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 deleteSelectedMenuItem = new JMenuItem();\r
  32   protected JMenuItem moveSelectedMenuItem = new JMenuItem();\r
  33   protected JMenuItem copySelectedMenuItem = new JMenuItem();\r
  34   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  35   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  36   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  37   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  38   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  39   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  40   protected JMenuItem fontNameMenuItem = new JMenuItem();\r
  41   protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
  42   protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
  43   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  44   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  45   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  46   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  47   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  48   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  50   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  51   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  52   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  53   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  54   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  55   BorderLayout borderLayout1 = new BorderLayout();\r
  56   public JLabel statusBar = new JLabel();\r
  57   protected JMenu saveAlignmentMenu = new JMenu();\r
  58   protected JMenu outputTextboxMenu = new JMenu();\r
  59   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  71   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  72   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  73   protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  75   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  76   JMenuItem htmlMenuItem = new JMenuItem();\r
  77   JMenuItem schemeKeyMenuItem = new JMenuItem();\r
  78   JMenuItem overviewMenuItem = new JMenuItem();\r
  79   protected JMenuItem undoMenuItem = new JMenuItem();\r
  80   protected JMenuItem redoMenuItem = new JMenuItem();\r
  81   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  82   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  83   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  84   JMenuItem pdbTest = new JMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   JMenu searchMenu = new JMenu();\r
  89   public GAlignFrame()\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(abovePIDColour);\r
 138     colours.add(userDefinedColour);\r
 139     colours.add(PIDColour);\r
 140     colours.add(BLOSUM62Colour);\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     groupEditingMenuItem.setText("Group editing mode");\r
 172     groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 173     {\r
 174       public void actionPerformed(ActionEvent e)\r
 175       {\r
 176         groupEditingMenuItem_actionPerformed(e);\r
 177       }\r
 178     });\r
 179     selectAllSequenceMenuItem.setText("Select all sequences");\r
 180     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 181     {\r
 182       public void actionPerformed(ActionEvent e)\r
 183       {\r
 184         selectAllSequenceMenuItem_actionPerformed(e);\r
 185       }\r
 186     });\r
 187     deselectAllSequenceMenuItem.setText("Clear sequence selection");\r
 188     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 189     {\r
 190       public void actionPerformed(ActionEvent e)\r
 191       {\r
 192         deselectAllSequenceMenuItem_actionPerformed(e);\r
 193       }\r
 194     });\r
 195     invertSequenceMenuItem.setText("Invert sequence selection");\r
 196     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 197     {\r
 198       public void actionPerformed(ActionEvent e)\r
 199       {\r
 200         invertSequenceMenuItem_actionPerformed(e);\r
 201       }\r
 202     });\r
 203     deleteSelectedMenuItem.setText("Delete selected sequences");\r
 204     deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 205     {\r
 206       public void actionPerformed(ActionEvent e)\r
 207       {\r
 208         deleteSelectedMenuItem_actionPerformed(e);\r
 209       }\r
 210     });\r
 211     moveSelectedMenuItem.setText("Move selected sequences to new alignment");\r
 212     moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 213     {\r
 214       public void actionPerformed(ActionEvent e)\r
 215       {\r
 216         moveSelectedMenuItem_actionPerformed(e);\r
 217       }\r
 218     });\r
 219     copySelectedMenuItem.setText("Copy selected sequences to new alignment");\r
 220     copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 221     {\r
