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 createPNG = new JMenuItem();\r
  89   protected JMenuItem font = new JMenuItem();\r
  90   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
  91   JMenuItem epsFile = new JMenuItem();\r
  92   public GAlignFrame()\r
  93   {\r
  94 \r
  95 \r
  96     try\r
  97     {\r
  98       jbInit();\r
  99       setJMenuBar(alignFrameMenuBar);\r
 100 \r
 101       JMenuItem item;\r
 102       // dynamically fill save as menu with available formats\r
 103       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {\r
 104         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 105         saveAlignmentMenu.add( item );\r
 106         item.addActionListener(new java.awt.event.ActionListener()\r
 107         {\r
 108           public void actionPerformed(ActionEvent e)\r
 109           {\r
 110             saveAs_actionPerformed(e);\r
 111           }\r
 112         });\r
 113 \r
 114         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));\r
 115         item.addActionListener(new java.awt.event.ActionListener()\r
 116         {\r
 117           public void actionPerformed(ActionEvent e)\r
 118           {\r
 119             outputText_actionPerformed(e);\r
 120           }\r
 121         });\r
 122 \r
 123         outputTextboxMenu.add( item );\r
 124       }\r
 125 \r
 126     }\r
 127     catch(Exception e)\r
 128     {\r
 129       e.printStackTrace();\r
 130     }\r
 131 \r
 132     ButtonGroup colours = new ButtonGroup();\r
 133     colours.add(noColourmenuItem);\r
 134     colours.add(clustalColour);\r
 135     colours.add(zappoColour);\r
 136     colours.add(taylorColour);\r
 137     colours.add(hydrophobicityColour);\r
 138     colours.add(helixColour);\r
 139     colours.add(strandColour);\r
 140     colours.add(turnColour);\r
 141     colours.add(buriedColour);\r
 142     colours.add(userDefinedColour);\r
 143     colours.add(PIDColour);\r
 144     colours.add(BLOSUM62Colour);\r
 145     colours.add(nucleotideColour);\r
 146   }\r
 147   private void jbInit() throws Exception\r
 148   {\r
 149     fileMenu.setMnemonic('F');\r
 150     fileMenu.setText("File");\r
 151     saveAlignmentMenu.setMnemonic('L');\r
 152     saveAlignmentMenu.setText("Save alignment to local file");\r
 153     closeMenuItem.setMnemonic('C');\r
 154     closeMenuItem.setText("Close");\r
 155     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 156     {\r
 157       public void actionPerformed(ActionEvent e)\r
 158       {\r
 159         closeMenuItem_actionPerformed(e);\r
 160       }\r
 161     });\r
 162     editMenu.setText("Edit");\r
 163     viewMenu.setText("View");\r
 164     colourMenu.setText("Colour");\r
 165     calculateMenu.setText("Calculate");\r
 166     alignMenu.setText("Web Service");\r
 167     groupsMenuItem.setVisible(false);\r
 168     groupsMenuItem.setText("Groups");\r
 169     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 170     {\r
 171       public void actionPerformed(ActionEvent e)\r
 172       {\r
 173         groupsMenuItem_actionPerformed(e);\r
 174       }\r
 175     });\r
 176     selectAllSequenceMenuItem.setText("Select all");\r
 177     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 178     {\r
 179       public void actionPerformed(ActionEvent e)\r
 180       {\r
 181         selectAllSequenceMenuItem_actionPerformed(e);\r
 182       }\r
 183     });\r
 184     deselectAllSequenceMenuItem.setText("Clear selection");\r
 185     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 186     {\r
 187       public void actionPerformed(ActionEvent e)\r
 188       {\r
 189         deselectAllSequenceMenuItem_actionPerformed(e);\r
 190       }\r
 191     });\r
 192     invertSequenceMenuItem.setText("Invert sequence selection");\r
 193     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 194     {\r
 195       public void actionPerformed(ActionEvent e)\r
 196       {\r
 197         invertSequenceMenuItem_actionPerformed(e);\r
 198       }\r
 199     });\r
 200     deselectAllColumnsMenuItem.setText("Deselect all columns");\r
 201     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 202     {\r
 203       public void actionPerformed(ActionEvent e)\r
 204       {\r
 205         deselectAllColumnsMenuItem_actionPerformed(e);\r
 206       }\r
 207     });\r
 208     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");\r
 209     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 210     {\r
 211       public void actionPerformed(ActionEvent e)\r
 212       {\r
 213         remove2LeftMenuItem_actionPerformed(e);\r
 214       }\r
 215     });\r
 216     remove2RightMenuItem.setText("Remove sequence -> right of selected column");\r
 217     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 218     {\r
