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   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     fontMenu.setText("Font");\r
 164     viewMenu.setText("View");\r
 165     colourMenu.setText("Colour");\r
 166     calculateMenu.setText("Calculate");\r
 167     alignMenu.setText("Web Service");\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     fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 249     {\r
 250       public void actionPerformed(ActionEvent e)\r
 251       {\r
 252         fontNameMenuItem_actionPerformed(e);\r
 253       }\r
 254     });\r
 255     fontSizeMenuItem.setText("10");\r
 256     fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 257     {\r
 258       public void actionPerformed(ActionEvent e)\r
 259       {\r
 260         fontSizeMenuItem_actionPerformed(e);\r
 261       }\r
 262     });\r
 263     fontStyleMenuItem.setText("Plain");\r
 264     fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 265     {\r
 266       public void actionPerformed(ActionEvent e)\r
 267       {\r
 268         fontStyleMenuItem_actionPerformed(e);\r
 269       }\r
 270     });\r
 271     viewBoxesMenuItem.setText("Boxes");\r
 272     viewBoxesMenuItem.setState(true);\r
 273     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 274     {\r
 275       public void actionPerformed(ActionEvent e)\r
 276       {\r
 277         viewBoxesMenuItem_actionPerformed(e);\r
 278       }\r
 279     });\r
 280     viewTextMenuItem.setText("Text");\r
 281     viewTextMenuItem.setState(true);\r
 282     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 283     {\r
 284       public void actionPerformed(ActionEvent e)\r
 285       {\r
 286         viewTextMenuItem_actionPerformed(e);\r
 287       }\r
 288     });\r
 289     sortPairwiseMenuItem.setText("Sort by pairwise identity");\r
 290     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 291     {\r
 292       public void actionPerformed(ActionEvent e)\r
 293       {\r
 294         sortPairwiseMenuItem_actionPerformed(e);\r
 295       }\r
 296     });\r
 297     sortIDMenuItem.setText("Sort by ID");\r
 298     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 299     {\r
 300       public void actionPerformed(ActionEvent e)\r
 301       {\r
 302         sortIDMenuItem_actionPerformed(e);\r
 303       }\r
 304     });\r
 305     sortGroupMenuItem.setText("Sort by group");\r
 306     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 307     {\r
 308       public void actionPerformed(ActionEvent e)\r
 309       {\r
 310         sortGroupMenuItem_actionPerformed(e);\r
 311       }\r
 312     });\r
 313     sortTreeOrderMenuItem.setText("Sort by tree order");\r
 314     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 315     {\r
 316       public void actionPerformed(ActionEvent e)\r
 317       {\r
 318         sortTreeOrderMenuItem_actionPerformed(e);\r
 319       }\r
 320     });\r
 321     removeRedundancyMenuItem.setText("Remove redundancy");\r
 322     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 323     {\r
 324       public void actionPerformed(ActionEvent e)\r
 325       {\r
 326         removeRedundancyMenuItem_actionPerformed(e);\r
 327       }\r
 328     });\r
 329     pairwiseAlignmentMenuItem.setText("Pairwise alignments");\r
 330     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 331     {\r
 332       public void actionPerformed(ActionEvent e)\r
 333       {\r
 334         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 335       }\r
 336     });\r
 337     PCAMenuItem.setText("Principal component analysis");\r
 338     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 339     {\r
 340       public void actionPerformed(ActionEvent e)\r
 341       {\r
 342         PCAMenuItem_actionPerformed(e);\r
 343       }\r
 344     });\r
 345     averageDistanceTreeMenuItem.setText("Average distance tree using PID");\r
 346     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 347     {\r
 348       public void actionPerformed(ActionEvent e)\r
 349       {\r
 350         averageDistanceTreeMenuItem_actionPerformed(e);\r
 351       }\r
 352     });\r
 353     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");\r
 354     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 355     {\r
 356       public void actionPerformed(ActionEvent e)\r
 357       {\r
 358         neighbourTreeMenuItem_actionPerformed(e);\r
 359       }\r
 360     });\r
 361     clustalAlignMenuItem.setText("Clustal alignment");\r
 362     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 363     {\r
 364       public void actionPerformed(ActionEvent e)\r
 365       {\r
 366         clustalAlignMenuItem_actionPerformed(e);\r
 367       }\r
 368     });\r
 369     this.getContentPane().setLayout(borderLayout1);\r
 370     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 371     statusBar.setBackground(Color.white);\r
