src/jalview/jbgui/GAlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 package jalview.jbgui;\r
  10 \r
  11 import javax.swing.*;\r
  12 import java.awt.event.*;\r
  13 import java.awt.*;\r
  14 \r
  15 public class GAlignFrame extends JInternalFrame\r
  16 {\r
  17   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  18   protected JMenu fileMenu = new JMenu();\r
  19   protected JMenuItem closeMenuItem = new JMenuItem();\r
  20   protected JMenu editMenu = new JMenu();\r
  21   protected JMenu fontMenu = new JMenu();\r
  22   protected JMenu viewMenu = new JMenu();\r
  23   protected JMenu colourMenu = new JMenu();\r
  24   protected JMenu calculateMenu = new JMenu();\r
  25   protected JMenu alignMenu = new JMenu();\r
  26   protected JMenuItem groupsMenuItem = new JMenuItem();\r
  27   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  28   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  29   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  30   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();\r
  31   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  32   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  33   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  34   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  35   protected JMenuItem setGapCharMenuItem = new JMenuItem();\r
  36   protected JMenuItem fontNameMenuItem = new JMenuItem();\r
  37   protected JMenuItem fontSizeMenuItem = new JMenuItem();\r
  38   protected JMenuItem fontStyleMenuItem = new JMenuItem();\r
  39   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  40   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  41   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  42   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  43   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  44   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();\r
  45   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  46   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  47   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  48   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  49   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  50   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  51   BorderLayout borderLayout1 = new BorderLayout();\r
  52   public JLabel statusBar = new JLabel();\r
  53   protected JMenu saveAlignmentMenu = new JMenu();\r
  54   protected JMenu outputTextboxMenu = new JMenu();\r
  55   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  58   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  59   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  60   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  61   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  66   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  67   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  68   protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();\r
  69   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  70   JMenuItem htmlMenuItem = new JMenuItem();\r
  71   JMenuItem overviewMenuItem = new JMenuItem();\r
  72   protected JMenuItem undoMenuItem = new JMenuItem();\r
  73   protected JMenuItem redoMenuItem = new JMenuItem();\r
  74   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  75   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  76   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  77   JMenuItem pdbTest = new JMenuItem();\r
  78   JMenuItem printMenuItem = new JMenuItem();\r
  79   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  80   JMenuItem findMenuItem = new JMenuItem();\r
  81   JMenu searchMenu = new JMenu();\r
  82   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  83   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  84   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  85   JMenuItem deleteGroups = new JMenuItem();\r
  86   JMenuItem delete = new JMenuItem();\r
  87   JMenuItem copy = new JMenuItem();\r
  88   JMenuItem cut = new JMenuItem();\r
  89   JMenu jMenu1 = new JMenu();\r
  90   JMenuItem pasteNew = new JMenuItem();\r
  91   JMenuItem pasteThis = new JMenuItem();\r
  92   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  93   public GAlignFrame()\r
  94   {\r
  95 \r
