\r
 603         noColourmenuItem_actionPerformed(e);\r
 604       }\r
 605     });\r
 606     wrapMenuItem.setEnabled(false);\r
 607     wrapMenuItem.setText("Wrap alignment");\r
 608     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 609     {\r
 610       public void actionPerformed(ActionEvent e)\r
 611       {\r
 612         wrapMenuItem_actionPerformed(e);\r
 613       }\r
 614     });\r
 615     pdbTest.setText("PDB Test Viewer");\r
 616     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 617     {\r
 618       public void actionPerformed(ActionEvent e)\r
 619       {\r
 620         pdbTest_actionPerformed(e);\r
 621       }\r
 622     });\r
 623     printMenuItem.setText("Print");\r
 624     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 625     {\r
 626       public void actionPerformed(ActionEvent e)\r
 627       {\r
 628         printMenuItem_actionPerformed(e);\r
 629       }\r
 630     });\r
 631     renderGapsMenuItem.setText("Render gaps");\r
 632     renderGapsMenuItem.setState(true);\r
 633     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 634     {\r
 635       public void actionPerformed(ActionEvent e)\r
 636       {\r
 637         renderGapsMenuItem_actionPerformed(e);\r
 638       }\r
 639     });\r
 640     findMenuItem.setText("Find");\r
 641     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 642     {\r
 643       public void actionPerformed(ActionEvent e)\r
 644       {\r
 645         findMenuItem_actionPerformed(e);\r
 646       }\r
 647     });\r
 648     alignFrameMenuBar.add(fileMenu);\r
 649     alignFrameMenuBar.add(editMenu);\r
 650     alignFrameMenuBar.add(fontMenu);\r
 651     alignFrameMenuBar.add(viewMenu);\r
 652     alignFrameMenuBar.add(colourMenu);\r
 653     alignFrameMenuBar.add(calculateMenu);\r
 654     alignFrameMenuBar.add(alignMenu);\r
 655     fileMenu.add(saveAlignmentMenu);\r
 656     fileMenu.add(outputTextboxMenu);\r
 657     fileMenu.add(htmlMenuItem);\r
 658     fileMenu.add(printMenuItem);\r
 659     fileMenu.addSeparator();\r
 660     fileMenu.add(closeMenuItem);\r
 661     editMenu.add(undoMenuItem);\r
 662     editMenu.add(redoMenuItem);\r
 663     editMenu.addSeparator();\r
 664     editMenu.add(groupsMenuItem);\r
 665     editMenu.add(groupEditingMenuItem);\r
 666     editMenu.addSeparator();\r
 667     editMenu.add(selectAllSequenceMenuItem);\r
 668     editMenu.add(deselectAllSequenceMenuItem);\r
 669     editMenu.add(invertSequenceMenuItem);\r
 670     editMenu.addSeparator();\r
 671     editMenu.add(copySelectedMenuItem);\r
 672     editMenu.add(moveSelectedMenuItem);\r
 673     editMenu.add(deleteSelectedMenuItem);\r
 674     editMenu.addSeparator();\r
 675     editMenu.add(deselectAllColumnsMenuItem);\r
 676     editMenu.add(remove2LeftMenuItem);\r
 677     editMenu.add(remove2RightMenuItem);\r
 678     editMenu.addSeparator();\r
 679     editMenu.add(removeGappedColumnMenuItem);\r
 680     editMenu.add(removeAllGapsMenuItem);\r
 681     editMenu.add(setGapCharMenuItem);\r
 682     editMenu.addSeparator();\r
 683     editMenu.add(findMenuItem);\r
 684     fontMenu.add(fontNameMenuItem);\r
 685     fontMenu.add(fontSizeMenuItem);\r
 686     fontMenu.add(fontStyleMenuItem);\r
 687     viewMenu.add(wrapMenuItem);\r
 688     viewMenu.add(viewBoxesMenuItem);\r
 689     viewMenu.add(viewTextMenuItem);\r
 690     viewMenu.add(colourTextMenuItem);\r
 691     viewMenu.add(renderGapsMenuItem);\r
 692     viewMenu.add(consensusGraphMenuItem);\r
 693     viewMenu.add(overviewMenuItem);\r
 694     colourMenu.add(noColourmenuItem);\r
 695     colourMenu.add(clustalColour);\r
 696     colourMenu.add(zappoColour);\r
 697     colourMenu.add(taylorColour);\r
 698     colourMenu.add(hydrophobicityColour);\r
 699     colourMenu.add(helixColour);\r
 700     colourMenu.add(strandColour);\r
 701     colourMenu.add(turnColour);\r
 702     colourMenu.add(buriedColour);\r
 703     colourMenu.add(userDefinedColour);\r
 704     colourMenu.addSeparator();\r
 705     colourMenu.add(conservationMenuItem);\r
 706     colourMenu.add(conservationColourIncMenuItem);\r
 707     colourMenu.addSeparator();\r
 708     colourMenu.add(abovePIDColour);\r
 709     colourMenu.add(PIDColour);\r
 710     colourMenu.add(BLOSUM62Colour);\r
 711     colourMenu.addSeparator();\r
 712     colourMenu.add(schemeKeyMenuItem);\r
 713     calculateMenu.add(sortPairwiseMenuItem);\r
 714     calculateMenu.add(sortIDMenuItem);\r
 715     calculateMenu.add(sortGroupMenuItem);\r
 716     calculateMenu.add(sortTreeOrderMenuItem);\r
 717     calculateMenu.add(removeRedundancyMenuItem);\r
 718     calculateMenu.addSeparator();\r
 719     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 720     calculateMenu.add(PCAMenuItem);\r
 721     calculateMenu.addSeparator();\r
 722     calculateMenu.add(averageDistanceTreeMenuItem);\r
 723     calculateMenu.add(neighbourTreeMenuItem);\r
 724     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 725     calculateMenu.add(njTreeBlosumMenuItem);\r
 726     alignMenu.add(clustalAlignMenuItem);\r
 727     alignMenu.add(pdbTest);\r
 728     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 729   }\r
 730 \r
 731   protected void saveAs_actionPerformed(ActionEvent e)\r
 732   {\r
 733 \r
 734   }\r
 735 \r
 736   protected void outputText_actionPerformed(ActionEvent e)\r
 737   {\r
 738 \r
 739   }\r
 740 \r
 741   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 742   {\r
 743 \r
 744   }\r
 745 \r
 746 \r
 747 \r
 748 \r
 749 \r
 750   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 751   {\r
 752 \r
 753   }\r
 754 \r
