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 sequenceFeatures = new JCheckBoxMenuItem();\r
  84   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  85   JMenuItem deleteGroups = new JMenuItem();\r
  86   JMenuItem delete = new JMenuItem();\r
  87   JMenuItem copy = new JMenuItem();\r
  88   JMenuItem cut = new JMenuItem();\r
  89   JMenu jMenu1 = new JMenu();\r
  90   JMenuItem pasteNew = new JMenuItem();\r
  91   JMenuItem pasteThis = new JMenuItem();\r
  92   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  93   JMenuItem createJPG = new JMenuItem();\r
  94   public GAlignFrame()\r
  95   {\r
  96 \r
  97 \r
  98     try\r
  99     {\r
 100       jbInit();\r
 101       setJMenuBar(alignFrameMenuBar);\r
 102 \r
 103       JMenuItem item;\r
 104       // dynamically fill save as menu with available formats\r
 105       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
 106         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 107         saveAlignmentMenu.add( item );\r
 108         item.addActionListener(new java.awt.event.ActionListener()\r
 109         {\r
 110           public void actionPerformed(ActionEvent e)\r
 111           {\r
 112             saveAs_actionPerformed(e);\r
 113           }\r
 114         });\r
 115 \r
 116         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 117         item.addActionListener(new java.awt.event.ActionListener()\r
 118         {\r
 119           public void actionPerformed(ActionEvent e)\r
 120           {\r
 121             outputText_actionPerformed(e);\r
 122           }\r
 123         });\r
 124 \r
 125         outputTextboxMenu.add( item );\r
 126       }\r
 127 \r
 128     }\r
 129     catch(Exception e)\r
 130     {\r
 131       e.printStackTrace();\r
 132     }\r
 133 \r
 134     ButtonGroup colours = new ButtonGroup();\r
 135     colours.add(noColourmenuItem);\r
 136     colours.add(clustalColour);\r
 137     colours.add(zappoColour);\r
 138     colours.add(taylorColour);\r
 139     colours.add(hydrophobicityColour);\r
 140     colours.add(helixColour);\r
 141     colours.add(strandColour);\r
 142     colours.add(turnColour);\r
 143     colours.add(buriedColour);\r
 144     colours.add(userDefinedColour);\r
 145     colours.add(PIDColour);\r
 146     colours.add(BLOSUM62Colour);\r
 147     colours.add(nucleotideColour);\r
 148   }\r
 149   private void jbInit() throws Exception\r
 150   {\r
 151     fileMenu.setMnemonic('F');\r
 152     fileMenu.setText("File");\r
 153     saveAlignmentMenu.setMnemonic('L');\r
 154     saveAlignmentMenu.setText("Save alignment to local file");\r
 155     closeMenuItem.setMnemonic('C');\r
 156     closeMenuItem.setText("Close");\r
 157     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 158     {\r
 159       public void actionPerformed(ActionEvent e)\r
 160       {\r
 161         closeMenuItem_actionPerformed(e);\r
 162       }\r
 163     });\r
 164     editMenu.setText("Edit");\r
 165     fontMenu.setText("Font");\r
 166     viewMenu.setText("View");\r
 167     colourMenu.setText("Colour");\r
 168     calculateMenu.setText("Calculate");\r
 169     alignMenu.setText("Web Service");\r
 170     groupsMenuItem.setEnabled(false);\r
 171     groupsMenuItem.setText("Groups");\r
 172     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 173     {\r
 174       public void actionPerformed(ActionEvent e)\r
 175       {\r
 176         groupsMenuItem_actionPerformed(e);\r
 177       }\r
 178     });\r
 179     selectAllSequenceMenuItem.setText("Select all");\r
 180     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 181     {\r
 182       public void actionPerformed(ActionEvent e)\r
 183       {\r
 184         selectAllSequenceMenuItem_actionPerformed(e);\r
 185       }\r
 186     });\r
 187     deselectAllSequenceMenuItem.setText("Clear selection");\r
 188     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 189     {\r
 190       public void actionPerformed(ActionEvent e)\r
 191       {\r
 192         deselectAllSequenceMenuItem_actionPerformed(e);\r
 193       }\r
 194     });\r
 195     invertSequenceMenuItem.setText("Invert sequence selection");\r
 196     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 197     {\r
 198       public void actionPerformed(ActionEvent e)\r
 199       {\r
 200         invertSequenceMenuItem_actionPerformed(e);\r
 201       }\r
 202     });\r
 203     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 204     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 205     {\r