  96 \r
  97     try\r
  98     {\r
  99       jbInit();\r
 100       setJMenuBar(alignFrameMenuBar);\r
 101 \r
 102       JMenuItem item;\r
 103       // dynamically fill save as menu with available formats\r
 104       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
 105         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 106         saveAlignmentMenu.add( item );\r
 107         item.addActionListener(new java.awt.event.ActionListener()\r
 108         {\r
 109           public void actionPerformed(ActionEvent e)\r
 110           {\r
 111             saveAs_actionPerformed(e);\r
 112           }\r
 113         });\r
 114 \r
 115         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 116         item.addActionListener(new java.awt.event.ActionListener()\r
 117         {\r
 118           public void actionPerformed(ActionEvent e)\r
 119           {\r
 120             outputText_actionPerformed(e);\r
 121           }\r
 122         });\r
 123 \r
 124         outputTextboxMenu.add( item );\r
 125       }\r
 126 \r
 127     }\r
 128     catch(Exception e)\r
 129     {\r
 130       e.printStackTrace();\r
 131     }\r
 132 \r
 133     ButtonGroup colours = new ButtonGroup();\r
 134     colours.add(noColourmenuItem);\r
 135     colours.add(clustalColour);\r
 136     colours.add(zappoColour);\r
 137     colours.add(taylorColour);\r
 138     colours.add(hydrophobicityColour);\r
 139     colours.add(helixColour);\r
 140     colours.add(strandColour);\r
 141     colours.add(turnColour);\r
 142     colours.add(buriedColour);\r
 143     colours.add(userDefinedColour);\r
 144     colours.add(PIDColour);\r
 145     colours.add(BLOSUM62Colour);\r
 146     colours.add(nucleotideColour);\r
 147   }\r
 148   private void jbInit() throws Exception\r
 149   {\r
 150     fileMenu.setMnemonic('F');\r
 151     fileMenu.setText("File");\r
 152     saveAlignmentMenu.setMnemonic('L');\r
 153     saveAlignmentMenu.setText("Save alignment to local file");\r
 154     closeMenuItem.setMnemonic('C');\r
 155     closeMenuItem.setText("Close");\r
 156     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 157     {\r
 158       public void actionPerformed(ActionEvent e)\r
 159       {\r
 160         closeMenuItem_actionPerformed(e);\r
 161       }\r
 162     });\r
 163     editMenu.setText("Edit");\r
 164     fontMenu.setText("Font");\r
 165     viewMenu.setText("View");\r
 166     colourMenu.setText("Colour");\r
 167     calculateMenu.setText("Calculate");\r
 168     alignMenu.setText("Web Service");\r
 169     groupsMenuItem.setText("Groups");\r
 170     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 171     {\r
 172       public void actionPerformed(ActionEvent e)\r
 173       {\r
 174         groupsMenuItem_actionPerformed(e);\r
 175       }\r
 176     });\r
 177     selectAllSequenceMenuItem.setText("Select all");\r
 178     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 179     {\r
 180       public void actionPerformed(ActionEvent e)\r
 181       {\r
 182         selectAllSequenceMenuItem_actionPerformed(e);\r
 183       }\r
 184     });\r
 185     deselectAllSequenceMenuItem.setText("Clear selection");\r
 186     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         deselectAllSequenceMenuItem_actionPerformed(e);\r
 191       }\r
 192     });\r
 193     invertSequenceMenuItem.setText("Invert sequence selection");\r
 194     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 195     {\r
 196       public void actionPerformed(ActionEvent e)\r
 197       {\r
 198         invertSequenceMenuItem_actionPerformed(e);\r
 199       }\r
 200     });\r
 201     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 202     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 203     {\r
 204       public void actionPerformed(ActionEvent e)\r
 205       {\r
 206         deselectAllColumnsMenuItem_actionPerformed(e);\r
 207       }\r
 208     });\r
 209     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 210     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 211     {\r
 212       public void actionPerformed(ActionEvent e)\r
 213       {\r
 214         remove2LeftMenuItem_actionPerformed(e);\r
 215       }\r
 216     });\r
 217     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 218     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 219     {\r
