src/jalview/jbgui/GAlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 package jalview.jbgui;\r
  10 \r
  11 import javax.swing.*;\r
  12 import java.awt.event.*;\r
  13 import java.awt.*;\r
  14 \r
  15 public class GAlignFrame extends JInternalFrame\r
  16 {\r
  17   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  18   protected JMenu fileMenu = new JMenu();\r
  19   protected JMenuItem closeMenuItem = new JMenuItem();\r
  20   protected JMenu editMenu = new JMenu();\r
  21   protected JMenu fontMenu = new JMenu();\r
  22   protected JMenu viewMenu = new JMenu();\r
  23   protected JMenu colourMenu = new JMenu();\r
  24   protected JMenu calculateMenu = new JMenu();\r
  25   protected JMenu alignMenu = new JMenu();\r
  26   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  27   protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();\r
  28   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  29   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  30   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  31   protected JMenuItem deleteSelectedMenuItem = new JMenuItem();\r
  32   protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
  33   protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
  34   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  35   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  36   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  37   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  38   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  39   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  40   protected JMenuItem fontNameMenuItem = new JMenuItem();\r
  41   protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
  42   protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
  43   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  44   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  45   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  46   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  47   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  48   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  50   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  51   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  52   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  53   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  54   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  55   BorderLayout borderLayout1 = new BorderLayout();\r
  56   public JLabel statusBar = new JLabel();\r
  57   protected JMenu saveAlignmentMenu = new JMenu();\r
  58   protected JMenu outputTextboxMenu = new JMenu();\r
  59   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  71   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  72   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  73   protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  75   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  76   JMenuItem htmlMenuItem = new JMenuItem();\r
  77   JMenuItem schemeKeyMenuItem = new JMenuItem();\r
  78   JMenuItem overviewMenuItem = new JMenuItem();\r
  79   protected JMenuItem undoMenuItem = new JMenuItem();\r
  80   protected JMenuItem redoMenuItem = new JMenuItem();\r
  81   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  82   JMenuItem noColourmenuItem = new JMenuItem();\r
  83   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  84   JMenuItem pdbTest = new JMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   JMenu searchMenu = new JMenu();\r
  89   public GAlignFrame()\r
  90   {\r
  91     try\r
  92     {\r
  93       jbInit();\r
  94       setJMenuBar(alignFrameMenuBar);\r
  95 \r
  96       JMenuItem item;\r
  97       // dynamically fill save as menu with available formats\r
  98       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
  99         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 100         saveAlignmentMenu.add( item );\r
 101         item.addActionListener(new java.awt.event.ActionListener()\r
 102         {\r
 103           public void actionPerformed(ActionEvent e)\r
 104           {\r
 105             saveAs_actionPerformed(e);\r
 106           }\r
 107         });\r
 108 \r
 109         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 110         item.addActionListener(new java.awt.event.ActionListener()\r
 111         {\r
 112           public void actionPerformed(ActionEvent e)\r
 113           {\r