 206       public void actionPerformed(ActionEvent e)\r
 207       {\r
 208         deselectAllColumnsMenuItem_actionPerformed(e);\r
 209       }\r
 210     });\r
 211     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 212     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 213     {\r
 214       public void actionPerformed(ActionEvent e)\r
 215       {\r
 216         remove2LeftMenuItem_actionPerformed(e);\r
 217       }\r
 218     });\r
 219     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 220     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 221     {\r
 222       public void actionPerformed(ActionEvent e)\r
 223       {\r
 224         remove2RightMenuItem_actionPerformed(e);\r
 225       }\r
 226     });\r
 227     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 228     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 229     {\r
 230       public void actionPerformed(ActionEvent e)\r
 231       {\r
 232         removeGappedColumnMenuItem_actionPerformed(e);\r
 233       }\r
 234     });\r
 235     removeAllGapsMenuItem.setText("Remove all gaps");\r
 236     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 237     {\r
 238       public void actionPerformed(ActionEvent e)\r
 239       {\r
 240         removeAllGapsMenuItem_actionPerformed(e);\r
 241       }\r
 242     });\r
 243     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 244     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 245     {\r
 246       public void actionPerformed(ActionEvent e)\r
 247       {\r
 248         setGapCharMenuItem_actionPerformed(e);\r
 249       }\r
 250     });\r
 251     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 252     {\r
 253       public void actionPerformed(ActionEvent e)\r
 254       {\r
 255         fontNameMenuItem_actionPerformed(e);\r
 256       }\r
 257     });\r
 258     fontSizeMenuItem.setText("10");\r
 259     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 260     {\r
 261       public void actionPerformed(ActionEvent e)\r
 262       {\r
 263         fontSizeMenuItem_actionPerformed(e);\r
 264       }\r
 265     });\r
 266     fontStyleMenuItem.setText("Plain");\r
 267     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 268     {\r
 269       public void actionPerformed(ActionEvent e)\r
 270       {\r
 271         fontStyleMenuItem_actionPerformed(e);\r
 272       }\r
 273     });\r
 274     viewBoxesMenuItem.setText("Boxes");\r
 275     viewBoxesMenuItem.setState(true);\r
 276     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 277     {\r
 278       public void actionPerformed(ActionEvent e)\r
 279       {\r
 280         viewBoxesMenuItem_actionPerformed(e);\r
 281       }\r
 282     });\r
 283     viewTextMenuItem.setText("Text");\r
 284     viewTextMenuItem.setState(true);\r
 285     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 286     {\r
 287       public void actionPerformed(ActionEvent e)\r
 288       {\r
 289         viewTextMenuItem_actionPerformed(e);\r
 290       }\r
 291     });\r
 292     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 293     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 294     {\r
 295       public void actionPerformed(ActionEvent e)\r
 296       {\r
 297         sortPairwiseMenuItem_actionPerformed(e);\r
 298       }\r
 299     });\r
 300     sortIDMenuItem.setText("Sort by ID");\r
 301     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 302     {\r
 303       public void actionPerformed(ActionEvent e)\r
 304       {\r
 305         sortIDMenuItem_actionPerformed(e);\r
 306       }\r
 307     });\r
 308     sortGroupMenuItem.setText("Sort by group");\r
 309     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 310     {\r
 311       public void actionPerformed(ActionEvent e)\r
 312       {\r
 313         sortGroupMenuItem_actionPerformed(e);\r
 314       }\r
 315     });\r
 316     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 317     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 318     {\r
 319       public void actionPerformed(ActionEvent e)\r
 320       {\r
 321         sortTreeOrderMenuItem_actionPerformed(e);\r
 322       }\r
 323     });\r
 324     removeRedundancyMenuItem.setText("Remove redundancy");\r
 325     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 326     {\r
 327       public void actionPerformed(ActionEvent e)\r
 328       {\r
 329         removeRedundancyMenuItem_actionPerformed(e);\r
 330       }\r
 331     });\r
 332     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 333     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 334     {\r
