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