 222       public void actionPerformed(ActionEvent e)\r
 223       {\r
 224         copySelectedMenuItem_actionPerformed(e);\r
 225       }\r
 226     });\r
 227     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 228     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 229     {\r
 230       public void actionPerformed(ActionEvent e)\r
 231       {\r
 232         deselectAllColumnsMenuItem_actionPerformed(e);\r
 233       }\r
 234     });\r
 235     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 236     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 237     {\r
 238       public void actionPerformed(ActionEvent e)\r
 239       {\r
 240         remove2LeftMenuItem_actionPerformed(e);\r
 241       }\r
 242     });\r
 243     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 244     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 245     {\r
 246       public void actionPerformed(ActionEvent e)\r
 247       {\r
 248         remove2RightMenuItem_actionPerformed(e);\r
 249       }\r
 250     });\r
 251     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 252     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 253     {\r
 254       public void actionPerformed(ActionEvent e)\r
 255       {\r
 256         removeGappedColumnMenuItem_actionPerformed(e);\r
 257       }\r
 258     });\r
 259     removeAllGapsMenuItem.setText("Remove all gaps");\r
 260     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 261     {\r
 262       public void actionPerformed(ActionEvent e)\r
 263       {\r
 264         removeAllGapsMenuItem_actionPerformed(e);\r
 265       }\r
 266     });\r
 267     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 268     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 269     {\r
 270       public void actionPerformed(ActionEvent e)\r
 271       {\r
 272         setGapCharMenuItem_actionPerformed(e);\r
 273       }\r
 274     });\r
 275     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 276     {\r
 277       public void actionPerformed(ActionEvent e)\r
 278       {\r
 279         fontNameMenuItem_actionPerformed(e);\r
 280       }\r
 281     });\r
 282     fontSizeMenuItem.setText("10");\r
 283     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 284     {\r
 285       public void actionPerformed(ActionEvent e)\r
 286       {\r
 287         fontSizeMenuItem_actionPerformed(e);\r
 288       }\r
 289     });\r
 290     fontStyleMenuItem.setText("Plain");\r
 291     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         fontStyleMenuItem_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     viewBoxesMenuItem.setText("Boxes");\r
 299     viewBoxesMenuItem.setState(true);\r
 300     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 301     {\r
 302       public void actionPerformed(ActionEvent e)\r
 303       {\r
 304         viewBoxesMenuItem_actionPerformed(e);\r
 305       }\r
 306     });\r
 307     viewTextMenuItem.setText("Text");\r
 308     viewTextMenuItem.setState(true);\r
 309     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 310     {\r
 311       public void actionPerformed(ActionEvent e)\r
 312       {\r
 313         viewTextMenuItem_actionPerformed(e);\r
 314       }\r
 315     });\r
 316     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 317     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 318     {\r
 319       public void actionPerformed(ActionEvent e)\r
 320       {\r
 321         sortPairwiseMenuItem_actionPerformed(e);\r
 322       }\r
 323     });\r
 324     sortIDMenuItem.setText("Sort by ID");\r
 325     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 326     {\r
 327       public void actionPerformed(ActionEvent e)\r
 328       {\r
 329         sortIDMenuItem_actionPerformed(e);\r
 330       }\r
 331     });\r
 332     sortGroupMenuItem.setText("Sort by group");\r
 333     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 334     {\r
 335       public void actionPerformed(ActionEvent e)\r
 336       {\r
 337         sortGroupMenuItem_actionPerformed(e);\r
 338       }\r
 339     });\r
 340     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 341     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 342     {\r
 343       public void actionPerformed(ActionEvent e)\r
 344       {\r
 345         sortTreeOrderMenuItem_actionPerformed(e);\r
 346       }\r
 347     });\r
 348     removeRedundancyMenuItem.setText("Remove redundancy");\r
 349     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 350     {\r
 351       public void actionPerformed(ActionEvent e)\r
 352       {\r
 353         removeRedundancyMenuItem_actionPerformed(e);\r
 354       }\r
 355     });\r
 356     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 357     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 358     {\r
