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 viewMenu = new JMenu();\r
  22   protected JMenu colourMenu = new JMenu();\r
  23   protected JMenu calculateMenu = new JMenu();\r
  24   protected JMenu alignMenu = new JMenu();\r
  25   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  26   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  27   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  28   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  29   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  30   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  31   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  32   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  33   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  34   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  35   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  36   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  37   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  38   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  39   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  40   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  41   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  42   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  43   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  44   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  45   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  46   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  47   BorderLayout borderLayout1 = new BorderLayout();\r
  48   public JLabel statusBar = new JLabel();\r
  49   protected JMenu saveAlignmentMenu = new JMenu();\r
  50   protected JMenu outputTextboxMenu = new JMenu();\r
  51   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  52   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  54   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  58   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  59   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  62   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  63   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  64   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  65   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  66   JMenuItem htmlMenuItem = new JMenuItem();\r
  67   JMenuItem overviewMenuItem = new JMenuItem();\r
  68   protected JMenuItem undoMenuItem = new JMenuItem();\r
  69   protected JMenuItem redoMenuItem = new JMenuItem();\r
  70   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  72   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  73   JMenuItem printMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  75   JMenuItem findMenuItem = new JMenuItem();\r
  76   JMenu searchMenu = new JMenu();\r
  77   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  78   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  79   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  80   JMenuItem deleteGroups = new JMenuItem();\r
  81   JMenuItem delete = new JMenuItem();\r
  82   JMenuItem copy = new JMenuItem();\r
  83   JMenuItem cut = new JMenuItem();\r
  84   JMenu jMenu1 = new JMenu();\r
  85   JMenuItem pasteNew = new JMenuItem();\r
  86   JMenuItem pasteThis = new JMenuItem();\r
  87   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  88   JMenuItem createJPG = new JMenuItem();\r
  89   protected JMenuItem font = new JMenuItem();\r
  90   public GAlignFrame()\r
  91   {\r
  92 \r
  93 \r
  94     try\r
  95     {\r
  96       jbInit();\r
  97       setJMenuBar(alignFrameMenuBar);\r
  98 \r
  99       JMenuItem item;\r
 100       // dynamically fill save as menu with available formats\r
 101       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
 102         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 103         saveAlignmentMenu.add( item );\r
 104         item.addActionListener(new java.awt.event.ActionListener()\r
 105         {\r
 106           public void actionPerformed(ActionEvent e)\r
 107           {\r
 108             saveAs_actionPerformed(e);\r
 109           }\r
 110         });\r
 111 \r
 112         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 113         item.addActionListener(new java.awt.event.ActionListener()\r
 114         {\r
 115           public void actionPerformed(ActionEvent e)\r
 116           {\r
 117             outputText_actionPerformed(e);\r
 118           }\r
 119         });\r
 120 \r
 121         outputTextboxMenu.add( item );\r
 122       }\r
 123 \r
 124     }\r
 125     catch(Exception e)\r
 126     {\r
 127       e.printStackTrace();\r
 128     }\r
 129 \r