 372     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 373     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 374     statusBar.setText("Status bar");\r
 375     outputTextboxMenu.setMnemonic('T');\r
 376     outputTextboxMenu.setText("Output alignment via textbox");\r
 377     clustalColour.setSelected(false);\r
 378     clustalColour.setText("Clustalx colours");\r
 379     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         clustalColour_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     zappoColour.setText("Zappo colour scheme");\r
 387     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         zappoColour_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     taylorColour.setText("Taylor colour scheme");\r
 395     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         taylorColour_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     hydrophobicityColour.setText("By hydrophobicity");\r
 403     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         hydrophobicityColour_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     helixColour.setText("Helix propensity");\r
 411     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 412     {\r
 413       public void actionPerformed(ActionEvent e)\r
 414       {\r
 415         helixColour_actionPerformed(e);\r
 416       }\r
 417     });\r
 418     strandColour.setText("Strand propensity");\r
 419     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 420     {\r
 421       public void actionPerformed(ActionEvent e)\r
 422       {\r
 423         strandColour_actionPerformed(e);\r
 424       }\r
 425     });\r
 426     turnColour.setText("Turn propensity");\r
 427     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 428     {\r
 429       public void actionPerformed(ActionEvent e)\r
 430       {\r
 431         turnColour_actionPerformed(e);\r
 432       }\r
 433     });\r
 434     buriedColour.setText("Buried index");\r
 435     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         buriedColour_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     userDefinedColour.setText("User defined colours");\r
 443     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 444     {\r
 445       public void actionPerformed(ActionEvent e)\r
 446       {\r
 447         userDefinedColour_actionPerformed(e);\r
 448       }\r
 449     });\r
 450     PIDColour.setText("Percentage Identity");\r
 451     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 452     {\r
 453       public void actionPerformed(ActionEvent e)\r
 454       {\r
 455         PIDColour_actionPerformed(e);\r
 456       }\r
 457     });\r
 458     BLOSUM62Colour.setText("BLOSUM62 score");\r
 459     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 460     {\r
 461       public void actionPerformed(ActionEvent e)\r
 462       {\r
 463         BLOSUM62Colour_actionPerformed(e);\r
 464       }\r
 465     });\r
 466     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");\r
 467     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 468     {\r
 469       public void actionPerformed(ActionEvent e)\r
 470       {\r
 471         avTreeBlosumMenuItem_actionPerformed(e);\r
 472       }\r
 473     });\r
 474     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");\r
 475     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 476     {\r
 477       public void actionPerformed(ActionEvent e)\r
 478       {\r
 479         njTreeBlosumMenuItem_actionPerformed(e);\r
 480       }\r
 481     });\r
 482     consensusGraphMenuItem.setActionCommand("");\r
 483     consensusGraphMenuItem.setText("Consensus graph");\r
 484     consensusGraphMenuItem.setState(true);\r
 485     consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         consensusGraphMenuItem_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     colourTextMenuItem.setText("Colour text");\r
 493     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         colourTextMenuItem_actionPerformed(e);\r
 498       }\r
 499     });\r
 500     htmlMenuItem.setText("Output as HTML");\r
 501     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         htmlMenuItem_actionPerformed(e);\r
 506       }\r
 507     });\r
 508     overviewMenuItem.setText("Overview window");\r
 509     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 510     {\r
 511       public void actionPerformed(ActionEvent e)\r
 512       {\r
 513         overviewMenuItem_actionPerformed(e);\r
 514       }\r
 515     });\r
 516     undoMenuItem.setEnabled(false);\r
 517     undoMenuItem.setMnemonic('Z');\r
 518     undoMenuItem.setText("Undo");\r
 519     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 520     {\r
 521       public void actionPerformed(ActionEvent e)\r
 522       {\r
 523         undoMenuItem_actionPerformed(e);\r
 524       }\r
 525     });\r
 526     redoMenuItem.setEnabled(false);\r
 527     redoMenuItem.setMnemonic('0');\r
 528     redoMenuItem.setText("Redo");\r