 335       public void actionPerformed(ActionEvent e)\r
 336       {\r
 337         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 338       }\r
 339     });\r
 340     PCAMenuItem.setText("Principal component analysis");\r
 341     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 342     {\r
 343       public void actionPerformed(ActionEvent e)\r
 344       {\r
 345         PCAMenuItem_actionPerformed(e);\r
 346       }\r
 347     });\r
 348     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 349     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 350     {\r
 351       public void actionPerformed(ActionEvent e)\r
 352       {\r
 353         averageDistanceTreeMenuItem_actionPerformed(e);\r
 354       }\r
 355     });\r
 356     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 357     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 358     {\r
 359       public void actionPerformed(ActionEvent e)\r
 360       {\r
 361         neighbourTreeMenuItem_actionPerformed(e);\r
 362       }\r
 363     });\r
 364     clustalAlignMenuItem.setText("Clustal alignment");\r
 365     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 366     {\r
 367       public void actionPerformed(ActionEvent e)\r
 368       {\r
 369         clustalAlignMenuItem_actionPerformed(e);\r
 370       }\r
 371     });\r
 372     this.getContentPane().setLayout(borderLayout1);\r
 373     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 374     statusBar.setBackground(Color.white);\r
 375     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 376     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 377     statusBar.setText("Status bar");\r
 378     outputTextboxMenu.setMnemonic('T');\r
 379     outputTextboxMenu.setText("Output alignment via textbox");\r
 380     clustalColour.setSelected(false);\r
 381     clustalColour.setText("Clustalx colours");\r
 382     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 383     {\r
 384       public void actionPerformed(ActionEvent e)\r
 385       {\r
 386         clustalColour_actionPerformed(e);\r
 387       }\r
 388     });\r
 389     zappoColour.setText("Zappo colour scheme");\r
 390     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 391     {\r
 392       public void actionPerformed(ActionEvent e)\r
 393       {\r
 394         zappoColour_actionPerformed(e);\r
 395       }\r
 396     });\r
 397     taylorColour.setText("Taylor colour scheme");\r
 398     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 399     {\r
 400       public void actionPerformed(ActionEvent e)\r
 401       {\r
 402         taylorColour_actionPerformed(e);\r
 403       }\r
 404     });\r
 405     hydrophobicityColour.setText("By hydrophobicity");\r
 406     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 407     {\r
 408       public void actionPerformed(ActionEvent e)\r
 409       {\r
 410         hydrophobicityColour_actionPerformed(e);\r
 411       }\r
 412     });\r
 413     helixColour.setText("Helix propensity");\r
 414     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 415     {\r
 416       public void actionPerformed(ActionEvent e)\r
 417       {\r
 418         helixColour_actionPerformed(e);\r
 419       }\r
 420     });\r
 421     strandColour.setText("Strand propensity");\r
 422     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 423     {\r
 424       public void actionPerformed(ActionEvent e)\r
 425       {\r
 426         strandColour_actionPerformed(e);\r
 427       }\r
 428     });\r
 429     turnColour.setText("Turn propensity");\r
 430     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 431     {\r
 432       public void actionPerformed(ActionEvent e)\r
 433       {\r
 434         turnColour_actionPerformed(e);\r
 435       }\r
 436     });\r
 437     buriedColour.setText("Buried index");\r
 438     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 439     {\r
 440       public void actionPerformed(ActionEvent e)\r
 441       {\r
 442         buriedColour_actionPerformed(e);\r
 443       }\r
 444     });\r
 445     userDefinedColour.setText("User defined colours");\r
 446     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 447     {\r
 448       public void actionPerformed(ActionEvent e)\r
 449       {\r
 450         userDefinedColour_actionPerformed(e);\r
 451       }\r
 452     });\r
 453     PIDColour.setText("Percentage Identity");\r
 454     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 455     {\r