 130     ButtonGroup colours = new ButtonGroup();\r
 131     colours.add(noColourmenuItem);\r
 132     colours.add(clustalColour);\r
 133     colours.add(zappoColour);\r
 134     colours.add(taylorColour);\r
 135     colours.add(hydrophobicityColour);\r
 136     colours.add(helixColour);\r
 137     colours.add(strandColour);\r
 138     colours.add(turnColour);\r
 139     colours.add(buriedColour);\r
 140     colours.add(userDefinedColour);\r
 141     colours.add(PIDColour);\r
 142     colours.add(BLOSUM62Colour);\r
 143     colours.add(nucleotideColour);\r
 144   }\r
 145   private void jbInit() throws Exception\r
 146   {\r
 147     fileMenu.setMnemonic('F');\r
 148     fileMenu.setText("File");\r
 149     saveAlignmentMenu.setMnemonic('L');\r
 150     saveAlignmentMenu.setText("Save alignment to local file");\r
 151     closeMenuItem.setMnemonic('C');\r
 152     closeMenuItem.setText("Close");\r
 153     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 154     {\r
 155       public void actionPerformed(ActionEvent e)\r
 156       {\r
 157         closeMenuItem_actionPerformed(e);\r
 158       }\r
 159     });\r
 160     editMenu.setText("Edit");\r
 161     viewMenu.setText("View");\r
 162     colourMenu.setText("Colour");\r
 163     calculateMenu.setText("Calculate");\r
 164     alignMenu.setText("Web Service");\r
 165     groupsMenuItem.setVisible(false);\r
 166     groupsMenuItem.setText("Groups");\r
 167     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 168     {\r
 169       public void actionPerformed(ActionEvent e)\r
 170       {\r
 171         groupsMenuItem_actionPerformed(e);\r
 172       }\r
 173     });\r
 174     selectAllSequenceMenuItem.setText("Select all");\r
 175     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 176     {\r
 177       public void actionPerformed(ActionEvent e)\r
 178       {\r
 179         selectAllSequenceMenuItem_actionPerformed(e);\r
 180       }\r
 181     });\r
 182     deselectAllSequenceMenuItem.setText("Clear selection");\r
 183     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 184     {\r
 185       public void actionPerformed(ActionEvent e)\r
 186       {\r
 187         deselectAllSequenceMenuItem_actionPerformed(e);\r
 188       }\r
 189     });\r
 190     invertSequenceMenuItem.setText("Invert sequence selection");\r
 191     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 192     {\r
 193       public void actionPerformed(ActionEvent e)\r
 194       {\r
 195         invertSequenceMenuItem_actionPerformed(e);\r
 196       }\r
 197     });\r
 198     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 199     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 200     {\r
 201       public void actionPerformed(ActionEvent e)\r
 202       {\r
 203         deselectAllColumnsMenuItem_actionPerformed(e);\r
 204       }\r
 205     });\r
 206     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 207     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 208     {\r
 209       public void actionPerformed(ActionEvent e)\r
 210       {\r
 211         remove2LeftMenuItem_actionPerformed(e);\r
 212       }\r
 213     });\r
 214     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 215     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 216     {\r
 217       public void actionPerformed(ActionEvent e)\r
 218       {\r
 219         remove2RightMenuItem_actionPerformed(e);\r
 220       }\r
 221     });\r
 222     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 223     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 224     {\r
 225       public void actionPerformed(ActionEvent e)\r
 226       {\r
 227         removeGappedColumnMenuItem_actionPerformed(e);\r
 228       }\r
 229     });\r
 230     removeAllGapsMenuItem.setText("Remove all gaps");\r
 231     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 232     {\r
 233       public void actionPerformed(ActionEvent e)\r
 234       {\r
 235         removeAllGapsMenuItem_actionPerformed(e);\r
 236       }\r
 237     });\r
 238     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 239     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 240     {\r
 241       public void actionPerformed(ActionEvent e)\r
 242       {\r
 243         setGapCharMenuItem_actionPerformed(e);\r
 244       }\r
 245     });\r
 246     viewBoxesMenuItem.setText("Boxes");\r
 247     viewBoxesMenuItem.setState(true);\r
 248     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 249     {\r
 250       public void actionPerformed(ActionEvent e)\r
 251       {\r
 252         viewBoxesMenuItem_actionPerformed(e);\r
 253       }\r
 254     });\r
 255     viewTextMenuItem.setText("Text");\r