 359       public void actionPerformed(ActionEvent e)\r
 360       {\r
 361         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 362       }\r
 363     });\r
 364     PCAMenuItem.setText("Principal component analysis");\r
 365     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 366     {\r
 367       public void actionPerformed(ActionEvent e)\r
 368       {\r
 369         PCAMenuItem_actionPerformed(e);\r
 370       }\r
 371     });\r
 372     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 373     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 374     {\r
 375       public void actionPerformed(ActionEvent e)\r
 376       {\r
 377         averageDistanceTreeMenuItem_actionPerformed(e);\r
 378       }\r
 379     });\r
 380     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 381     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 382     {\r
 383       public void actionPerformed(ActionEvent e)\r
 384       {\r
 385         neighbourTreeMenuItem_actionPerformed(e);\r
 386       }\r
 387     });\r
 388     clustalAlignMenuItem.setText("Clustal alignment");\r
 389     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 390     {\r
 391       public void actionPerformed(ActionEvent e)\r
 392       {\r
 393         clustalAlignMenuItem_actionPerformed(e);\r
 394       }\r
 395     });\r
 396     this.getContentPane().setLayout(borderLayout1);\r
 397     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 398     statusBar.setBackground(Color.white);\r
 399     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 400     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 401     statusBar.setText("Status bar");\r
 402     outputTextboxMenu.setMnemonic('T');\r
 403     outputTextboxMenu.setText("Output alignment via textbox");\r
 404     clustalColour.setEnabled(false);\r
 405     clustalColour.setSelected(false);\r
 406     clustalColour.setText("Clustalx colours");\r
 407     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 408     {\r
 409       public void actionPerformed(ActionEvent e)\r
 410       {\r
 411         clustalColour_actionPerformed(e);\r
 412       }\r
 413     });\r
 414     zappoColour.setText("Zappo colour scheme");\r
 415     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 416     {\r
 417       public void actionPerformed(ActionEvent e)\r
 418       {\r
 419         zappoColour_actionPerformed(e);\r
 420       }\r
 421     });\r
 422     taylorColour.setText("Taylor colour scheme");\r
 423     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 424     {\r
 425       public void actionPerformed(ActionEvent e)\r
 426       {\r
 427         taylorColour_actionPerformed(e);\r
 428       }\r
 429     });\r
 430     hydrophobicityColour.setText("By hydrophobicity");\r
 431     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 432     {\r
 433       public void actionPerformed(ActionEvent e)\r
 434       {\r
 435         hydrophobicityColour_actionPerformed(e);\r
 436       }\r
 437     });\r
 438     helixColour.setText("Helix propensity");\r
 439     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 440     {\r
 441       public void actionPerformed(ActionEvent e)\r
 442       {\r
 443         helixColour_actionPerformed(e);\r
 444       }\r
 445     });\r
 446     strandColour.setText("Strand propensity");\r
 447     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 448     {\r
 449       public void actionPerformed(ActionEvent e)\r
 450       {\r
 451         strandColour_actionPerformed(e);\r
 452       }\r
 453     });\r
 454     turnColour.setText("Turn propensity");\r
 455     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 456     {\r
 457       public void actionPerformed(ActionEvent e)\r
 458       {\r
 459         turnColour_actionPerformed(e);\r
 460       }\r
 461     });\r
 462     buriedColour.setText("Buried index");\r
 463     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 464     {\r
 465       public void actionPerformed(ActionEvent e)\r
 466       {\r
 467         buriedColour_actionPerformed(e);\r
 468       }\r
 469     });\r
 470     abovePIDColour.setEnabled(false);\r
 471     abovePIDColour.setText("Above PID threshold only");\r
 472     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         abovePIDColour_actionPerformed(e);\r
 477       }\r
 478     });\r
 479     userDefinedColour.setText("User defined colours");\r
 480     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 481     {\r
 482       public void actionPerformed(ActionEvent e)\r
 483       {\r
 484         userDefinedColour_actionPerformed(e);\r
 485       }\r
 486     });\r
 487     PIDColour.setEnabled(false);\r
 488     PIDColour.setText("By PID");\r
 489     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 490     {\r
 491       public void actionPerformed(ActionEvent e)\r
 492       {\r