 220       public void actionPerformed(ActionEvent e)\r
 221       {\r
 222         remove2RightMenuItem_actionPerformed(e);\r
 223       }\r
 224     });\r
 225     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 226     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 227     {\r
 228       public void actionPerformed(ActionEvent e)\r
 229       {\r
 230         removeGappedColumnMenuItem_actionPerformed(e);\r
 231       }\r
 232     });\r
 233     removeAllGapsMenuItem.setText("Remove all gaps");\r
 234     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 235     {\r
 236       public void actionPerformed(ActionEvent e)\r
 237       {\r
 238         removeAllGapsMenuItem_actionPerformed(e);\r
 239       }\r
 240     });\r
 241     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 242     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 243     {\r
 244       public void actionPerformed(ActionEvent e)\r
 245       {\r
 246         setGapCharMenuItem_actionPerformed(e);\r
 247       }\r
 248     });\r
 249     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 250     {\r
 251       public void actionPerformed(ActionEvent e)\r
 252       {\r
 253         fontNameMenuItem_actionPerformed(e);\r
 254       }\r
 255     });\r
 256     fontSizeMenuItem.setText("10");\r
 257     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 258     {\r
 259       public void actionPerformed(ActionEvent e)\r
 260       {\r
 261         fontSizeMenuItem_actionPerformed(e);\r
 262       }\r
 263     });\r
 264     fontStyleMenuItem.setText("Plain");\r
 265     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 266     {\r
 267       public void actionPerformed(ActionEvent e)\r
 268       {\r
 269         fontStyleMenuItem_actionPerformed(e);\r
 270       }\r
 271     });\r
 272     viewBoxesMenuItem.setText("Boxes");\r
 273     viewBoxesMenuItem.setState(true);\r
 274     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 275     {\r
 276       public void actionPerformed(ActionEvent e)\r
 277       {\r
 278         viewBoxesMenuItem_actionPerformed(e);\r
 279       }\r
 280     });\r
 281     viewTextMenuItem.setText("Text");\r
 282     viewTextMenuItem.setState(true);\r
 283     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 284     {\r
 285       public void actionPerformed(ActionEvent e)\r
 286       {\r
 287         viewTextMenuItem_actionPerformed(e);\r
 288       }\r
 289     });\r
 290     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 291     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         sortPairwiseMenuItem_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     sortIDMenuItem.setText("Sort by ID");\r
 299     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         sortIDMenuItem_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     sortGroupMenuItem.setText("Sort by group");\r
 307     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 308     {\r
 309       public void actionPerformed(ActionEvent e)\r
 310       {\r
 311         sortGroupMenuItem_actionPerformed(e);\r
 312       }\r
 313     });\r
 314     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 315     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         sortTreeOrderMenuItem_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     removeRedundancyMenuItem.setText("Remove redundancy");\r
 323     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 324     {\r
 325       public void actionPerformed(ActionEvent e)\r
 326       {\r
 327         removeRedundancyMenuItem_actionPerformed(e);\r
 328       }\r
 329     });\r
 330     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 331     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 332     {\r
 333       public void actionPerformed(ActionEvent e)\r
 334       {\r
 335         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 336       }\r
 337     });\r
 338     PCAMenuItem.setText("Principal component analysis");\r
 339     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 340     {\r
 341       public void actionPerformed(ActionEvent e)\r
 342       {\r
 343         PCAMenuItem_actionPerformed(e);\r
 344       }\r
 345     });\r