 256     viewTextMenuItem.setState(true);\r
 257     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 258     {\r
 259       public void actionPerformed(ActionEvent e)\r
 260       {\r
 261         viewTextMenuItem_actionPerformed(e);\r
 262       }\r
 263     });\r
 264     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 265     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 266     {\r
 267       public void actionPerformed(ActionEvent e)\r
 268       {\r
 269         sortPairwiseMenuItem_actionPerformed(e);\r
 270       }\r
 271     });\r
 272     sortIDMenuItem.setText("Sort by ID");\r
 273     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 274     {\r
 275       public void actionPerformed(ActionEvent e)\r
 276       {\r
 277         sortIDMenuItem_actionPerformed(e);\r
 278       }\r
 279     });\r
 280     sortGroupMenuItem.setText("Sort by group");\r
 281     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 282     {\r
 283       public void actionPerformed(ActionEvent e)\r
 284       {\r
 285         sortGroupMenuItem_actionPerformed(e);\r
 286       }\r
 287     });\r
 288     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 289     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 290     {\r
 291       public void actionPerformed(ActionEvent e)\r
 292       {\r
 293         sortTreeOrderMenuItem_actionPerformed(e);\r
 294       }\r
 295     });\r
 296     removeRedundancyMenuItem.setText("Remove redundancy");\r
 297     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 298     {\r
 299       public void actionPerformed(ActionEvent e)\r
 300       {\r
 301         removeRedundancyMenuItem_actionPerformed(e);\r
 302       }\r
 303     });\r
 304     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 305     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 306     {\r
 307       public void actionPerformed(ActionEvent e)\r
 308       {\r
 309         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 310       }\r
 311     });\r
 312     PCAMenuItem.setText("Principal component analysis");\r
 313     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 314     {\r
 315       public void actionPerformed(ActionEvent e)\r
 316       {\r
 317         PCAMenuItem_actionPerformed(e);\r
 318       }\r
 319     });\r
 320     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 321     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 322     {\r
 323       public void actionPerformed(ActionEvent e)\r
 324       {\r
 325         averageDistanceTreeMenuItem_actionPerformed(e);\r
 326       }\r
 327     });\r
 328     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 329     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 330     {\r
 331       public void actionPerformed(ActionEvent e)\r
 332       {\r
 333         neighbourTreeMenuItem_actionPerformed(e);\r
 334       }\r
 335     });\r
 336     clustalAlignMenuItem.setText("Clustal alignment");\r
 337     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 338     {\r
 339       public void actionPerformed(ActionEvent e)\r
 340       {\r
 341         clustalAlignMenuItem_actionPerformed(e);\r
 342       }\r
 343     });\r
 344     this.getContentPane().setLayout(borderLayout1);\r
 345     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 346     statusBar.setBackground(Color.white);\r
 347     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 348     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 349     statusBar.setText("Status bar");\r
 350     outputTextboxMenu.setMnemonic('T');\r
 351     outputTextboxMenu.setText("Output alignment via textbox");\r
 352     clustalColour.setSelected(false);\r
 353     clustalColour.setText("Clustalx colours");\r
 354     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 355     {\r
 356       public void actionPerformed(ActionEvent e)\r
 357       {\r
 358         clustalColour_actionPerformed(e);\r
 359       }\r
 360     });\r
 361     zappoColour.setText("Zappo colour scheme");\r
 362     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 363     {\r
 364       public void actionPerformed(ActionEvent e)\r
 365       {\r
 366         zappoColour_actionPerformed(e);\r
 367       }\r
 368     });\r
 369     taylorColour.setText("Taylor colour scheme");\r
 370     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 371     {\r
 372       public void actionPerformed(ActionEvent e)\r
 373       {\r
 374         taylorColour_actionPerformed(e);\r
 375       }\r
 376     });\r
 377     hydrophobicityColour.setText("By hydrophobicity");\r
 378     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 379     {\r