 493         PIDColour_actionPerformed(e);\r
 494       }\r
 495     });\r
 496     BLOSUM62Colour.setText("By BLOSUM62 score");\r
 497     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         BLOSUM62Colour_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 505     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         avTreeBlosumMenuItem_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 513     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 514     {\r
 515       public void actionPerformed(ActionEvent e)\r
 516       {\r
 517         njTreeBlosumMenuItem_actionPerformed(e);\r
 518       }\r
 519     });\r
 520     conservationColourIncMenuItem.setEnabled(false);\r
 521     conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
 522     conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         conservationColourIncMenuItem_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     consensusGraphMenuItem.setActionCommand("");\r
 530     consensusGraphMenuItem.setText("Consensus graph");\r
 531     consensusGraphMenuItem.setState(true);\r
 532     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 533     {\r
 534       public void actionPerformed(ActionEvent e)\r
 535       {\r
 536         consensusGraphMenuItem_actionPerformed(e);\r
 537       }\r
 538     });\r
 539     colourTextMenuItem.setText("Colour text");\r
 540     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 541     {\r
 542       public void actionPerformed(ActionEvent e)\r
 543       {\r
 544         colourTextMenuItem_actionPerformed(e);\r
 545       }\r
 546     });\r
 547     htmlMenuItem.setText("Output as HTML");\r
 548     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 549     {\r
 550       public void actionPerformed(ActionEvent e)\r
 551       {\r
 552         htmlMenuItem_actionPerformed(e);\r
 553       }\r
 554     });\r
 555     schemeKeyMenuItem.setText("Colour Scheme Key");\r
 556     schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 557     {\r
 558       public void actionPerformed(ActionEvent e)\r
 559       {\r
 560         schemeKeyMenuItem_actionPerformed(e);\r
 561       }\r
 562     });\r
 563     overviewMenuItem.setText("Overview window");\r
 564     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 565     {\r
 566       public void actionPerformed(ActionEvent e)\r
 567       {\r
 568         overviewMenuItem_actionPerformed(e);\r
 569       }\r
 570     });\r
 571     undoMenuItem.setEnabled(false);\r
 572     undoMenuItem.setMnemonic('Z');\r
 573     undoMenuItem.setText("Undo");\r
 574     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         undoMenuItem_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     redoMenuItem.setEnabled(false);\r
 582     redoMenuItem.setMnemonic('0');\r
 583     redoMenuItem.setText("Redo");\r
 584     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 585     {\r
 586       public void actionPerformed(ActionEvent e)\r
 587       {\r
 588         redoMenuItem_actionPerformed(e);\r
 589       }\r
 590     });\r
 591     conservationMenuItem.setText("By conservation");\r
 592     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 593     {\r
 594       public void actionPerformed(ActionEvent e)\r
 595       {\r
 596         conservationMenuItem_actionPerformed(e);\r
 597       }\r
 598     });\r
 599     noColourmenuItem.setText("None");\r
 600     noColourmenuItem.setSelected(true);\r
 601     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 602     {\r
 603       public void actionPerformed(ActionEvent e)\r
 604       {\r
 605         noColourmenuItem_actionPerformed(e);\r
 606       }\r
 607     });\r
 608     wrapMenuItem.setEnabled(false);\r
 609     wrapMenuItem.setText("Wrap alignment");\r
 610     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 611     {\r
 612       public void actionPerformed(ActionEvent e)\r
 613       {\r
 614         wrapMenuItem_actionPerformed(e);\r
 615       }\r
 616     });\r
 617     pdbTest.setText("PDB Test Viewer");\r
 618     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 619     {\r
 620       public void actionPerformed(ActionEvent e)\r
 621       {\r
 622         pdbTest_actionPerformed(e);\r
 623       }\r
 624     });\r
 625     printMenuItem.setText("Print");\r
 626     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         printMenuItem_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     renderGapsMenuItem.setText("Render gaps");\r
 634     renderGapsMenuItem.setState(true);\r
 635     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 636     {\r
 637       public void actionPerformed(ActionEvent e)\r
 638       {\r
 639         renderGapsMenuItem_actionPerformed(e);\r
 640       }\r
 641     });\r
 642     findMenuItem.setText("Find");\r
 643     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 644     {\r
