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