 380       public void actionPerformed(ActionEvent e)\r
 381       {\r
 382         hydrophobicityColour_actionPerformed(e);\r
 383       }\r
 384     });\r
 385     helixColour.setText("Helix propensity");\r
 386     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 387     {\r
 388       public void actionPerformed(ActionEvent e)\r
 389       {\r
 390         helixColour_actionPerformed(e);\r
 391       }\r
 392     });\r
 393     strandColour.setText("Strand propensity");\r
 394     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         strandColour_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     turnColour.setText("Turn propensity");\r
 402     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 403     {\r
 404       public void actionPerformed(ActionEvent e)\r
 405       {\r
 406         turnColour_actionPerformed(e);\r
 407       }\r
 408     });\r
 409     buriedColour.setText("Buried index");\r
 410     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 411     {\r
 412       public void actionPerformed(ActionEvent e)\r
 413       {\r
 414         buriedColour_actionPerformed(e);\r
 415       }\r
 416     });\r
 417     userDefinedColour.setText("User defined colours");\r
 418     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 419     {\r
 420       public void actionPerformed(ActionEvent e)\r
 421       {\r
 422         userDefinedColour_actionPerformed(e);\r
 423       }\r
 424     });\r
 425     PIDColour.setText("Percentage Identity");\r
 426     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 427     {\r
 428       public void actionPerformed(ActionEvent e)\r
 429       {\r
 430         PIDColour_actionPerformed(e);\r
 431       }\r
 432     });\r
 433     BLOSUM62Colour.setText("BLOSUM62 score");\r
 434     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 435     {\r
 436       public void actionPerformed(ActionEvent e)\r
 437       {\r
 438         BLOSUM62Colour_actionPerformed(e);\r
 439       }\r
 440     });\r
 441     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 442     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 443     {\r
 444       public void actionPerformed(ActionEvent e)\r
 445       {\r
 446         avTreeBlosumMenuItem_actionPerformed(e);\r
 447       }\r
 448     });\r
 449     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 450     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         njTreeBlosumMenuItem_actionPerformed(e);\r
 455       }\r
 456     });\r
 457     consensusGraphMenuItem.setActionCommand("");\r
 458     consensusGraphMenuItem.setText("Consensus graph");\r
 459     consensusGraphMenuItem.setState(true);\r
 460     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 461     {\r
 462       public void actionPerformed(ActionEvent e)\r
 463       {\r
 464         consensusGraphMenuItem_actionPerformed(e);\r
 465       }\r
 466     });\r
 467     colourTextMenuItem.setText("Colour text");\r
 468     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 469     {\r
 470       public void actionPerformed(ActionEvent e)\r
 471       {\r
 472         colourTextMenuItem_actionPerformed(e);\r
 473       }\r
 474     });\r
 475     htmlMenuItem.setText("Output as HTML");\r
 476     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 477     {\r
 478       public void actionPerformed(ActionEvent e)\r
 479       {\r
 480         htmlMenuItem_actionPerformed(e);\r
 481       }\r
 482     });\r
 483     overviewMenuItem.setText("Overview window");\r
 484     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 485     {\r
 486       public void actionPerformed(ActionEvent e)\r
 487       {\r
 488         overviewMenuItem_actionPerformed(e);\r
 489       }\r
 490     });\r
 491     undoMenuItem.setEnabled(false);\r
 492     undoMenuItem.setMnemonic('Z');\r
 493     undoMenuItem.setText("Undo");\r
 494     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         undoMenuItem_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     redoMenuItem.setEnabled(false);\r
 502     redoMenuItem.setMnemonic('0');\r
 503     redoMenuItem.setText("Redo");\r
 504     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 505     {\r
 506       public void actionPerformed(ActionEvent e)\r
 507       {\r
 508         redoMenuItem_actionPerformed(e);\r
 509       }\r
 510     });\r
 511     conservationMenuItem.setText("By conservation");\r
 512     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 513     {\r
 514       public void actionPerformed(ActionEvent e)\r
 515       {\r
 516         conservationMenuItem_actionPerformed(e);\r
 517       }\r
 518     });\r
 519     noColourmenuItem.setText("None");\r