 219       public void actionPerformed(ActionEvent e)\r
 220       {\r
 221         remove2RightMenuItem_actionPerformed(e);\r
 222       }\r
 223     });\r
 224     removeGappedColumnMenuItem.setText("Remove gapped columns");\r
 225     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 226     {\r
 227       public void actionPerformed(ActionEvent e)\r
 228       {\r
 229         removeGappedColumnMenuItem_actionPerformed(e);\r
 230       }\r
 231     });\r
 232     removeAllGapsMenuItem.setText("Remove all gaps");\r
 233     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 234     {\r
 235       public void actionPerformed(ActionEvent e)\r
 236       {\r
 237         removeAllGapsMenuItem_actionPerformed(e);\r
 238       }\r
 239     });\r
 240     setGapCharMenuItem.setText("Set gap character to \".\"");\r
 241     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 242     {\r
 243       public void actionPerformed(ActionEvent e)\r
 244       {\r
 245         setGapCharMenuItem_actionPerformed(e);\r
 246       }\r
 247     });\r
 248     viewBoxesMenuItem.setText("Boxes");\r
 249     viewBoxesMenuItem.setState(true);\r
 250     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 251     {\r
 252       public void actionPerformed(ActionEvent e)\r
 253       {\r
 254         viewBoxesMenuItem_actionPerformed(e);\r
 255       }\r
 256     });\r
 257     viewTextMenuItem.setText("Text");\r
 258     viewTextMenuItem.setState(true);\r
 259     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 260     {\r
 261       public void actionPerformed(ActionEvent e)\r
 262       {\r
 263         viewTextMenuItem_actionPerformed(e);\r
 264       }\r
 265     });\r
 266     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 267     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 268     {\r
 269       public void actionPerformed(ActionEvent e)\r
 270       {\r
 271         sortPairwiseMenuItem_actionPerformed(e);\r
 272       }\r
 273     });\r
 274     sortIDMenuItem.setText("Sort by ID");\r
 275     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 276     {\r
 277       public void actionPerformed(ActionEvent e)\r
 278       {\r
 279         sortIDMenuItem_actionPerformed(e);\r
 280       }\r
 281     });\r
 282     sortGroupMenuItem.setText("Sort by group");\r
 283     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 284     {\r
 285       public void actionPerformed(ActionEvent e)\r
 286       {\r
 287         sortGroupMenuItem_actionPerformed(e);\r
 288       }\r
 289     });\r
 290     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 291     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         sortTreeOrderMenuItem_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     removeRedundancyMenuItem.setText("Remove redundancy");\r
 299     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         removeRedundancyMenuItem_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 307     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 308     {\r
 309       public void actionPerformed(ActionEvent e)\r
 310       {\r
 311         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 312       }\r
 313     });\r
 314     PCAMenuItem.setText("Principal component analysis");\r
 315     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         PCAMenuItem_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 323     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 324     {\r
 325       public void actionPerformed(ActionEvent e)\r
 326       {\r
 327         averageDistanceTreeMenuItem_actionPerformed(e);\r
 328       }\r
 329     });\r
 330     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 331     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 332     {\r
 333       public void actionPerformed(ActionEvent e)\r
 334       {\r
 335         neighbourTreeMenuItem_actionPerformed(e);\r
 336       }\r
 337     });\r
 338     clustalAlignMenuItem.setText("Clustal alignment");\r
 339     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 340     {\r
 341       public void actionPerformed(ActionEvent e)\r
 342       {\r
 343         clustalAlignMenuItem_actionPerformed(e);\r
 344       }\r
 345     });\r
 346     this.getContentPane().setLayout(borderLayout1);\r
 347     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 348     statusBar.setBackground(Color.white);\r
 349     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 350     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 351     statusBar.setText("Status bar");\r
 352     outputTextboxMenu.setMnemonic('T');\r
 353     outputTextboxMenu.setText("Output alignment via textbox");\r
 354     clustalColour.setSelected(false);\r