 114             outputText_actionPerformed(e);\r
 115           }\r
 116         });\r
 117 \r
 118         outputTextboxMenu.add( item );\r
 119       }\r
 120 \r
 121     }\r
 122     catch(Exception e)\r
 123     {\r
 124       e.printStackTrace();\r
 125     }\r
 126 \r
 127     ButtonGroup colours = new ButtonGroup();\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(abovePIDColour);\r
 137     colours.add(userDefinedColour);\r
 138     colours.add(PIDColour);\r
 139     colours.add(BLOSUM62Colour);\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     groupEditingMenuItem.setText("Group editing mode");\r
 171     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 172     {\r
 173       public void actionPerformed(ActionEvent e)\r
 174       {\r
 175         groupEditingMenuItem_actionPerformed(e);\r
 176       }\r
 177     });\r
 178     selectAllSequenceMenuItem.setText("Select all sequences");\r
 179     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 180     {\r
 181       public void actionPerformed(ActionEvent e)\r
 182       {\r
 183         selectAllSequenceMenuItem_actionPerformed(e);\r
 184       }\r
 185     });\r
 186     deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
 187     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 188     {\r
 189       public void actionPerformed(ActionEvent e)\r
 190       {\r
 191         deselectAllSequenceMenuItem_actionPerformed(e);\r
 192       }\r
 193     });\r
 194     invertSequenceMenuItem.setText("Invert sequence selection");\r
 195     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 196     {\r
 197       public void actionPerformed(ActionEvent e)\r
 198       {\r
 199         invertSequenceMenuItem_actionPerformed(e);\r
 200       }\r
 201     });\r
 202     deleteSelectedMenuItem.setText("Delete selected sequences");\r
 203     deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 204     {\r
 205       public void actionPerformed(ActionEvent e)\r
 206       {\r
 207         deleteSelectedMenuItem_actionPerformed(e);\r
 208       }\r
 209     });\r
 210     moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
 211     moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 212     {\r
 213       public void actionPerformed(ActionEvent e)\r
 214       {\r
 215         moveSelectedMenuItem_actionPerformed(e);\r
 216       }\r
 217     });\r
 218     copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
 219     copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 220     {\r
 221       public void actionPerformed(ActionEvent e)\r
 222       {\r
 223         copySelectedMenuItem_actionPerformed(e);\r
 224       }\r
 225     });\r
 226     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 227     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 228     {\r
 229       public void actionPerformed(ActionEvent e)\r
 230       {\r
 231         deselectAllColumnsMenuItem_actionPerformed(e);\r
 232       }\r
 233     });\r
 234     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 235     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 236     {\r
 237       public void actionPerformed(ActionEvent e)\r
 238       {\r
 239         remove2LeftMenuItem_actionPerformed(e);\r
 240       }\r
 241     });\r
 242     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 243     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 244     {\r
 245       public void actionPerformed(ActionEvent e)\r
 246       {\r
 247         remove2RightMenuItem_actionPerformed(e);\r
 248       }\r
 249     });\r
 250     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 251     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 252     {\r
 253       public void actionPerformed(ActionEvent e)\r
 254       {\r
 255         removeGappedColumnMenuItem_actionPerformed(e);\r
 256       }\r
 257     });\r
 258     removeAllGapsMenuItem.setText("Remove all gaps");\r
 259     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 260     {\r
 261       public void actionPerformed(ActionEvent e)\r
 262       {\r
 263         removeAllGapsMenuItem_actionPerformed(e);\r
 264       }\r
 265     });\r
 266     setGapCharMenuItem.setText("Set gap character to \"-\"");\r
 267     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 268     {\r
 269       public void actionPerformed(ActionEvent e)\r
 270       {\r
 271         setGapCharMenuItem_actionPerformed(e);\r
 272       }\r
 273     });\r