 755   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 756   {\r
 757 \r
 758   }\r
 759 \r
 760   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 761   {\r
 762 \r
 763   }\r
 764 \r
 765 \r
 766   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 767   {\r
 768 \r
 769   }\r
 770 \r
 771   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 772   {\r
 773 \r
 774   }\r
 775 \r
 776   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 777   {\r
 778 \r
 779   }\r
 780 \r
 781   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 782   {\r
 783 \r
 784   }\r
 785 \r
 786   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 787   {\r
 788 \r
 789   }\r
 790 \r
 791   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793 \r
 794   }\r
 795 \r
 796   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798 \r
 799   }\r
 800 \r
 801   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 802   {\r
 803 \r
 804   }\r
 805 \r
 806   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 807   {\r
 808 \r
 809   }\r
 810 \r
 811   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 812   {\r
 813 \r
 814   }\r
 815 \r
 816   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 817   {\r
 818 \r
 819   }\r
 820 \r
 821   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 822   {\r
 823 \r
 824   }\r
 825 \r
 826   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 827   {\r
 828 \r
 829   }\r
 830 \r
 831   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 832   {\r
 833 \r
 834   }\r
 835 \r
 836 \r
 837   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 838   {\r
 839 \r
 840   }\r
 841 \r
 842   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844 \r
 845   }\r
 846 \r
 847   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849 \r
 850   }\r
 851 \r
 852   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 853   {\r
 854 \r
 855   }\r
 856 \r
 857 \r
 858   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 859   {\r
 860 \r
 861   }\r
 862 \r
 863   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 864   {\r
 865 \r
 866   }\r
 867 \r
 868 \r
 869   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871 \r
 872   }\r
 873 \r
 874 \r
 875 \r
 876   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878 \r
 879   }\r
 880 \r
 881   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 882   {\r
 883 \r
 884   }\r
 885 \r
 886   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 887   {\r
 888 \r
 889   }\r
 890 \r
 891   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 892   {\r
 893 \r
 894   }\r
 895 \r
 896   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 897   {\r
 898 \r
 899   }\r
 900 \r
 901   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 902   {\r
 903 \r
 904   }\r
 905 \r
 906   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 907   {\r
 908 \r
 909   }\r
 910 \r
 911   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 912   {\r
 913 \r
 914   }\r
 915 \r
 916   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 917   {\r
 918 \r
 919   }\r
 920 \r
 921   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 922   {\r
 923 \r
 924   }\r
 925 \r
 926   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928 \r
 929   }\r
 930 \r
 931 \r
 932   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 933   {\r
 934 \r
 935   }\r
 936 \r
 937   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 938   {\r
 939 \r
 940   }\r
 941 \r
 942 \r
 943 \r
 944   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946 \r
 947   }\r
 948 \r
 949 \r
 950 \r
 951 \r
 952   protected void clustalColour_actionPerformed(ActionEvent e)\r
 953   {\r
 954 \r
 955   }\r
 956 \r
 957   protected void zappoColour_actionPerformed(ActionEvent e)\r
 958   {\r
 959 \r
 960   }\r
 961 \r
 962   protected void taylorColour_actionPerformed(ActionEvent e)\r
 963   {\r
 964 \r
 965   }\r
 966 \r
 967 \r
 968   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 969   {\r
 970 \r
 971   }\r
 972 \r
 973   protected void helixColour_actionPerformed(ActionEvent e)\r
 974   {\r
 975 \r
 976   }\r
 977 \r
 978   protected void strandColour_actionPerformed(ActionEvent e)\r
 979   {\r
 980 \r
 981   }\r
 982 \r
 983   protected void turnColour_actionPerformed(ActionEvent e)\r
 984   {\r
 985 \r
 986   }\r
 987 \r
 988   protected void buriedColour_actionPerformed(ActionEvent e)\r
 989   {\r
 990 \r
 991   }\r
 992 \r
 993 \r
 994   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 995  {\r
 996 \r
 997  }\r
 998 \r
 999 \r
1000   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
1001   {\r
1002 \r
1003   }\r
1004 \r
1005 \r
1006   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1007   {\r
1008 \r
1009   }\r
1010 \r
1011   protected void PIDColour_actionPerformed(ActionEvent e)\r
1012   {\r
1013 \r
1014   }\r
1015 \r
1016   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1017   {\r
1018 \r
1019   }\r
1020 \r
1021   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
1022   {\r
1023 \r
1024   }\r
1025 \r
1026   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1027   {\r
1028 \r
1029   }\r
1030 \r
1031   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1032   {\r
1033 \r
1034   }\r
1035 \r
1036   protected void pdbTest_actionPerformed(ActionEvent e)\r
1037   {\r
1038 \r
1039   }\r
1040 \r
1041   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1042   {\r
1043 \r
1044   }\r
1045 \r
1046   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1047   {\r
1048 \r
1049   }\r
1050 \r
1051   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1052   {\r
1053 \r
1054   }\r
1055 \r
1056 }\r