 355     clustalColour.setText("Clustalx colours");\r
 356     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 357     {\r
 358       public void actionPerformed(ActionEvent e)\r
 359       {\r
 360         clustalColour_actionPerformed(e);\r
 361       }\r
 362     });\r
 363     zappoColour.setText("Zappo colour scheme");\r
 364     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 365     {\r
 366       public void actionPerformed(ActionEvent e)\r
 367       {\r
 368         zappoColour_actionPerformed(e);\r
 369       }\r
 370     });\r
 371     taylorColour.setText("Taylor colour scheme");\r
 372     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 373     {\r
 374       public void actionPerformed(ActionEvent e)\r
 375       {\r
 376         taylorColour_actionPerformed(e);\r
 377       }\r
 378     });\r
 379     hydrophobicityColour.setText("By hydrophobicity");\r
 380     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 381     {\r
 382       public void actionPerformed(ActionEvent e)\r
 383       {\r
 384         hydrophobicityColour_actionPerformed(e);\r
 385       }\r
 386     });\r
 387     helixColour.setText("Helix propensity");\r
 388     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 389     {\r
 390       public void actionPerformed(ActionEvent e)\r
 391       {\r
 392         helixColour_actionPerformed(e);\r
 393       }\r
 394     });\r
 395     strandColour.setText("Strand propensity");\r
 396     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 397     {\r
 398       public void actionPerformed(ActionEvent e)\r
 399       {\r
 400         strandColour_actionPerformed(e);\r
 401       }\r
 402     });\r
 403     turnColour.setText("Turn propensity");\r
 404     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 405     {\r
 406       public void actionPerformed(ActionEvent e)\r
 407       {\r
 408         turnColour_actionPerformed(e);\r
 409       }\r
 410     });\r
 411     buriedColour.setText("Buried index");\r
 412     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 413     {\r
 414       public void actionPerformed(ActionEvent e)\r
 415       {\r
 416         buriedColour_actionPerformed(e);\r
 417       }\r
 418     });\r
 419     userDefinedColour.setText("User defined colours");\r
 420     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 421     {\r
 422       public void actionPerformed(ActionEvent e)\r
 423       {\r
 424         userDefinedColour_actionPerformed(e);\r
 425       }\r
 426     });\r
 427     PIDColour.setText("Percentage Identity");\r
 428     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         PIDColour_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     BLOSUM62Colour.setText("BLOSUM62 score");\r
 436     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 437     {\r
 438       public void actionPerformed(ActionEvent e)\r
 439       {\r
 440         BLOSUM62Colour_actionPerformed(e);\r
 441       }\r
 442     });\r
 443     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 444     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         avTreeBlosumMenuItem_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 452     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 453     {\r
 454       public void actionPerformed(ActionEvent e)\r
 455       {\r
 456         njTreeBlosumMenuItem_actionPerformed(e);\r
 457       }\r
 458     });\r
 459     consensusGraphMenuItem.setActionCommand("");\r
 460     consensusGraphMenuItem.setText("Consensus graph");\r
 461     consensusGraphMenuItem.setState(true);\r
 462     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         consensusGraphMenuItem_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     colourTextMenuItem.setText("Colour text");\r
 470     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 471     {\r
 472       public void actionPerformed(ActionEvent e)\r
 473       {\r
 474         colourTextMenuItem_actionPerformed(e);\r
 475       }\r
 476     });\r
 477     htmlMenuItem.setText("Output as HTML");\r
 478     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 479     {\r
 480       public void actionPerformed(ActionEvent e)\r
 481       {\r
 482         htmlMenuItem_actionPerformed(e);\r
 483       }\r
 484     });\r
 485     overviewMenuItem.setText("Overview window");\r
 486     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         overviewMenuItem_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     undoMenuItem.setEnabled(false);\r
 494     undoMenuItem.setMnemonic('Z');\r
 495     undoMenuItem.setText("Undo");\r
 496     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 497     {\r
 498       public void actionPerformed(ActionEvent e)\r
 499       {\r
 500         undoMenuItem_actionPerformed(e);\r
