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