 274     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 275     {\r
 276       public void actionPerformed(ActionEvent e)\r
 277       {\r
 278         fontNameMenuItem_actionPerformed(e);\r
 279       }\r
 280     });\r
 281     fontSizeMenuItem.setText("10");\r
 282     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 283     {\r
 284       public void actionPerformed(ActionEvent e)\r
 285       {\r
 286         fontSizeMenuItem_actionPerformed(e);\r
 287       }\r
 288     });\r
 289     fontStyleMenuItem.setText("Plain");\r
 290     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 291     {\r
 292       public void actionPerformed(ActionEvent e)\r
 293       {\r
 294         fontStyleMenuItem_actionPerformed(e);\r
 295       }\r
 296     });\r
 297     viewBoxesMenuItem.setText("Boxes");\r
 298     viewBoxesMenuItem.setState(true);\r
 299     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         viewBoxesMenuItem_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     viewTextMenuItem.setText("Text");\r
 307     viewTextMenuItem.setState(true);\r
 308     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 309     {\r
 310       public void actionPerformed(ActionEvent e)\r
 311       {\r
 312         viewTextMenuItem_actionPerformed(e);\r
 313       }\r
 314     });\r
 315     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 316     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 317     {\r
 318       public void actionPerformed(ActionEvent e)\r
 319       {\r
 320         sortPairwiseMenuItem_actionPerformed(e);\r
 321       }\r
 322     });\r
 323     sortIDMenuItem.setText("Sort by ID");\r
 324     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         sortIDMenuItem_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     sortGroupMenuItem.setText("Sort by group");\r
 332     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 333     {\r
 334       public void actionPerformed(ActionEvent e)\r
 335       {\r
 336         sortGroupMenuItem_actionPerformed(e);\r
 337       }\r
 338     });\r
 339     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 340     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 341     {\r
 342       public void actionPerformed(ActionEvent e)\r
 343       {\r
 344         sortTreeOrderMenuItem_actionPerformed(e);\r
 345       }\r
 346     });\r
 347     removeRedundancyMenuItem.setText("Remove redundancy");\r
 348     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 349     {\r
 350       public void actionPerformed(ActionEvent e)\r
 351       {\r
 352         removeRedundancyMenuItem_actionPerformed(e);\r
 353       }\r
 354     });\r
 355     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 356     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 357     {\r
 358       public void actionPerformed(ActionEvent e)\r
 359       {\r
 360         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 361       }\r
 362     });\r
 363     PCAMenuItem.setText("Principal component analysis");\r
 364     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 365     {\r
 366       public void actionPerformed(ActionEvent e)\r
 367       {\r
 368         PCAMenuItem_actionPerformed(e);\r
 369       }\r
 370     });\r
 371     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 372     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 373     {\r
 374       public void actionPerformed(ActionEvent e)\r
 375       {\r
 376         averageDistanceTreeMenuItem_actionPerformed(e);\r
 377       }\r
 378     });\r
 379     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 380     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 381     {\r
 382       public void actionPerformed(ActionEvent e)\r
 383       {\r
 384         neighbourTreeMenuItem_actionPerformed(e);\r
 385       }\r
 386     });\r
 387     clustalAlignMenuItem.setText("Clustal alignment");\r
 388     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 389     {\r
 390       public void actionPerformed(ActionEvent e)\r
 391       {\r
 392         clustalAlignMenuItem_actionPerformed(e);\r
 393       }\r
 394     });\r
 395     this.getContentPane().setLayout(borderLayout1);\r
 396     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 397     statusBar.setBackground(Color.white);\r
 398     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 399     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 400     statusBar.setText("Status bar");\r
 401     outputTextboxMenu.setMnemonic('T');\r