 645       public void actionPerformed(ActionEvent e)\r
 646       {\r
 647         findMenuItem_actionPerformed(e);\r
 648       }\r
 649     });\r
 650     searchMenu.setText("Search");\r
 651     alignFrameMenuBar.add(fileMenu);\r
 652     alignFrameMenuBar.add(editMenu);\r
 653     alignFrameMenuBar.add(searchMenu);\r
 654     alignFrameMenuBar.add(fontMenu);\r
 655     alignFrameMenuBar.add(viewMenu);\r
 656     alignFrameMenuBar.add(colourMenu);\r
 657     alignFrameMenuBar.add(calculateMenu);\r
 658     alignFrameMenuBar.add(alignMenu);\r
 659     fileMenu.add(saveAlignmentMenu);\r
 660     fileMenu.add(outputTextboxMenu);\r
 661     fileMenu.add(htmlMenuItem);\r
 662     fileMenu.add(printMenuItem);\r
 663     fileMenu.addSeparator();\r
 664     fileMenu.add(closeMenuItem);\r
 665     editMenu.add(undoMenuItem);\r
 666     editMenu.add(redoMenuItem);\r
 667     editMenu.addSeparator();\r
 668     editMenu.add(groupsMenuItem);\r
 669     editMenu.add(groupEditingMenuItem);\r
 670     editMenu.addSeparator();\r
 671     editMenu.add(selectAllSequenceMenuItem);\r
 672     editMenu.add(deselectAllSequenceMenuItem);\r
 673     editMenu.add(invertSequenceMenuItem);\r
 674     editMenu.addSeparator();\r
 675     editMenu.add(copySelectedMenuItem);\r
 676     editMenu.add(moveSelectedMenuItem);\r
 677     editMenu.add(deleteSelectedMenuItem);\r
 678     editMenu.addSeparator();\r
 679     editMenu.add(deselectAllColumnsMenuItem);\r
 680     editMenu.add(remove2LeftMenuItem);\r
 681     editMenu.add(remove2RightMenuItem);\r
 682     editMenu.addSeparator();\r
 683     editMenu.add(removeGappedColumnMenuItem);\r
 684     editMenu.add(removeAllGapsMenuItem);\r
 685     editMenu.add(setGapCharMenuItem);\r
 686     searchMenu.add(findMenuItem);\r
 687     fontMenu.add(fontNameMenuItem);\r
 688     fontMenu.add(fontSizeMenuItem);\r
 689     fontMenu.add(fontStyleMenuItem);\r
 690     viewMenu.add(wrapMenuItem);\r
 691     viewMenu.add(viewBoxesMenuItem);\r
 692     viewMenu.add(viewTextMenuItem);\r
 693     viewMenu.add(colourTextMenuItem);\r
 694     viewMenu.add(renderGapsMenuItem);\r
 695     viewMenu.add(consensusGraphMenuItem);\r
 696     viewMenu.add(overviewMenuItem);\r
 697     colourMenu.add(noColourmenuItem);\r
 698     colourMenu.add(clustalColour);\r
 699     colourMenu.add(zappoColour);\r
 700     colourMenu.add(taylorColour);\r
 701     colourMenu.add(hydrophobicityColour);\r
 702     colourMenu.add(helixColour);\r
 703     colourMenu.add(strandColour);\r
 704     colourMenu.add(turnColour);\r
 705     colourMenu.add(buriedColour);\r
 706     colourMenu.add(userDefinedColour);\r
 707     colourMenu.addSeparator();\r
 708     colourMenu.add(conservationMenuItem);\r
 709     colourMenu.add(conservationColourIncMenuItem);\r
 710     colourMenu.addSeparator();\r
 711     colourMenu.add(abovePIDColour);\r
 712     colourMenu.add(PIDColour);\r
 713     colourMenu.add(BLOSUM62Colour);\r
 714     colourMenu.addSeparator();\r
 715     colourMenu.add(schemeKeyMenuItem);\r
 716     calculateMenu.add(sortPairwiseMenuItem);\r
 717     calculateMenu.add(sortIDMenuItem);\r
 718     calculateMenu.add(sortGroupMenuItem);\r
 719     calculateMenu.add(sortTreeOrderMenuItem);\r
 720     calculateMenu.add(removeRedundancyMenuItem);\r
 721     calculateMenu.addSeparator();\r
 722     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 723     calculateMenu.add(PCAMenuItem);\r
 724     calculateMenu.addSeparator();\r
 725     calculateMenu.add(averageDistanceTreeMenuItem);\r
 726     calculateMenu.add(neighbourTreeMenuItem);\r
 727     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 728     calculateMenu.add(njTreeBlosumMenuItem);\r
 729     alignMenu.add(clustalAlignMenuItem);\r
 730     alignMenu.add(pdbTest);\r
 731     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 732   }\r
 733 \r
 734   protected void saveAs_actionPerformed(ActionEvent e)\r
 735   {\r
 736 \r
 737   }\r
 738 \r
 739   protected void outputText_actionPerformed(ActionEvent e)\r
 740   {\r
 741 \r
 742   }\r
 743 \r
 744   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 745   {\r
 746 \r
 747   }\r
 748 \r
 749 \r
 750 \r
 751 \r
 752 \r
 753   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 754   {\r
 755 \r
 756   }\r
 757 \r
 758   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 759   {\r
 760 \r
 761   }\r
 762 \r
 763   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 764   {\r
 765 \r
 766   }\r
 767 \r
 768 \r
 769   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771 \r
 772   }\r
 773 \r
 774   protected void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781 \r
 782   }\r
 783 \r
 784   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786 \r
 787   }\r
 788 \r
 789   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 790   {\r