 346     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 347     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 348     {\r
 349       public void actionPerformed(ActionEvent e)\r
 350       {\r
 351         averageDistanceTreeMenuItem_actionPerformed(e);\r
 352       }\r
 353     });\r
 354     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 355     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 356     {\r
 357       public void actionPerformed(ActionEvent e)\r
 358       {\r
 359         neighbourTreeMenuItem_actionPerformed(e);\r
 360       }\r
 361     });\r
 362     clustalAlignMenuItem.setText("Clustal alignment");\r
 363     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 364     {\r
 365       public void actionPerformed(ActionEvent e)\r
 366       {\r
 367         clustalAlignMenuItem_actionPerformed(e);\r
 368       }\r
 369     });\r
 370     this.getContentPane().setLayout(borderLayout1);\r
 371     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 372     statusBar.setBackground(Color.white);\r
 373     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 374     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 375     statusBar.setText("Status bar");\r
 376     outputTextboxMenu.setMnemonic('T');\r
 377     outputTextboxMenu.setText("Output alignment via textbox");\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("Percentage Identity");\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("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     consensusGraphMenuItem.setActionCommand("");\r
 484     consensusGraphMenuItem.setText("Consensus graph");\r
 485     consensusGraphMenuItem.setState(true);\r
 486     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         consensusGraphMenuItem_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     colourTextMenuItem.setText("Colour text");\r
 494     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         colourTextMenuItem_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     htmlMenuItem.setText("Output as HTML");\r
 502     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         htmlMenuItem_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     overviewMenuItem.setText("Overview window");\r
 510     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         overviewMenuItem_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     undoMenuItem.setEnabled(false);\r
 518     undoMenuItem.setMnemonic('Z');\r
 519     undoMenuItem.setText("Undo");\r
 520     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 521     {\r
 522       public void actionPerformed(ActionEvent e)\r
 523       {\r
 524         undoMenuItem_actionPerformed(e);\r
 525       }\r
 526     });\r
 527     redoMenuItem.setEnabled(false);\r
 528     redoMenuItem.setMnemonic('0');\r
 529     redoMenuItem.setText("Redo");\r
 530     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         redoMenuItem_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     conservationMenuItem.setText("By conservation");\r
 538     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 539     {\r
 540       public void actionPerformed(ActionEvent e)\r
 541       {\r
 542         conservationMenuItem_actionPerformed(e);\r
 543       }\r
 544     });\r
 545     noColourmenuItem.setText("None");\r
 546     noColourmenuItem.setSelected(true);\r
 547     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 548     {\r
 549       public void actionPerformed(ActionEvent e)\r
 550       {\r
 551         noColourmenuItem_actionPerformed(e);\r
 552       }\r
 553     });\r
 554     wrapMenuItem.setText("Wrap alignment");\r
 555     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 556     {\r
 557       public void actionPerformed(ActionEvent e)\r
 558       {\r
 559         wrapMenuItem_actionPerformed(e);\r
 560       }\r
 561     });\r
 562     pdbTest.setText("PDB Test Viewer");\r
 563     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 564     {\r
 565       public void actionPerformed(ActionEvent e)\r
 566       {\r
 567         pdbTest_actionPerformed(e);\r
 568       }\r
 569     });\r
 570     printMenuItem.setText("Print");\r
 571     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 572     {\r
 573       public void actionPerformed(ActionEvent e)\r
 574       {\r
