src/jalview/jbgui/GAlignFrame.java

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