 501       }\r
 502     });\r
 503     redoMenuItem.setEnabled(false);\r
 504     redoMenuItem.setMnemonic('0');\r
 505     redoMenuItem.setText("Redo");\r
 506     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 507     {\r
 508       public void actionPerformed(ActionEvent e)\r
 509       {\r
 510         redoMenuItem_actionPerformed(e);\r
 511       }\r
 512     });\r
 513     conservationMenuItem.setText("By conservation");\r
 514     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 515     {\r
 516       public void actionPerformed(ActionEvent e)\r
 517       {\r
 518         conservationMenuItem_actionPerformed(e);\r
 519       }\r
 520     });\r
 521     noColourmenuItem.setText("None");\r
 522     noColourmenuItem.setSelected(true);\r
 523     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 524     {\r
 525       public void actionPerformed(ActionEvent e)\r
 526       {\r
 527         noColourmenuItem_actionPerformed(e);\r
 528       }\r
 529     });\r
 530     wrapMenuItem.setText("Wrap alignment");\r
 531     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 532     {\r
 533       public void actionPerformed(ActionEvent e)\r
 534       {\r
 535         wrapMenuItem_actionPerformed(e);\r
 536       }\r
 537     });\r
 538     printMenuItem.setText("Print");\r
 539     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 540     {\r
 541       public void actionPerformed(ActionEvent e)\r
 542       {\r
 543         printMenuItem_actionPerformed(e);\r
 544       }\r
 545     });\r
 546     renderGapsMenuItem.setText("Render gaps");\r
 547     renderGapsMenuItem.setState(true);\r
 548     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 549     {\r
 550       public void actionPerformed(ActionEvent e)\r
 551       {\r
 552         renderGapsMenuItem_actionPerformed(e);\r
 553       }\r
 554     });\r
 555     findMenuItem.setText("Find");\r
 556     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 557     {\r
 558       public void actionPerformed(ActionEvent e)\r
 559       {\r
 560         findMenuItem_actionPerformed(e);\r
 561       }\r
 562     });\r
 563     searchMenu.setText("Search");\r
 564 \r
 565     abovePIDThreshold.setText("Above PID threshold");\r
 566     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 567       public void actionPerformed(ActionEvent e) {\r
 568         abovePIDThreshold_actionPerformed(e);\r
 569       }\r
 570     });\r
 571     sequenceFeatures.setText("Sequence Features");\r
 572     sequenceFeatures.addActionListener(new ActionListener()\r
 573     {\r
 574       public void actionPerformed(ActionEvent actionEvent)\r
 575       {\r
 576         sequenceFeatures_actionPerformed(actionEvent);\r
 577       }\r
 578     });\r
 579     nucleotideColour.setText("Nucleotide colours");\r
 580     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 581     {\r
 582       public void actionPerformed(ActionEvent e)\r
 583       {\r
 584         nucleotideColour_actionPerformed(e);\r
 585       }\r
 586     });\r
 587     deleteGroups.setSelected(false);\r
 588     deleteGroups.setText("Delete all groups");\r
 589     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 590     {\r
 591       public void actionPerformed(ActionEvent e)\r
 592       {\r
 593         deleteGroups_actionPerformed(e);\r
 594       }\r
 595     });\r
 596     copy.setText("Copy");\r
 597     copy.setMnemonic(KeyEvent.VK_C);\r
 598 \r
 599     copy.addActionListener(new java.awt.event.ActionListener()\r
 600     {\r
 601       public void actionPerformed(ActionEvent e)\r
 602       {\r
 603         copy_actionPerformed(e);\r
 604       }\r
 605     });\r
 606     cut.setText("Cut");\r
 607     cut.setMnemonic(KeyEvent.VK_X);\r
 608     cut.addActionListener(new java.awt.event.ActionListener()\r
 609     {\r
 610       public void actionPerformed(ActionEvent e)\r
 611       {\r
 612         cut_actionPerformed(e);\r
 613       }\r
 614     });\r
 615     delete.setText("Delete");\r
 616     delete.addActionListener(new java.awt.event.ActionListener()\r
 617     {\r
 618       public void actionPerformed(ActionEvent e)\r
 619       {\r
 620         delete_actionPerformed(e);\r
 621       }\r
 622     });\r
 623     jMenu1.setMnemonic('V');\r
 624     jMenu1.setText("Paste");\r
 625     pasteNew.setText("to new alignment");\r
 626     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         pasteNew_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     pasteThis.setText("add to this alignment");\r
 634     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         pasteThis_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     applyToAllGroups.setText("Apply colour to all groups");\r
 642     applyToAllGroups.setState(true);\r