 575         printMenuItem_actionPerformed(e);\r
 576       }\r
 577     });\r
 578     renderGapsMenuItem.setText("Render gaps");\r
 579     renderGapsMenuItem.setState(true);\r
 580     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 581     {\r
 582       public void actionPerformed(ActionEvent e)\r
 583       {\r
 584         renderGapsMenuItem_actionPerformed(e);\r
 585       }\r
 586     });\r
 587     findMenuItem.setText("Find");\r
 588     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 589     {\r
 590       public void actionPerformed(ActionEvent e)\r
 591       {\r
 592         findMenuItem_actionPerformed(e);\r
 593       }\r
 594     });\r
 595     searchMenu.setText("Search");\r
 596 \r
 597     abovePIDThreshold.setText("Above PID threshold");\r
 598     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 599       public void actionPerformed(ActionEvent e) {\r
 600         abovePIDThreshold_actionPerformed(e);\r
 601       }\r
 602     });\r
 603     sequenceFeatures.setSelected(true);\r
 604     sequenceFeatures.setText("Sequence Features");\r
 605     sequenceFeatures.addActionListener(new ActionListener()\r
 606     {\r
 607       public void actionPerformed(ActionEvent actionEvent)\r
 608       {\r
 609         sequenceFeatures_actionPerformed(actionEvent);\r
 610       }\r
 611     });\r
 612     nucleotideColour.setText("Nucleotide colours");\r
 613     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 614     {\r
 615       public void actionPerformed(ActionEvent e)\r
 616       {\r
 617         nucleotideColour_actionPerformed(e);\r
 618       }\r
 619     });\r
 620     deleteGroups.setSelected(false);\r
 621     deleteGroups.setText("Delete all groups");\r
 622     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 623     {\r
 624       public void actionPerformed(ActionEvent e)\r
 625       {\r
 626         deleteGroups_actionPerformed(e);\r
 627       }\r
 628     });\r
 629     copy.setText("Copy");\r
 630     copy.setMnemonic(KeyEvent.VK_C);\r
 631 \r
 632     copy.addActionListener(new java.awt.event.ActionListener()\r
 633     {\r
 634       public void actionPerformed(ActionEvent e)\r
 635       {\r
 636         copy_actionPerformed(e);\r
 637       }\r
 638     });\r
 639     cut.setText("Cut");\r
 640     cut.setMnemonic(KeyEvent.VK_X);\r
 641     cut.addActionListener(new java.awt.event.ActionListener()\r
 642     {\r
 643       public void actionPerformed(ActionEvent e)\r
 644       {\r
 645         cut_actionPerformed(e);\r
 646       }\r
 647     });\r
 648     delete.setText("Delete");\r
 649     delete.addActionListener(new java.awt.event.ActionListener()\r
 650     {\r
 651       public void actionPerformed(ActionEvent e)\r
 652       {\r
 653         delete_actionPerformed(e);\r
 654       }\r
 655     });\r
 656     jMenu1.setMnemonic('V');\r
 657     jMenu1.setText("Paste");\r
 658     pasteNew.setText("to new alignment");\r
 659     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 660     {\r
 661       public void actionPerformed(ActionEvent e)\r
 662       {\r
 663         pasteNew_actionPerformed(e);\r
 664       }\r
 665     });\r
 666     pasteThis.setText("add to this alignment");\r
 667     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 668     {\r
 669       public void actionPerformed(ActionEvent e)\r
 670       {\r
 671         pasteThis_actionPerformed(e);\r
 672       }\r
 673     });\r
 674     applyToAllGroups.setText("Apply colour to all groups");\r
 675     applyToAllGroups.setState(true);\r
 676     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 677     {\r
 678       public void actionPerformed(ActionEvent e)\r
 679       {\r
 680         applyToAllGroups_actionPerformed(e);\r
 681       }\r
 682     });\r
 683     alignFrameMenuBar.add(fileMenu);\r
 684     alignFrameMenuBar.add(editMenu);\r
 685     alignFrameMenuBar.add(searchMenu);\r
 686     alignFrameMenuBar.add(fontMenu);\r
 687     alignFrameMenuBar.add(viewMenu);\r
 688     alignFrameMenuBar.add(colourMenu);\r
 689     alignFrameMenuBar.add(calculateMenu);\r
 690     alignFrameMenuBar.add(alignMenu);\r
 691     fileMenu.add(saveAlignmentMenu);\r
 692     fileMenu.add(outputTextboxMenu);\r
 693     fileMenu.add(htmlMenuItem);\r
 694     fileMenu.add(printMenuItem);\r
