src/jalview/jbgui/GAlignFrame.java

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