 643     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 644     {\r
 645       public void actionPerformed(ActionEvent e)\r
 646       {\r
 647         applyToAllGroups_actionPerformed(e);\r
 648       }\r
 649     });\r
 650     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 651     {\r
 652       public void actionPerformed(ActionEvent e)\r
 653       {\r
 654         createPNG_actionPerformed(e);\r
 655       }\r
 656     });\r
 657     createPNG.setActionCommand("Save as PNG Image");\r
 658     createPNG.setText("Save as PNG Image");\r
 659     font.setText("Change Font");\r
 660     font.addActionListener(new java.awt.event.ActionListener()\r
 661     {\r
 662       public void actionPerformed(ActionEvent e)\r
 663       {\r
 664         font_actionPerformed(e);\r
 665       }\r
 666     });\r
 667     fullSeqId.setText("Show full sequence id");\r
 668     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
 669     {\r
 670       public void actionPerformed(ActionEvent e)\r
 671       {\r
 672         fullSeqId_actionPerformed(e);\r
 673       }\r
 674     });\r
 675     epsFile.setText("Save as EPS file");\r
 676     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 677     {\r
 678       public void actionPerformed(ActionEvent e)\r
 679       {\r
 680         epsFile_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(viewMenu);\r
 687     alignFrameMenuBar.add(colourMenu);\r
 688     alignFrameMenuBar.add(calculateMenu);\r
 689     alignFrameMenuBar.add(alignMenu);\r
 690     fileMenu.add(saveAlignmentMenu);\r
 691     fileMenu.add(outputTextboxMenu);\r
 692     fileMenu.add(htmlMenuItem);\r
 693     fileMenu.add(epsFile);\r
 694     fileMenu.add(createPNG);\r
 695     fileMenu.add(printMenuItem);\r
 696     fileMenu.addSeparator();\r
 697     fileMenu.add(closeMenuItem);\r
 698     editMenu.add(copy);\r
 699     editMenu.add(jMenu1);\r
 700     editMenu.add(cut);\r
 701     editMenu.add(delete);\r
 702     editMenu.addSeparator();\r
 703     editMenu.add(undoMenuItem);\r
 704     editMenu.add(redoMenuItem);\r
 705     editMenu.addSeparator();\r
 706     editMenu.add(deselectAllSequenceMenuItem);\r
 707     editMenu.add(selectAllSequenceMenuItem);\r
 708     editMenu.add(invertSequenceMenuItem);\r
 709     editMenu.add(deleteGroups);\r
 710     editMenu.add(groupsMenuItem);\r
 711     editMenu.addSeparator();\r
 712     editMenu.add(deselectAllColumnsMenuItem);\r
 713     editMenu.add(remove2LeftMenuItem);\r
 714     editMenu.add(remove2RightMenuItem);\r
 715     editMenu.addSeparator();\r
 716     editMenu.add(removeGappedColumnMenuItem);\r
 717     editMenu.add(removeAllGapsMenuItem);\r
 718     editMenu.add(setGapCharMenuItem);\r
 719     searchMenu.add(findMenuItem);\r
 720     viewMenu.add(font);\r
 721     viewMenu.add(fullSeqId);\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     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 762     jMenu1.add(pasteNew);\r
 763     jMenu1.add(pasteThis);\r
 764   }\r
 765 \r
 766   protected void saveAs_actionPerformed(ActionEvent e)\r
 767   {\r
 768 \r
 769   }\r
 770 \r
 771   protected void outputText_actionPerformed(ActionEvent e)\r
 772   {\r
 773 \r
 774   }\r
 775 \r
 776   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 777   {\r
 778 \r
 779   }\r
 780 \r
 781 \r
 782 \r
 783 \r
 784 \r
 785   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 786   {\r
 787 \r
 788   }\r
 789 \r
 790   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792 \r
 793   }\r
 794 \r
 795   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 796   {\r
 797 \r
 798   }\r
 799 \r
 800 \r
 801   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 802   {\r
 803 \r
 804   }\r
 805 \r
 806 \r
 807   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 808   {\r
 809 \r
 810   }\r
 811 \r
 812   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 813   {\r
 814 \r
 815   }\r
 816 \r
 817   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 818   {\r
 819 \r
 820   }\r
 821 \r
 822 \r
 823   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 824   {\r
 825 \r
 826   }\r
 827 \r
 828   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 829   {\r
 830 \r
 831   }\r
 832 \r
 833   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835 \r
 836   }\r
 837 \r
 838   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 839   {\r
 840 \r
 841   }\r
 842 \r
 843   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 844   {\r
 845 \r
 846   }\r
 847 \r
 848   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 849   {\r
 850 \r
 851   }\r
 852 \r
 853 \r
 854 \r
 855 \r
 856 \r
 857   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 858   {\r
 859 \r
 860   }\r
 861 \r
 862 \r