 456       public void actionPerformed(ActionEvent e)\r
 457       {\r
 458         PIDColour_actionPerformed(e);\r
 459       }\r
 460     });\r
 461     BLOSUM62Colour.setText("BLOSUM62 score");\r
 462     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         BLOSUM62Colour_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 470     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 471     {\r
 472       public void actionPerformed(ActionEvent e)\r
 473       {\r
 474         avTreeBlosumMenuItem_actionPerformed(e);\r
 475       }\r
 476     });\r
 477     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 478     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 479     {\r
 480       public void actionPerformed(ActionEvent e)\r
 481       {\r
 482         njTreeBlosumMenuItem_actionPerformed(e);\r
 483       }\r
 484     });\r
 485     consensusGraphMenuItem.setActionCommand("");\r
 486     consensusGraphMenuItem.setText("Consensus graph");\r
 487     consensusGraphMenuItem.setState(true);\r
 488     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 489     {\r
 490       public void actionPerformed(ActionEvent e)\r
 491       {\r
 492         consensusGraphMenuItem_actionPerformed(e);\r
 493       }\r
 494     });\r
 495     colourTextMenuItem.setText("Colour text");\r
 496     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 497     {\r
 498       public void actionPerformed(ActionEvent e)\r
 499       {\r
 500         colourTextMenuItem_actionPerformed(e);\r
 501       }\r
 502     });\r
 503     htmlMenuItem.setText("Output as HTML");\r
 504     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 505     {\r
 506       public void actionPerformed(ActionEvent e)\r
 507       {\r
 508         htmlMenuItem_actionPerformed(e);\r
 509       }\r
 510     });\r
 511     overviewMenuItem.setText("Overview window");\r
 512     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 513     {\r
 514       public void actionPerformed(ActionEvent e)\r
 515       {\r
 516         overviewMenuItem_actionPerformed(e);\r
 517       }\r
 518     });\r
 519     undoMenuItem.setEnabled(false);\r
 520     undoMenuItem.setMnemonic('Z');\r
 521     undoMenuItem.setText("Undo");\r
 522     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         undoMenuItem_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     redoMenuItem.setEnabled(false);\r
 530     redoMenuItem.setMnemonic('0');\r
 531     redoMenuItem.setText("Redo");\r
 532     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 533     {\r
 534       public void actionPerformed(ActionEvent e)\r
 535       {\r
 536         redoMenuItem_actionPerformed(e);\r
 537       }\r
 538     });\r
 539     conservationMenuItem.setText("By conservation");\r
 540     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 541     {\r
 542       public void actionPerformed(ActionEvent e)\r
 543       {\r
 544         conservationMenuItem_actionPerformed(e);\r
 545       }\r
 546     });\r
 547     noColourmenuItem.setText("None");\r
 548     noColourmenuItem.setSelected(true);\r
 549     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 550     {\r
 551       public void actionPerformed(ActionEvent e)\r
 552       {\r
 553         noColourmenuItem_actionPerformed(e);\r
 554       }\r
 555     });\r
 556     wrapMenuItem.setText("Wrap alignment");\r
 557     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 558     {\r
 559       public void actionPerformed(ActionEvent e)\r
 560       {\r
 561         wrapMenuItem_actionPerformed(e);\r
 562       }\r
 563     });\r
 564     pdbTest.setText("PDB Test Viewer");\r
 565     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 566     {\r
 567       public void actionPerformed(ActionEvent e)\r
 568       {\r
 569         pdbTest_actionPerformed(e);\r
 570       }\r
 571     });\r
 572     printMenuItem.setText("Print");\r
 573     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 574     {\r
 575       public void actionPerformed(ActionEvent e)\r
 576       {\r
 577         printMenuItem_actionPerformed(e);\r
 578       }\r
 579     });\r
 580     renderGapsMenuItem.setText("Render gaps");\r
 581     renderGapsMenuItem.setState(true);\r
 582     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 583     {\r
 584       public void actionPerformed(ActionEvent e)\r
 585       {\r
 586         renderGapsMenuItem_actionPerformed(e);\r
 587       }\r
 588     });\r
 589     findMenuItem.setText("Find");\r
 590     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 591     {\r
