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