 402     outputTextboxMenu.setText("Output alignment via textbox");\r
 403     clustalColour.setEnabled(false);\r
 404     clustalColour.setSelected(false);\r
 405     clustalColour.setText("Clustalx colours");\r
 406     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 407     {\r
 408       public void actionPerformed(ActionEvent e)\r
 409       {\r
 410         clustalColour_actionPerformed(e);\r
 411       }\r
 412     });\r
 413     zappoColour.setSelected(true);\r
 414     zappoColour.setText("Zappo colour scheme");\r
 415     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 416     {\r
 417       public void actionPerformed(ActionEvent e)\r
 418       {\r
 419         zappoColour_actionPerformed(e);\r
 420       }\r
 421     });\r
 422     taylorColour.setText("Taylor colour scheme");\r
 423     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 424     {\r
 425       public void actionPerformed(ActionEvent e)\r
 426       {\r
 427         taylorColour_actionPerformed(e);\r
 428       }\r
 429     });\r
 430     hydrophobicityColour.setText("By hydrophobicity");\r
 431     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 432     {\r
 433       public void actionPerformed(ActionEvent e)\r
 434       {\r
 435         hydrophobicityColour_actionPerformed(e);\r
 436       }\r
 437     });\r
 438     helixColour.setText("Helix propensity");\r
 439     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 440     {\r
 441       public void actionPerformed(ActionEvent e)\r
 442       {\r
 443         helixColour_actionPerformed(e);\r
 444       }\r
 445     });\r
 446     strandColour.setText("Strand propensity");\r
 447     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 448     {\r
 449       public void actionPerformed(ActionEvent e)\r
 450       {\r
 451         strandColour_actionPerformed(e);\r
 452       }\r
 453     });\r
 454     turnColour.setText("Turn propensity");\r
 455     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 456     {\r
 457       public void actionPerformed(ActionEvent e)\r
 458       {\r
 459         turnColour_actionPerformed(e);\r
 460       }\r
 461     });\r
 462     buriedColour.setText("Buried index");\r
 463     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 464     {\r
 465       public void actionPerformed(ActionEvent e)\r
 466       {\r
 467         buriedColour_actionPerformed(e);\r
 468       }\r
 469     });\r
 470     abovePIDColour.setEnabled(false);\r
 471     abovePIDColour.setText("Above PID threshold only");\r
 472     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         abovePIDColour_actionPerformed(e);\r
 477       }\r
 478     });\r
 479     userDefinedColour.setText("User defined colours");\r
 480     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 481     {\r
 482       public void actionPerformed(ActionEvent e)\r
 483       {\r
 484         userDefinedColour_actionPerformed(e);\r
 485       }\r
 486     });\r
 487     PIDColour.setEnabled(false);\r
 488     PIDColour.setText("By PID");\r
 489     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 490     {\r
 491       public void actionPerformed(ActionEvent e)\r
 492       {\r
 493         PIDColour_actionPerformed(e);\r
 494       }\r
 495     });\r
 496     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 497     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         BLOSUM62Colour_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 505     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         avTreeBlosumMenuItem_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 513     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 514     {\r
 515       public void actionPerformed(ActionEvent e)\r
 516       {\r
 517         njTreeBlosumMenuItem_actionPerformed(e);\r
 518       }\r
 519     });\r
 520     conservationColourIncMenuItem.setEnabled(false);\r
 521     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 522     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         conservationColourIncMenuItem_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     consensusGraphMenuItem.setActionCommand("");\r
 530     consensusGraphMenuItem.setText("Consensus graph");\r
 531     consensusGraphMenuItem.setState(true);\r
 532     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 533     {\r
 534       public void actionPerformed(ActionEvent e)\r
 535       {\r
 536         consensusGraphMenuItem_actionPerformed(e);\r