 863   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 864   {\r
 865 \r
 866   }\r
 867 \r
 868   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 869   {\r
 870 \r
 871   }\r
 872 \r
 873 \r
 874   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 875   {\r
 876 \r
 877   }\r
 878 \r
 879 \r
 880 \r
 881   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 882   {\r
 883 \r
 884   }\r
 885 \r
 886   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 887   {\r
 888 \r
 889   }\r
 890 \r
 891   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 892   {\r
 893 \r
 894   }\r
 895 \r
 896   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 897   {\r
 898 \r
 899   }\r
 900 \r
 901   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 902   {\r
 903 \r
 904   }\r
 905 \r
 906   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 907   {\r
 908 \r
 909   }\r
 910 \r
 911   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 912   {\r
 913 \r
 914   }\r
 915 \r
 916   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 917   {\r
 918 \r
 919   }\r
 920 \r
 921   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 922   {\r
 923 \r
 924   }\r
 925 \r
 926   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928 \r
 929   }\r
 930 \r
 931   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933 \r
 934   }\r
 935 \r
 936 \r
 937   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 938   {\r
 939 \r
 940   }\r
 941 \r
 942   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 943   {\r
 944 \r
 945   }\r
 946 \r
 947 \r
 948 \r
 949   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 950   {\r
 951 \r
 952   }\r
 953 \r
 954 \r
 955 \r
 956 \r
 957   protected void clustalColour_actionPerformed(ActionEvent e)\r
 958   {\r
 959 \r
 960   }\r
 961 \r
 962   protected void zappoColour_actionPerformed(ActionEvent e)\r
 963   {\r
 964 \r
 965   }\r
 966 \r
 967   protected void taylorColour_actionPerformed(ActionEvent e)\r
 968   {\r
 969 \r
 970   }\r
 971 \r
 972 \r
 973   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 974   {\r
 975 \r
 976   }\r
 977 \r
 978   protected void helixColour_actionPerformed(ActionEvent e)\r
 979   {\r
 980 \r
 981   }\r
 982 \r
 983   protected void strandColour_actionPerformed(ActionEvent e)\r
 984   {\r
 985 \r
 986   }\r
 987 \r
 988   protected void turnColour_actionPerformed(ActionEvent e)\r
 989   {\r
 990 \r
 991   }\r
 992 \r
 993   protected void buriedColour_actionPerformed(ActionEvent e)\r
 994   {\r
 995 \r
 996   }\r
 997 \r
 998 \r
 999 \r
1000   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1001   {\r
1002 \r
1003   }\r
1004 \r
1005   protected void PIDColour_actionPerformed(ActionEvent e)\r
1006   {\r
1007 \r
1008   }\r
1009 \r
1010   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1011   {\r
1012 \r
1013   }\r
1014 \r
1015 \r
1016   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018 \r
1019   }\r
1020 \r
1021   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1022   {\r
1023 \r
1024   }\r
1025 \r
1026 \r
1027   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1028   {\r
1029 \r
1030   }\r
1031 \r
1032   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1033   {\r
1034 \r
1035   }\r
1036 \r
1037   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1038   {\r
1039 \r
1040   }\r
1041 \r
1042 \r
1043   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1044 \r
1045   }\r
1046 \r
1047   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1048   {\r
1049 \r
1050   }\r
1051 \r
1052   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1053   {\r
1054 \r
1055   }\r
1056 \r
1057   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1058   {\r
1059 \r
1060   }\r
1061 \r
1062  protected void copy_actionPerformed(ActionEvent e)\r
1063   {\r
1064 \r
1065   }\r
1066 \r
1067 \r
1068   protected void cut_actionPerformed(ActionEvent e)\r
1069   {\r
1070 \r
1071   }\r
1072 \r
1073   protected void delete_actionPerformed(ActionEvent e)\r
1074   {\r
1075 \r
1076   }\r
1077 \r
1078   protected void pasteNew_actionPerformed(ActionEvent e)\r
1079   {\r
1080 \r
1081   }\r
1082 \r
1083   protected void pasteThis_actionPerformed(ActionEvent e)\r
1084   {\r
1085 \r
1086   }\r
1087 \r
1088   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1089   {\r
1090 \r
1091   }\r
1092 \r
1093   protected void createPNG_actionPerformed(ActionEvent e)\r
1094   {\r
1095 \r
1096   }\r
1097 \r
1098   protected void font_actionPerformed(ActionEvent e)\r
1099   {\r
1100 \r
1101   }\r
1102 \r
1103   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1104   {\r
1105 \r
1106   }\r
1107 \r
1108   protected void epsFile_actionPerformed(ActionEvent e)\r
1109   {\r
1110 \r
1111   }\r
1112 \r
1113 \r
1114 \r
1115 }\r