 592       public void actionPerformed(ActionEvent e)\r
 593       {\r
 594         findMenuItem_actionPerformed(e);\r
 595       }\r
 596     });\r
 597     searchMenu.setText("Search");\r
 598 \r
 599     abovePIDThreshold.setText("Above PID threshold");\r
 600     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 601       public void actionPerformed(ActionEvent e) {\r
 602         abovePIDThreshold_actionPerformed(e);\r
 603       }\r
 604     });\r
 605     sequenceFeatures.setSelected(true);\r
 606     sequenceFeatures.setText("Sequence Features");\r
 607     sequenceFeatures.addActionListener(new ActionListener()\r
 608     {\r
 609       public void actionPerformed(ActionEvent actionEvent)\r
 610       {\r
 611         sequenceFeatures_actionPerformed(actionEvent);\r
 612       }\r
 613     });\r
 614     nucleotideColour.setText("Nucleotide colours");\r
 615     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 616     {\r
 617       public void actionPerformed(ActionEvent e)\r
 618       {\r
 619         nucleotideColour_actionPerformed(e);\r
 620       }\r
 621     });\r
 622     deleteGroups.setSelected(false);\r
 623     deleteGroups.setText("Delete all groups");\r
 624     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 625     {\r
 626       public void actionPerformed(ActionEvent e)\r
 627       {\r
 628         deleteGroups_actionPerformed(e);\r
 629       }\r
 630     });\r
 631     copy.setText("Copy");\r
 632     copy.setMnemonic(KeyEvent.VK_C);\r
 633 \r
 634     copy.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         copy_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     cut.setText("Cut");\r
 642     cut.setMnemonic(KeyEvent.VK_X);\r
 643     cut.addActionListener(new java.awt.event.ActionListener()\r
 644     {\r
 645       public void actionPerformed(ActionEvent e)\r
 646       {\r
 647         cut_actionPerformed(e);\r
 648       }\r
 649     });\r
 650     delete.setText("Delete");\r
 651     delete.addActionListener(new java.awt.event.ActionListener()\r
 652     {\r
 653       public void actionPerformed(ActionEvent e)\r
 654       {\r
 655         delete_actionPerformed(e);\r
 656       }\r
 657     });\r
 658     jMenu1.setMnemonic('V');\r
 659     jMenu1.setText("Paste");\r
 660     pasteNew.setText("to new alignment");\r
 661     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 662     {\r
 663       public void actionPerformed(ActionEvent e)\r
 664       {\r
 665         pasteNew_actionPerformed(e);\r
 666       }\r
 667     });\r
 668     pasteThis.setText("add to this alignment");\r
 669     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 670     {\r
 671       public void actionPerformed(ActionEvent e)\r
 672       {\r
 673         pasteThis_actionPerformed(e);\r
 674       }\r
 675     });\r
 676     applyToAllGroups.setText("Apply colour to all groups");\r
 677     applyToAllGroups.setState(true);\r
 678     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 679     {\r
 680       public void actionPerformed(ActionEvent e)\r
 681       {\r
 682         applyToAllGroups_actionPerformed(e);\r
 683       }\r
 684     });\r
 685     createJPG.addActionListener(new java.awt.event.ActionListener()\r
 686     {\r
 687       public void actionPerformed(ActionEvent e)\r
 688       {\r
 689         createJPG_actionPerformed(e);\r
 690       }\r
 691     });\r
 692     createJPG.setText("Save as JPG Image");\r
 693     alignFrameMenuBar.add(fileMenu);\r
 694     alignFrameMenuBar.add(editMenu);\r
 695     alignFrameMenuBar.add(searchMenu);\r
 696     alignFrameMenuBar.add(fontMenu);\r
 697     alignFrameMenuBar.add(viewMenu);\r
 698     alignFrameMenuBar.add(colourMenu);\r
 699     alignFrameMenuBar.add(calculateMenu);\r
 700     alignFrameMenuBar.add(alignMenu);\r
 701     fileMenu.add(saveAlignmentMenu);\r
 702     fileMenu.add(outputTextboxMenu);\r
 703     fileMenu.add(htmlMenuItem);\r
 704     fileMenu.add(createJPG);\r
 705     fileMenu.add(printMenuItem);\r
 706     fileMenu.addSeparator();\r
 707     fileMenu.add(closeMenuItem);\r
 708     editMenu.add(copy);\r
 709     editMenu.add(jMenu1);\r
 710     editMenu.add(cut);\r
 711     editMenu.add(delete);\r
 712     editMenu.addSeparator();\r
 713     editMenu.add(undoMenuItem);\r
 714     editMenu.add(redoMenuItem);\r
 715     editMenu.addSeparator();\r
 716     editMenu.add(deselectAllSequenceMenuItem);\r
 717     editMenu.add(selectAllSequenceMenuItem);\r
 718     editMenu.add(invertSequenceMenuItem);\r