 537       }\r
 538     });\r
 539     colourTextMenuItem.setText("Colour text");\r
 540     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 541     {\r
 542       public void actionPerformed(ActionEvent e)\r
 543       {\r
 544         colourTextMenuItem_actionPerformed(e);\r
 545       }\r
 546     });\r
 547     htmlMenuItem.setText("Output as HTML");\r
 548     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 549     {\r
 550       public void actionPerformed(ActionEvent e)\r
 551       {\r
 552         htmlMenuItem_actionPerformed(e);\r
 553       }\r
 554     });\r
 555     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 556     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 557     {\r
 558       public void actionPerformed(ActionEvent e)\r
 559       {\r
 560         schemeKeyMenuItem_actionPerformed(e);\r
 561       }\r
 562     });\r
 563     overviewMenuItem.setText("Overview window");\r
 564     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 565     {\r
 566       public void actionPerformed(ActionEvent e)\r
 567       {\r
 568         overviewMenuItem_actionPerformed(e);\r
 569       }\r
 570     });\r
 571     undoMenuItem.setEnabled(false);\r
 572     undoMenuItem.setMnemonic('Z');\r
 573     undoMenuItem.setText("Undo");\r
 574     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         undoMenuItem_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     redoMenuItem.setEnabled(false);\r
 582     redoMenuItem.setMnemonic('0');\r
 583     redoMenuItem.setText("Redo");\r
 584     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 585     {\r
 586       public void actionPerformed(ActionEvent e)\r
 587       {\r
 588         redoMenuItem_actionPerformed(e);\r
 589       }\r
 590     });\r
 591     conservationMenuItem.setText("By conservation");\r
 592     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 593     {\r
 594       public void actionPerformed(ActionEvent e)\r
 595       {\r
 596         conservationMenuItem_actionPerformed(e);\r
 597       }\r
 598     });\r
 599     noColourmenuItem.setText("None");\r
 600     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 601     {\r
 602       public void actionPerformed(ActionEvent e)\r
 603       {\r
 604         noColourmenuItem_actionPerformed(e);\r
 605       }\r
 606     });\r
 607     wrapMenuItem.setEnabled(false);\r
 608     wrapMenuItem.setText("Wrap alignment");\r
 609     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 610     {\r
 611       public void actionPerformed(ActionEvent e)\r
 612       {\r
 613         wrapMenuItem_actionPerformed(e);\r
 614       }\r
 615     });\r
 616     pdbTest.setText("PDB Test Viewer");\r
 617     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 618     {\r
 619       public void actionPerformed(ActionEvent e)\r
 620       {\r
 621         pdbTest_actionPerformed(e);\r
 622       }\r
 623     });\r
 624     printMenuItem.setText("Print");\r
 625     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 626     {\r
 627       public void actionPerformed(ActionEvent e)\r
 628       {\r
 629         printMenuItem_actionPerformed(e);\r
 630       }\r
 631     });\r
 632     renderGapsMenuItem.setText("Render gaps");\r
 633     renderGapsMenuItem.setState(true);\r
 634     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         renderGapsMenuItem_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     findMenuItem.setText("Find");\r
 642     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 643     {\r
 644       public void actionPerformed(ActionEvent e)\r
 645       {\r
 646         findMenuItem_actionPerformed(e);\r
 647       }\r
 648     });\r
 649     searchMenu.setText("Search");\r
 650     alignFrameMenuBar.add(fileMenu);\r
 651     alignFrameMenuBar.add(editMenu);\r
 652     alignFrameMenuBar.add(searchMenu);\r
 653     alignFrameMenuBar.add(fontMenu);\r
 654     alignFrameMenuBar.add(viewMenu);\r
 655     alignFrameMenuBar.add(colourMenu);\r
 656     alignFrameMenuBar.add(calculateMenu);\r
 657     alignFrameMenuBar.add(alignMenu);\r
 658     fileMenu.add(saveAlignmentMenu);\r
 659     fileMenu.add(outputTextboxMenu);\r
 660     fileMenu.add(htmlMenuItem);\r
 661     fileMenu.add(printMenuItem);\r
 662     fileMenu.addSeparator();\r
 663     fileMenu.add(closeMenuItem);\r
 664     editMenu.add(undoMenuItem);\r
 665     editMenu.add(redoMenuItem);\r
 666     editMenu.addSeparator();\r
 667     editMenu.add(groupsMenuItem);\r