 695     fileMenu.addSeparator();\r
 696     fileMenu.add(closeMenuItem);\r
 697     editMenu.add(copy);\r
 698     editMenu.add(jMenu1);\r
 699     editMenu.add(cut);\r
 700     editMenu.add(delete);\r
 701     editMenu.addSeparator();\r
 702     editMenu.add(undoMenuItem);\r
 703     editMenu.add(redoMenuItem);\r
 704     editMenu.addSeparator();\r
 705     editMenu.add(deselectAllSequenceMenuItem);\r
 706     editMenu.add(selectAllSequenceMenuItem);\r
 707     editMenu.add(invertSequenceMenuItem);\r
 708     editMenu.add(deleteGroups);\r
 709     editMenu.add(groupsMenuItem);\r
 710     editMenu.addSeparator();\r
 711     editMenu.add(deselectAllColumnsMenuItem);\r
 712     editMenu.add(remove2LeftMenuItem);\r
 713     editMenu.add(remove2RightMenuItem);\r
 714     editMenu.addSeparator();\r
 715     editMenu.add(removeGappedColumnMenuItem);\r
 716     editMenu.add(removeAllGapsMenuItem);\r
 717     editMenu.add(setGapCharMenuItem);\r
 718     searchMenu.add(findMenuItem);\r
 719     fontMenu.add(fontNameMenuItem);\r
 720     fontMenu.add(fontSizeMenuItem);\r
 721     fontMenu.add(fontStyleMenuItem);\r
 722     viewMenu.add(wrapMenuItem);\r
 723     viewMenu.add(viewBoxesMenuItem);\r
 724     viewMenu.add(viewTextMenuItem);\r
 725     viewMenu.add(colourTextMenuItem);\r
 726     viewMenu.add(renderGapsMenuItem);\r
 727     viewMenu.add(consensusGraphMenuItem);\r
 728     viewMenu.add(overviewMenuItem);\r
 729     viewMenu.add(sequenceFeatures);\r
 730     colourMenu.add(applyToAllGroups);\r
 731     colourMenu.add(noColourmenuItem);\r
 732     colourMenu.add(clustalColour);\r
 733     colourMenu.add(zappoColour);\r
 734     colourMenu.add(taylorColour);\r
 735     colourMenu.add(hydrophobicityColour);\r
 736     colourMenu.add(helixColour);\r
 737     colourMenu.add(strandColour);\r
 738     colourMenu.add(turnColour);\r
 739     colourMenu.add(buriedColour);\r
 740     colourMenu.add(nucleotideColour);\r
 741     colourMenu.add(userDefinedColour);\r
 742     colourMenu.add(PIDColour);\r
 743     colourMenu.add(BLOSUM62Colour);\r
 744     colourMenu.addSeparator();\r
 745     colourMenu.add(abovePIDThreshold);\r
 746     colourMenu.add(conservationMenuItem);\r
 747     calculateMenu.add(sortPairwiseMenuItem);\r
 748     calculateMenu.add(sortIDMenuItem);\r
 749     calculateMenu.add(sortGroupMenuItem);\r
 750     calculateMenu.add(sortTreeOrderMenuItem);\r
 751     calculateMenu.add(removeRedundancyMenuItem);\r
 752     calculateMenu.addSeparator();\r
 753     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 754     calculateMenu.add(PCAMenuItem);\r
 755     calculateMenu.addSeparator();\r
 756     calculateMenu.add(averageDistanceTreeMenuItem);\r
 757     calculateMenu.add(neighbourTreeMenuItem);\r
 758     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 759     calculateMenu.add(njTreeBlosumMenuItem);\r
 760     alignMenu.add(clustalAlignMenuItem);\r
 761     alignMenu.add(pdbTest);\r
 762     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 763     jMenu1.add(pasteNew);\r
 764     jMenu1.add(pasteThis);\r
 765   }\r
 766 \r
 767   protected void saveAs_actionPerformed(ActionEvent e)\r
 768   {\r
 769 \r
 770   }\r
 771 \r
 772   protected void outputText_actionPerformed(ActionEvent e)\r
 773   {\r
 774 \r
 775   }\r
 776 \r
 777   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 778   {\r
 779 \r
 780   }\r
 781 \r
 782 \r
 783 \r
 784 \r
 785 \r
 786   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 787   {\r
 788 \r
 789   }\r
 790 \r
 791   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793 \r
 794   }\r
 795 \r
 796   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798 \r
 799   }\r
 800 \r
 801 \r
 802   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804 \r
 805   }\r
 806 \r
 807 \r
 808   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 809   {\r
 810 \r
 811   }\r
 812 \r
 813   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 814   {\r
 815 \r
 816   }\r
 817 \r
 818   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 819   {\r
 820 \r
 821   }\r
 822 \r
 823 \r
 824   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 825   {\r
 826 \r
 827   }\r
 828 \r
 829   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831 \r
 832   }\r
 833 \r