 520     noColourmenuItem.setSelected(true);\r
 521     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         noColourmenuItem_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     wrapMenuItem.setText("Wrap alignment");\r
 529     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         wrapMenuItem_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     printMenuItem.setText("Print");\r
 537     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         printMenuItem_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     renderGapsMenuItem.setText("Render gaps");\r
 545     renderGapsMenuItem.setState(true);\r
 546     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         renderGapsMenuItem_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     findMenuItem.setText("Find");\r
 554     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         findMenuItem_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     searchMenu.setText("Search");\r
 562 \r
 563     abovePIDThreshold.setText("Above PID threshold");\r
 564     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 565       public void actionPerformed(ActionEvent e) {\r
 566         abovePIDThreshold_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     sequenceFeatures.setText("Sequence Features");\r
 570     sequenceFeatures.addActionListener(new ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent actionEvent)\r
 573       {\r
 574         sequenceFeatures_actionPerformed(actionEvent);\r
 575       }\r
 576     });\r
 577     nucleotideColour.setText("Nucleotide colours");\r
 578     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent e)\r
 581       {\r
 582         nucleotideColour_actionPerformed(e);\r
 583       }\r
 584     });\r
 585     deleteGroups.setSelected(false);\r
 586     deleteGroups.setText("Delete all groups");\r
 587     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent e)\r
 590       {\r
 591         deleteGroups_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     copy.setText("Copy");\r
 595     copy.setMnemonic(KeyEvent.VK_C);\r
 596 \r
 597     copy.addActionListener(new java.awt.event.ActionListener()\r
 598     {\r
 599       public void actionPerformed(ActionEvent e)\r
 600       {\r
 601         copy_actionPerformed(e);\r
 602       }\r
 603     });\r
 604     cut.setText("Cut");\r
 605     cut.setMnemonic(KeyEvent.VK_X);\r
 606     cut.addActionListener(new java.awt.event.ActionListener()\r
 607     {\r
 608       public void actionPerformed(ActionEvent e)\r
 609       {\r
 610         cut_actionPerformed(e);\r
 611       }\r
 612     });\r
 613     delete.setText("Delete");\r
 614     delete.addActionListener(new java.awt.event.ActionListener()\r
 615     {\r
 616       public void actionPerformed(ActionEvent e)\r
 617       {\r
 618         delete_actionPerformed(e);\r
 619       }\r
 620     });\r
 621     jMenu1.setMnemonic('V');\r
 622     jMenu1.setText("Paste");\r
 623     pasteNew.setText("to new alignment");\r
 624     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 625     {\r
 626       public void actionPerformed(ActionEvent e)\r
 627       {\r
 628         pasteNew_actionPerformed(e);\r
 629       }\r
 630     });\r
 631     pasteThis.setText("add to this alignment");\r
 632     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 633     {\r
 634       public void actionPerformed(ActionEvent e)\r
 635       {\r
 636         pasteThis_actionPerformed(e);\r
 637       }\r
 638     });\r
 639     applyToAllGroups.setText("Apply colour to all groups");\r
 640     applyToAllGroups.setState(true);\r
 641     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 642     {\r
 643       public void actionPerformed(ActionEvent e)\r
 644       {\r
 645         applyToAllGroups_actionPerformed(e);\r
 646       }\r
 647     });\r
 648     createJPG.addActionListener(new java.awt.event.ActionListener()\r
 649     {\r
 650       public void actionPerformed(ActionEvent e)\r
 651       {\r
 652         createJPG_actionPerformed(e);\r
 653       }\r
 654     });\r
 655     createJPG.setText("Save as JPG Image");\r
 656     font.setText("Change Font");\r
 657     font.addActionListener(new java.awt.event.ActionListener()\r
 658     {\r
 659       public void actionPerformed(ActionEvent e)\r
 660       {\r
 661         font_actionPerformed(e);\r
 662       }\r
 663     });\r
 664     alignFrameMenuBar.add(fileMenu);\r
 665     alignFrameMenuBar.add(editMenu);\r
 666     alignFrameMenuBar.add(searchMenu);\r
 667     alignFrameMenuBar.add(viewMenu);\r
 668     alignFrameMenuBar.add(colourMenu);\r
 669     alignFrameMenuBar.add(calculateMenu);\r