 668     editMenu.add(groupEditingMenuItem);\r
 669     editMenu.addSeparator();\r
 670     editMenu.add(selectAllSequenceMenuItem);\r
 671     editMenu.add(deselectAllSequenceMenuItem);\r
 672     editMenu.add(invertSequenceMenuItem);\r
 673     editMenu.addSeparator();\r
 674     editMenu.add(copySelectedMenuItem);\r
 675     editMenu.add(moveSelectedMenuItem);\r
 676     editMenu.add(deleteSelectedMenuItem);\r
 677     editMenu.addSeparator();\r
 678     editMenu.add(deselectAllColumnsMenuItem);\r
 679     editMenu.add(remove2LeftMenuItem);\r
 680     editMenu.add(remove2RightMenuItem);\r
 681     editMenu.addSeparator();\r
 682     editMenu.add(removeGappedColumnMenuItem);\r
 683     editMenu.add(removeAllGapsMenuItem);\r
 684     editMenu.add(setGapCharMenuItem);\r
 685     searchMenu.add(findMenuItem);\r
 686     fontMenu.add(fontNameMenuItem);\r
 687     fontMenu.add(fontSizeMenuItem);\r
 688     fontMenu.add(fontStyleMenuItem);\r
 689     viewMenu.add(wrapMenuItem);\r
 690     viewMenu.add(viewBoxesMenuItem);\r
 691     viewMenu.add(viewTextMenuItem);\r
 692     viewMenu.add(colourTextMenuItem);\r
 693     viewMenu.add(renderGapsMenuItem);\r
 694     viewMenu.add(consensusGraphMenuItem);\r
 695     viewMenu.add(overviewMenuItem);\r
 696     colourMenu.add(noColourmenuItem);\r
 697     colourMenu.add(clustalColour);\r
 698     colourMenu.add(zappoColour);\r
 699     colourMenu.add(taylorColour);\r
 700     colourMenu.add(hydrophobicityColour);\r
 701     colourMenu.add(helixColour);\r
 702     colourMenu.add(strandColour);\r
 703     colourMenu.add(turnColour);\r
 704     colourMenu.add(buriedColour);\r
 705     colourMenu.add(userDefinedColour);\r
 706     colourMenu.addSeparator();\r
 707     colourMenu.add(conservationMenuItem);\r
 708     colourMenu.add(conservationColourIncMenuItem);\r
 709     colourMenu.addSeparator();\r
 710     colourMenu.add(abovePIDColour);\r
 711     colourMenu.add(PIDColour);\r
 712     colourMenu.add(BLOSUM62Colour);\r
 713     colourMenu.addSeparator();\r
 714     colourMenu.add(schemeKeyMenuItem);\r
 715     calculateMenu.add(sortPairwiseMenuItem);\r
 716     calculateMenu.add(sortIDMenuItem);\r
 717     calculateMenu.add(sortGroupMenuItem);\r
 718     calculateMenu.add(sortTreeOrderMenuItem);\r
 719     calculateMenu.add(removeRedundancyMenuItem);\r
 720     calculateMenu.addSeparator();\r
 721     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 722     calculateMenu.add(PCAMenuItem);\r
 723     calculateMenu.addSeparator();\r
 724     calculateMenu.add(averageDistanceTreeMenuItem);\r
 725     calculateMenu.add(neighbourTreeMenuItem);\r
 726     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 727     calculateMenu.add(njTreeBlosumMenuItem);\r
 728     alignMenu.add(clustalAlignMenuItem);\r
 729     alignMenu.add(pdbTest);\r
 730     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 731   }\r
 732 \r
 733   protected void saveAs_actionPerformed(ActionEvent e)\r
 734   {\r
 735 \r
 736   }\r
 737 \r
 738   protected void outputText_actionPerformed(ActionEvent e)\r
 739   {\r
 740 \r
 741   }\r
 742 \r
 743   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 744   {\r
 745 \r
 746   }\r
 747 \r
 748 \r
 749 \r
 750 \r
 751 \r
 752   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 753   {\r
 754 \r
 755   }\r
 756 \r
 757   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 758   {\r
 759 \r
 760   }\r
 761 \r
 762   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 763   {\r
 764 \r
 765   }\r
 766 \r
 767 \r
 768   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 769   {\r
 770 \r
 771   }\r
 772 \r
 773   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 774   {\r
 775 \r
 776   }\r
 777 \r
 778   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 779   {\r
 780 \r
 781   }\r
 782 \r
 783   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 784   {\r
 785 \r
 786   }\r
 787 \r
 788   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 789   {\r
 790 \r
 791   }\r
 792 \r
 793   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 794   {\r
 795 \r
 796   }\r
 797 \r
 798   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 799   {\r
 800 \r
 801   }\r
 802 \r
 803   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 804   {\r
 805 \r
 806   }\r
 807 \r
 808   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 809   {\r
 810 \r
 811   }\r
 812 \r
 813   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 814   {\r