 791 \r
 792   }\r
 793 \r
 794   protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
 795   {\r
 796 \r
 797   }\r
 798 \r
 799   protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
 800   {\r
 801 \r
 802   }\r
 803 \r
 804   protected void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
 805   {\r
 806 \r
 807   }\r
 808 \r
 809   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 810   {\r
 811 \r
 812   }\r
 813 \r
 814   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 815   {\r
 816 \r
 817   }\r
 818 \r
 819   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 820   {\r
 821 \r
 822   }\r
 823 \r
 824   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 825   {\r
 826 \r
 827   }\r
 828 \r
 829   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831 \r
 832   }\r
 833 \r
 834   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 835   {\r
 836 \r
 837   }\r
 838 \r
 839 \r
 840   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 841   {\r
 842 \r
 843   }\r
 844 \r
 845   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 846   {\r
 847 \r
 848   }\r
 849 \r
 850   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 851   {\r
 852 \r
 853   }\r
 854 \r
 855   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857 \r
 858   }\r
 859 \r
 860 \r
 861   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863 \r
 864   }\r
 865 \r
 866   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 867   {\r
 868 \r
 869   }\r
 870 \r
 871 \r
 872   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 873   {\r
 874 \r
 875   }\r
 876 \r
 877 \r
 878 \r
 879   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 880   {\r
 881 \r
 882   }\r
 883 \r
 884   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886 \r
 887   }\r
 888 \r
 889   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 890   {\r
 891 \r
 892   }\r
 893 \r
 894   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 905   {\r
 906 \r
 907   }\r
 908 \r
 909   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912   }\r
 913 \r
 914   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916 \r
 917   }\r
 918 \r
 919   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921 \r
 922   }\r
 923 \r
 924   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 925   {\r
 926 \r
 927   }\r
 928 \r
 929   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 930   {\r
 931 \r
 932   }\r
 933 \r
 934 \r
 935   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 936   {\r
 937 \r
 938   }\r
 939 \r
 940   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 941   {\r
 942 \r
 943   }\r
 944 \r
 945 \r
 946 \r
 947   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949 \r
 950   }\r
 951 \r
 952 \r
 953 \r
 954 \r
 955   protected void clustalColour_actionPerformed(ActionEvent e)\r
 956   {\r
 957 \r
 958   }\r
 959 \r
 960   protected void zappoColour_actionPerformed(ActionEvent e)\r
 961   {\r
 962 \r
 963   }\r
 964 \r
 965   protected void taylorColour_actionPerformed(ActionEvent e)\r
 966   {\r
 967 \r
 968   }\r
 969 \r
 970 \r
 971   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 972   {\r
 973 \r
 974   }\r
 975 \r
 976   protected void helixColour_actionPerformed(ActionEvent e)\r
 977   {\r
 978 \r
 979   }\r
 980 \r
 981   protected void strandColour_actionPerformed(ActionEvent e)\r
 982   {\r
 983 \r
 984   }\r
 985 \r
 986   protected void turnColour_actionPerformed(ActionEvent e)\r
 987   {\r
 988 \r
 989   }\r
 990 \r
 991   protected void buriedColour_actionPerformed(ActionEvent e)\r
 992   {\r
 993 \r
 994   }\r
 995 \r
 996 \r
 997   protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
 998  {\r
 999 \r
1000  }\r
1001 \r
1002 \r
1003   protected void abovePIDColour_actionPerformed(ActionEvent e)\r
1004   {\r
1005 \r
1006   }\r
1007 \r
1008 \r
1009   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1010   {\r
1011 \r
1012   }\r
1013 \r
1014   protected void PIDColour_actionPerformed(ActionEvent e)\r
1015   {\r
1016 \r
1017   }\r
1018 \r
1019   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1020   {\r
1021 \r
1022   }\r
1023 \r
1024   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
1025   {\r
1026 \r
1027   }\r
1028 \r
1029   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1030   {\r
1031 \r
1032   }\r
1033 \r
1034   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1035   {\r
1036 \r
1037   }\r
1038 \r
1039   protected void pdbTest_actionPerformed(ActionEvent e)\r
1040   {\r
1041 \r
1042   }\r
1043 \r
1044   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046 \r
1047   }\r
1048 \r
1049   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1050   {\r
1051 \r
1052   }\r
1053 \r
1054   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1055   {\r
1056 \r
1057   }\r
1058 \r
1059 }\r