 670     alignFrameMenuBar.add(alignMenu);\r
 671     fileMenu.add(saveAlignmentMenu);\r
 672     fileMenu.add(outputTextboxMenu);\r
 673     fileMenu.add(htmlMenuItem);\r
 674     fileMenu.add(createJPG);\r
 675     fileMenu.add(printMenuItem);\r
 676     fileMenu.addSeparator();\r
 677     fileMenu.add(closeMenuItem);\r
 678     editMenu.add(copy);\r
 679     editMenu.add(jMenu1);\r
 680     editMenu.add(cut);\r
 681     editMenu.add(delete);\r
 682     editMenu.addSeparator();\r
 683     editMenu.add(undoMenuItem);\r
 684     editMenu.add(redoMenuItem);\r
 685     editMenu.addSeparator();\r
 686     editMenu.add(deselectAllSequenceMenuItem);\r
 687     editMenu.add(selectAllSequenceMenuItem);\r
 688     editMenu.add(invertSequenceMenuItem);\r
 689     editMenu.add(deleteGroups);\r
 690     editMenu.add(groupsMenuItem);\r
 691     editMenu.addSeparator();\r
 692     editMenu.add(deselectAllColumnsMenuItem);\r
 693     editMenu.add(remove2LeftMenuItem);\r
 694     editMenu.add(remove2RightMenuItem);\r
 695     editMenu.addSeparator();\r
 696     editMenu.add(removeGappedColumnMenuItem);\r
 697     editMenu.add(removeAllGapsMenuItem);\r
 698     editMenu.add(setGapCharMenuItem);\r
 699     searchMenu.add(findMenuItem);\r
 700     viewMenu.add(font);\r
 701     viewMenu.add(wrapMenuItem);\r
 702     viewMenu.add(viewBoxesMenuItem);\r
 703     viewMenu.add(viewTextMenuItem);\r
 704     viewMenu.add(colourTextMenuItem);\r
 705     viewMenu.add(renderGapsMenuItem);\r
 706     viewMenu.add(consensusGraphMenuItem);\r
 707     viewMenu.add(overviewMenuItem);\r
 708     viewMenu.add(sequenceFeatures);\r
 709     colourMenu.add(applyToAllGroups);\r
 710     colourMenu.add(noColourmenuItem);\r
 711     colourMenu.add(clustalColour);\r
 712     colourMenu.add(zappoColour);\r
 713     colourMenu.add(taylorColour);\r
 714     colourMenu.add(hydrophobicityColour);\r
 715     colourMenu.add(helixColour);\r
 716     colourMenu.add(strandColour);\r
 717     colourMenu.add(turnColour);\r
 718     colourMenu.add(buriedColour);\r
 719     colourMenu.add(nucleotideColour);\r
 720     colourMenu.add(userDefinedColour);\r
 721     colourMenu.add(PIDColour);\r
 722     colourMenu.add(BLOSUM62Colour);\r
 723     colourMenu.addSeparator();\r
 724     colourMenu.add(abovePIDThreshold);\r
 725     colourMenu.add(conservationMenuItem);\r
 726     calculateMenu.add(sortPairwiseMenuItem);\r
 727     calculateMenu.add(sortIDMenuItem);\r
 728     calculateMenu.add(sortGroupMenuItem);\r
 729     calculateMenu.add(sortTreeOrderMenuItem);\r
 730     calculateMenu.add(removeRedundancyMenuItem);\r
 731     calculateMenu.addSeparator();\r
 732     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 733     calculateMenu.add(PCAMenuItem);\r
 734     calculateMenu.addSeparator();\r
 735     calculateMenu.add(averageDistanceTreeMenuItem);\r
 736     calculateMenu.add(neighbourTreeMenuItem);\r
 737     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 738     calculateMenu.add(njTreeBlosumMenuItem);\r
 739     alignMenu.add(clustalAlignMenuItem);\r
 740     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 741     jMenu1.add(pasteNew);\r
 742     jMenu1.add(pasteThis);\r
 743   }\r
 744 \r
 745   protected void saveAs_actionPerformed(ActionEvent e)\r
 746   {\r
 747 \r
 748   }\r
 749 \r
 750   protected void outputText_actionPerformed(ActionEvent e)\r
 751   {\r
 752 \r
 753   }\r
 754 \r
 755   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 756   {\r
 757 \r
 758   }\r
 759 \r
 760 \r
 761 \r
 762 \r
 763 \r
 764   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766 \r
 767   }\r
 768 \r
 769   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771 \r
 772   }\r
 773 \r
 774   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 775   {\r
 776 \r
 777   }\r
 778 \r
 779 \r
 780   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 781   {\r
 782 \r
 783   }\r
 784 \r
 785 \r
 786   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 787   {\r
 788 \r
 789   }\r
 790 \r
 791   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793 \r
 794   }\r
 795 \r
 796   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798 \r
 799   }\r
 800 \r
 801 \r
 802   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804 \r
 805   }\r
 806 \r
 807   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 808   {\r
 809 \r
 810   }\r
 811 \r
 812   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 813   {\r
 814 \r
 815   }\r
 816 \r
 817   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 818   {\r
 819 \r
 820   }\r
 821 \r
 822   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 823   {\r
 824 \r
 825   }\r
 826 \r