 834   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 835   {\r
 836 \r
 837   }\r
 838 \r
 839   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 840   {\r
 841 \r
 842   }\r
 843 \r
 844   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 845   {\r
 846 \r
 847   }\r
 848 \r
 849   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 850   {\r
 851 \r
 852   }\r
 853 \r
 854 \r
 855   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857 \r
 858   }\r
 859 \r
 860   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 866   {\r
 867 \r
 868   }\r
 869 \r
 870   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 871   {\r
 872 \r
 873   }\r
 874 \r
 875 \r
 876   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878 \r
 879   }\r
 880 \r
 881   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 882   {\r
 883 \r
 884   }\r
 885 \r
 886 \r
 887   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 888   {\r
 889 \r
 890   }\r
 891 \r
 892 \r
 893 \r
 894   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 905   {\r
 906 \r
 907   }\r
 908 \r
 909   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912   }\r
 913 \r
 914   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916 \r
 917   }\r
 918 \r
 919   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921 \r
 922   }\r
 923 \r
 924   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 925   {\r
 926 \r
 927   }\r
 928 \r
 929   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 930   {\r
 931 \r
 932   }\r
 933 \r
 934   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 935   {\r
 936 \r
 937   }\r
 938 \r
 939   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941 \r
 942   }\r
 943 \r
 944   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946 \r
 947   }\r
 948 \r
 949 \r
 950   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 951   {\r
 952 \r
 953   }\r
 954 \r
 955   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 956   {\r
 957 \r
 958   }\r
 959 \r
 960 \r
 961 \r
 962   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 963   {\r
 964 \r
 965   }\r
 966 \r
 967 \r
 968 \r
 969 \r
 970   protected void clustalColour_actionPerformed(ActionEvent e)\r
 971   {\r
 972 \r
 973   }\r
 974 \r
 975   protected void zappoColour_actionPerformed(ActionEvent e)\r
 976   {\r
 977 \r
 978   }\r
 979 \r
 980   protected void taylorColour_actionPerformed(ActionEvent e)\r
 981   {\r
 982 \r
 983   }\r
 984 \r
 985 \r
 986   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 987   {\r
 988 \r
 989   }\r
 990 \r
 991   protected void helixColour_actionPerformed(ActionEvent e)\r
 992   {\r
 993 \r
 994   }\r
 995 \r
 996   protected void strandColour_actionPerformed(ActionEvent e)\r
 997   {\r
 998 \r
 999   }\r
1000 \r
1001   protected void turnColour_actionPerformed(ActionEvent e)\r
1002   {\r
1003 \r
1004   }\r
1005 \r
1006   protected void buriedColour_actionPerformed(ActionEvent e)\r
1007   {\r
1008 \r
1009   }\r
1010 \r
1011 \r
1012 \r
1013   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1014   {\r
1015 \r
1016   }\r
1017 \r
1018   protected void PIDColour_actionPerformed(ActionEvent e)\r
1019   {\r
1020 \r
1021   }\r
1022 \r
1023   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1024   {\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
1060   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1061 \r
1062   }\r
1063 \r
1064   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1065   {\r
1066 \r
1067   }\r
1068 \r
1069   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1070   {\r
1071 \r
1072   }\r
1073 \r
1074   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1075   {\r
1076 \r
1077   }\r
1078 \r
1079  protected void copy_actionPerformed(ActionEvent e)\r
1080   {\r
1081 \r
1082   }\r
1083 \r
1084 \r
1085   protected void cut_actionPerformed(ActionEvent e)\r
1086   {\r
1087 \r
1088   }\r
1089 \r
1090   protected void delete_actionPerformed(ActionEvent e)\r
1091   {\r
1092 \r
1093   }\r
1094 \r
1095   protected void pasteNew_actionPerformed(ActionEvent e)\r
1096   {\r
1097 \r
1098   }\r
1099 \r
1100   protected void pasteThis_actionPerformed(ActionEvent e)\r
1101   {\r
1102 \r
1103   }\r
1104 \r
1105   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1106   {\r
1107 \r
1108   }\r
1109 \r
1110 \r
1111 \r
1112 }\r