 719     editMenu.add(deleteGroups);\r
 720     editMenu.add(groupsMenuItem);\r
 721     editMenu.addSeparator();\r
 722     editMenu.add(deselectAllColumnsMenuItem);\r
 723     editMenu.add(remove2LeftMenuItem);\r
 724     editMenu.add(remove2RightMenuItem);\r
 725     editMenu.addSeparator();\r
 726     editMenu.add(removeGappedColumnMenuItem);\r
 727     editMenu.add(removeAllGapsMenuItem);\r
 728     editMenu.add(setGapCharMenuItem);\r
 729     searchMenu.add(findMenuItem);\r
 730     fontMenu.add(fontNameMenuItem);\r
 731     fontMenu.add(fontSizeMenuItem);\r
 732     fontMenu.add(fontStyleMenuItem);\r
 733     viewMenu.add(wrapMenuItem);\r
 734     viewMenu.add(viewBoxesMenuItem);\r
 735     viewMenu.add(viewTextMenuItem);\r
 736     viewMenu.add(colourTextMenuItem);\r
 737     viewMenu.add(renderGapsMenuItem);\r
 738     viewMenu.add(consensusGraphMenuItem);\r
 739     viewMenu.add(overviewMenuItem);\r
 740     viewMenu.add(sequenceFeatures);\r
 741     colourMenu.add(applyToAllGroups);\r
 742     colourMenu.add(noColourmenuItem);\r
 743     colourMenu.add(clustalColour);\r
 744     colourMenu.add(zappoColour);\r
 745     colourMenu.add(taylorColour);\r
 746     colourMenu.add(hydrophobicityColour);\r
 747     colourMenu.add(helixColour);\r
 748     colourMenu.add(strandColour);\r
 749     colourMenu.add(turnColour);\r
 750     colourMenu.add(buriedColour);\r
 751     colourMenu.add(nucleotideColour);\r
 752     colourMenu.add(userDefinedColour);\r
 753     colourMenu.add(PIDColour);\r
 754     colourMenu.add(BLOSUM62Colour);\r
 755     colourMenu.addSeparator();\r
 756     colourMenu.add(abovePIDThreshold);\r
 757     colourMenu.add(conservationMenuItem);\r
 758     calculateMenu.add(sortPairwiseMenuItem);\r
 759     calculateMenu.add(sortIDMenuItem);\r
 760     calculateMenu.add(sortGroupMenuItem);\r
 761     calculateMenu.add(sortTreeOrderMenuItem);\r
 762     calculateMenu.add(removeRedundancyMenuItem);\r
 763     calculateMenu.addSeparator();\r
 764     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 765     calculateMenu.add(PCAMenuItem);\r
 766     calculateMenu.addSeparator();\r
 767     calculateMenu.add(averageDistanceTreeMenuItem);\r
 768     calculateMenu.add(neighbourTreeMenuItem);\r
 769     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 770     calculateMenu.add(njTreeBlosumMenuItem);\r
 771     alignMenu.add(clustalAlignMenuItem);\r
 772     alignMenu.add(pdbTest);\r
 773     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 774     jMenu1.add(pasteNew);\r
 775     jMenu1.add(pasteThis);\r
 776   }\r
 777 \r
 778   protected void saveAs_actionPerformed(ActionEvent e)\r
 779   {\r
 780 \r
 781   }\r
 782 \r
 783   protected void outputText_actionPerformed(ActionEvent e)\r
 784   {\r
 785 \r
 786   }\r
 787 \r
 788   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 789   {\r
 790 \r
 791   }\r
 792 \r
 793 \r
 794 \r
 795 \r
 796 \r
 797   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 798   {\r
 799 \r
 800   }\r
 801 \r
 802   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804 \r
 805   }\r
 806 \r
 807   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 808   {\r
 809 \r
 810   }\r
 811 \r
 812 \r
 813   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 814   {\r
 815 \r
 816   }\r
 817 \r
 818 \r
 819   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 820   {\r
 821 \r
 822   }\r
 823 \r
 824   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 825   {\r
 826 \r
 827   }\r
 828 \r
 829   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831 \r
 832   }\r
 833 \r
 834 \r
 835   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 836   {\r
 837 \r
 838   }\r
 839 \r
 840   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 841   {\r
 842 \r
 843   }\r
 844 \r
 845   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 846   {\r
 847 \r
 848   }\r
 849 \r
 850   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 851   {\r
 852 \r
 853   }\r
 854 \r
 855   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857 \r
 858   }\r
 859 \r
 860   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865 \r
 866   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 867   {\r
 868 \r
 869   }\r
 870 \r
 871   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 872   {\r
 873 \r
 874   }\r
 875 \r
 876   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878 \r
 879   }\r
 880 \r
 881   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 882   {\r
 883 \r
 884   }\r
 885 \r
 886 \r