 827   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 828   {\r
 829 \r
 830   }\r
 831 \r
 832 \r
 833 \r
 834 \r
 835 \r
 836   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 837   {\r
 838 \r
 839   }\r
 840 \r
 841 \r
 842   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844 \r
 845   }\r
 846 \r
 847   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849 \r
 850   }\r
 851 \r
 852 \r
 853   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 854   {\r
 855 \r
 856   }\r
 857 \r
 858 \r
 859 \r
 860   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 866   {\r
 867 \r
 868   }\r
 869 \r
 870   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 871   {\r
 872 \r
 873   }\r
 874 \r
 875   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 876   {\r
 877 \r
 878   }\r
 879 \r
 880   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 881   {\r
 882 \r
 883   }\r
 884 \r
 885   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 886   {\r
 887 \r
 888   }\r
 889 \r
 890   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 891   {\r
 892 \r
 893   }\r
 894 \r
 895   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 896   {\r
 897 \r
 898   }\r
 899 \r
 900   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 901   {\r
 902 \r
 903   }\r
 904 \r
 905   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 906   {\r
 907 \r
 908   }\r
 909 \r
 910   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 911   {\r
 912 \r
 913   }\r
 914 \r
 915 \r
 916   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 917   {\r
 918 \r
 919   }\r
 920 \r
 921   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 922   {\r
 923 \r
 924   }\r
 925 \r
 926 \r
 927 \r
 928   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930 \r
 931   }\r
 932 \r
 933 \r
 934 \r
 935 \r
 936   protected void clustalColour_actionPerformed(ActionEvent e)\r
 937   {\r
 938 \r
 939   }\r
 940 \r
 941   protected void zappoColour_actionPerformed(ActionEvent e)\r
 942   {\r
 943 \r
 944   }\r
 945 \r
 946   protected void taylorColour_actionPerformed(ActionEvent e)\r
 947   {\r
 948 \r
 949   }\r
 950 \r
 951 \r
 952   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 953   {\r
 954 \r
 955   }\r
 956 \r
 957   protected void helixColour_actionPerformed(ActionEvent e)\r
 958   {\r
 959 \r
 960   }\r
 961 \r
 962   protected void strandColour_actionPerformed(ActionEvent e)\r
 963   {\r
 964 \r
 965   }\r
 966 \r
 967   protected void turnColour_actionPerformed(ActionEvent e)\r
 968   {\r
 969 \r
 970   }\r
 971 \r
 972   protected void buriedColour_actionPerformed(ActionEvent e)\r
 973   {\r
 974 \r
 975   }\r
 976 \r
 977 \r
 978 \r
 979   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 980   {\r
 981 \r
 982   }\r
 983 \r
 984   protected void PIDColour_actionPerformed(ActionEvent e)\r
 985   {\r
 986 \r
 987   }\r
 988 \r
 989   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 990   {\r
 991 \r
 992   }\r
 993 \r
 994 \r
 995   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 996   {\r
 997 \r
 998   }\r
 999 \r
1000   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1001   {\r
1002 \r
1003   }\r
1004 \r
1005 \r
1006   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1007   {\r
1008 \r
1009   }\r
1010 \r
1011   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1012   {\r
1013 \r
1014   }\r
1015 \r
1016   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018 \r
1019   }\r
1020 \r
1021 \r
1022   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1023 \r
1024   }\r
1025 \r
1026   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1027   {\r
1028 \r
1029   }\r
1030 \r
1031   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1032   {\r
1033 \r
1034   }\r
1035 \r
1036   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1037   {\r
1038 \r
1039   }\r
1040 \r
1041  protected void copy_actionPerformed(ActionEvent e)\r
1042   {\r
1043 \r
1044   }\r
1045 \r
1046 \r
1047   protected void cut_actionPerformed(ActionEvent e)\r
1048   {\r
1049 \r
1050   }\r
1051 \r
1052   protected void delete_actionPerformed(ActionEvent e)\r
1053   {\r
1054 \r
1055   }\r
1056 \r
1057   protected void pasteNew_actionPerformed(ActionEvent e)\r
1058   {\r
1059 \r
1060   }\r
1061 \r
1062   protected void pasteThis_actionPerformed(ActionEvent e)\r
1063   {\r
1064 \r
1065   }\r
1066 \r
1067   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1068   {\r
1069 \r
1070   }\r
1071 \r
1072   protected void createJPG_actionPerformed(ActionEvent e)\r
1073   {\r
1074 \r
1075   }\r
1076 \r
1077   protected void font_actionPerformed(ActionEvent e)\r
1078   {\r
1079 \r
1080   }\r
1081 \r
1082 \r
1083 \r
1084 }\r