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