 887   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 888   {\r
 889 \r
 890   }\r
 891 \r
 892   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 893   {\r
 894 \r
 895   }\r
 896 \r
 897 \r
 898   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 899   {\r
 900 \r
 901   }\r
 902 \r
 903 \r
 904 \r
 905   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 906   {\r
 907 \r
 908   }\r
 909 \r
 910   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913   }\r
 914 \r
 915   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917 \r
 918   }\r
 919 \r
 920   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922 \r
 923   }\r
 924 \r
 925   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 926   {\r
 927 \r
 928   }\r
 929 \r
 930   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932 \r
 933   }\r
 934 \r
 935   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 936   {\r
 937 \r
 938   }\r
 939 \r
 940   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 941   {\r
 942 \r
 943   }\r
 944 \r
 945   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 946   {\r
 947 \r
 948   }\r
 949 \r
 950   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 951   {\r
 952 \r
 953   }\r
 954 \r
 955   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 956   {\r
 957 \r
 958   }\r
 959 \r
 960 \r
 961   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 962   {\r
 963 \r
 964   }\r
 965 \r
 966   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 967   {\r
 968 \r
 969   }\r
 970 \r
 971 \r
 972 \r
 973   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 974   {\r
 975 \r
 976   }\r
 977 \r
 978 \r
 979 \r
 980 \r
 981   protected void clustalColour_actionPerformed(ActionEvent e)\r
 982   {\r
 983 \r
 984   }\r
 985 \r
 986   protected void zappoColour_actionPerformed(ActionEvent e)\r
 987   {\r
 988 \r
 989   }\r
 990 \r
 991   protected void taylorColour_actionPerformed(ActionEvent e)\r
 992   {\r
 993 \r
 994   }\r
 995 \r
 996 \r
 997   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 998   {\r
 999 \r
1000   }\r
1001 \r
1002   protected void helixColour_actionPerformed(ActionEvent e)\r
1003   {\r
1004 \r
1005   }\r
1006 \r
1007   protected void strandColour_actionPerformed(ActionEvent e)\r
1008   {\r
1009 \r
1010   }\r
1011 \r
1012   protected void turnColour_actionPerformed(ActionEvent e)\r
1013   {\r
1014 \r
1015   }\r
1016 \r
1017   protected void buriedColour_actionPerformed(ActionEvent e)\r
1018   {\r
1019 \r
1020   }\r
1021 \r
1022 \r
1023 \r
1024   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1025   {\r
1026 \r
1027   }\r
1028 \r
1029   protected void PIDColour_actionPerformed(ActionEvent e)\r
1030   {\r
1031 \r
1032   }\r
1033 \r
1034   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1035   {\r
1036 \r
1037   }\r
1038 \r
1039 \r
1040   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1041   {\r
1042 \r
1043   }\r
1044 \r
1045   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1046   {\r
1047 \r
1048   }\r
1049 \r
1050   protected void pdbTest_actionPerformed(ActionEvent e)\r
1051   {\r
1052 \r
1053   }\r
1054 \r
1055   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1056   {\r
1057 \r
1058   }\r
1059 \r
1060   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1061   {\r
1062 \r
1063   }\r
1064 \r
1065   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1066   {\r
1067 \r
1068   }\r
1069 \r
1070 \r
1071   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1072 \r
1073   }\r
1074 \r
1075   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1076   {\r
1077 \r
1078   }\r
1079 \r
1080   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1081   {\r
1082 \r
1083   }\r
1084 \r
1085   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1086   {\r
1087 \r
1088   }\r
1089 \r
1090  protected void copy_actionPerformed(ActionEvent e)\r
1091   {\r
1092 \r
1093   }\r
1094 \r
1095 \r
1096   protected void cut_actionPerformed(ActionEvent e)\r
1097   {\r
1098 \r
1099   }\r
1100 \r
1101   protected void delete_actionPerformed(ActionEvent e)\r
1102   {\r
1103 \r
1104   }\r
1105 \r
1106   protected void pasteNew_actionPerformed(ActionEvent e)\r
1107   {\r
1108 \r
1109   }\r
1110 \r
1111   protected void pasteThis_actionPerformed(ActionEvent e)\r
1112   {\r
1113 \r
1114   }\r
1115 \r
1116   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1117   {\r
1118 \r
1119   }\r
1120 \r
1121   protected void createJPG_actionPerformed(ActionEvent e)\r
1122   {\r
1123 \r
1124   }\r
1125 \r
1126 \r
1127 \r
1128 }\r