 815 \r
 816   }\r
 817 \r
 818   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 819   {\r
 820 \r
 821   }\r
 822 \r
 823   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 824   {\r
 825 \r
 826   }\r
 827 \r
 828   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 829   {\r
 830 \r
 831   }\r
 832 \r
 833   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835 \r
 836   }\r
 837 \r
 838 \r
 839   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 840   {\r
 841 \r
 842   }\r
 843 \r
 844   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 845   {\r
 846 \r
 847   }\r
 848 \r
 849   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 850   {\r
 851 \r
 852   }\r
 853 \r
 854   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 855   {\r
 856 \r
 857   }\r
 858 \r
 859 \r
 860   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 866   {\r
 867 \r
 868   }\r
 869 \r
 870 \r
 871   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 872   {\r
 873 \r
 874   }\r
 875 \r
 876 \r
 877 \r
 878   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 879   {\r
 880 \r
 881   }\r
 882 \r
 883   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 884   {\r
 885 \r
 886   }\r
 887 \r
 888   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 889   {\r
 890 \r
 891   }\r
 892 \r
 893   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 894   {\r
 895 \r
 896   }\r
 897 \r
 898   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 899   {\r
 900 \r
 901   }\r
 902 \r
 903   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 904   {\r
 905 \r
 906   }\r
 907 \r
 908   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 909   {\r
 910 \r
 911   }\r
 912 \r
 913   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 914   {\r
 915 \r
 916   }\r
 917 \r
 918   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 919   {\r
 920 \r
 921   }\r
 922 \r
 923   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 924   {\r
 925 \r
 926   }\r
 927 \r
 928   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930 \r
 931   }\r
 932 \r
 933 \r
 934   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 935   {\r
 936 \r
 937   }\r
 938 \r
 939   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941 \r
 942   }\r
 943 \r
 944 \r
 945 \r
 946   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 947   {\r
 948 \r
 949   }\r
 950 \r
 951 \r
 952 \r
 953 \r
 954   protected void clustalColour_actionPerformed(ActionEvent e)\r
 955   {\r
 956 \r
 957   }\r
 958 \r
 959   protected void zappoColour_actionPerformed(ActionEvent e)\r
 960   {\r
 961 \r
 962   }\r
 963 \r
 964   protected void taylorColour_actionPerformed(ActionEvent e)\r
 965   {\r
 966 \r
 967   }\r
 968 \r
 969 \r
 970   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 971   {\r
 972 \r
 973   }\r
 974 \r
 975   protected void helixColour_actionPerformed(ActionEvent e)\r
 976   {\r
 977 \r
 978   }\r
 979 \r
 980   protected void strandColour_actionPerformed(ActionEvent e)\r
 981   {\r
 982 \r
 983   }\r
 984 \r
 985   protected void turnColour_actionPerformed(ActionEvent e)\r
 986   {\r
 987 \r
 988   }\r
 989 \r
 990   protected void buriedColour_actionPerformed(ActionEvent e)\r
 991   {\r
 992 \r
 993   }\r
 994 \r
 995 \r
 996   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 997  {\r
 998 \r
 999  }\r
1000 \r
1001 \r
1002   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
1003   {\r
1004 \r
1005   }\r
1006 \r
1007 \r
1008   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1009   {\r
1010 \r
1011   }\r
1012 \r
1013   protected void PIDColour_actionPerformed(ActionEvent e)\r
1014   {\r
1015 \r
1016   }\r
1017 \r
1018   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1019   {\r
1020 \r
1021   }\r
1022 \r
1023   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
1024   {\r
1025 \r
1026   }\r
1027 \r
1028   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1029   {\r
1030 \r
1031   }\r
1032 \r
1033   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1034   {\r
1035 \r
1036   }\r
1037 \r
1038   protected void pdbTest_actionPerformed(ActionEvent e)\r
1039   {\r
1040 \r
1041   }\r
1042 \r
1043   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1044   {\r
1045 \r
1046   }\r
1047 \r
1048   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1049   {\r
1050 \r
1051   }\r
1052 \r
1053   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1054   {\r
1055 \r
1056   }\r
1057 \r
1058 }\r