 529     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         redoMenuItem_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     conservationMenuItem.setText("By conservation");\r
 537     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         conservationMenuItem_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     noColourmenuItem.setText("None");\r
 545     noColourmenuItem.setSelected(true);\r
 546     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         noColourmenuItem_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     wrapMenuItem.setText("Wrap alignment");\r
 554     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         wrapMenuItem_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     pdbTest.setText("PDB Test Viewer");\r
 562     pdbTest.addActionListener(new java.awt.event.ActionListener()\r
 563     {\r
 564       public void actionPerformed(ActionEvent e)\r
 565       {\r
 566         pdbTest_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     printMenuItem.setText("Print");\r
 570     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent e)\r
 573       {\r
 574         printMenuItem_actionPerformed(e);\r
 575       }\r
 576     });\r
 577     renderGapsMenuItem.setText("Render gaps");\r
 578     renderGapsMenuItem.setState(true);\r
 579     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent e)\r
 582       {\r
 583         renderGapsMenuItem_actionPerformed(e);\r
 584       }\r
 585     });\r
 586     findMenuItem.setText("Find");\r
 587     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent e)\r
 590       {\r
 591         findMenuItem_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     searchMenu.setText("Search");\r
 595 \r
 596     abovePIDThreshold.setText("Above PID threshold");\r
 597     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 598       public void actionPerformed(ActionEvent e) {\r
 599         abovePIDThreshold_actionPerformed(e);\r
 600       }\r
 601     });\r
 602     sequenceFeatures.setSelected(true);\r
 603     sequenceFeatures.setText("Sequence Features");\r
 604     sequenceFeatures.addActionListener(new ActionListener()\r
 605     {\r
 606       public void actionPerformed(ActionEvent actionEvent)\r
 607       {\r
 608         sequenceFeatures_actionPerformed(actionEvent);\r
 609       }\r
 610     });\r
 611     nucleotideColour.setText("Nucleotide colours");\r
 612     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 613     {\r
 614       public void actionPerformed(ActionEvent e)\r
 615       {\r
 616         nucleotideColour_actionPerformed(e);\r
 617       }\r
 618     });\r
 619     deleteGroups.setSelected(false);\r
 620     deleteGroups.setText("Delete all groups");\r
 621     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 622     {\r
 623       public void actionPerformed(ActionEvent e)\r
 624       {\r
 625         deleteGroups_actionPerformed(e);\r
 626       }\r
 627     });\r
 628     copy.setText("Copy");\r
 629     copy.setMnemonic(KeyEvent.VK_C);\r
 630 \r
 631     copy.addActionListener(new java.awt.event.ActionListener()\r
 632     {\r
 633       public void actionPerformed(ActionEvent e)\r
 634       {\r
 635         copy_actionPerformed(e);\r
 636       }\r
 637     });\r
 638    // pasteNew.setText("Paste (as new alignment)");\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("as 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     alignFrameMenuBar.add(fileMenu);\r
 675     alignFrameMenuBar.add(editMenu);\r
 676     alignFrameMenuBar.add(searchMenu);\r
 677     alignFrameMenuBar.add(fontMenu);\r
 678     alignFrameMenuBar.add(viewMenu);\r
 679     alignFrameMenuBar.add(colourMenu);\r
 680     alignFrameMenuBar.add(calculateMenu);\r
 681     alignFrameMenuBar.add(alignMenu);\r
 682     fileMenu.add(saveAlignmentMenu);\r
 683     fileMenu.add(outputTextboxMenu);\r
 684     fileMenu.add(htmlMenuItem);\r
 685     fileMenu.add(printMenuItem);\r
 686     fileMenu.addSeparator();\r
 687     fileMenu.add(closeMenuItem);\r
 688     editMenu.add(copy);\r
 689     editMenu.add(jMenu1);\r
 690     editMenu.add(cut);\r
 691     editMenu.add(delete);\r
 692     editMenu.addSeparator();\r
 693     editMenu.add(undoMenuItem);\r
 694     editMenu.add(redoMenuItem);\r
 695     editMenu.addSeparator();\r
 696     editMenu.add(deselectAllSequenceMenuItem);\r
 697     editMenu.add(selectAllSequenceMenuItem);\r
 698     editMenu.add(invertSequenceMenuItem);\r
 699     editMenu.add(deleteGroups);\r
 700     editMenu.add(groupsMenuItem);\r
 701     editMenu.addSeparator();\r
 702     editMenu.add(deselectAllColumnsMenuItem);\r
 703     editMenu.add(remove2LeftMenuItem);\r
 704     editMenu.add(remove2RightMenuItem);\r
 705     editMenu.addSeparator();\r
 706     editMenu.add(removeGappedColumnMenuItem);\r
 707     editMenu.add(removeAllGapsMenuItem);\r
 708     editMenu.add(setGapCharMenuItem);\r
 709     searchMenu.add(findMenuItem);\r
 710     fontMenu.add(fontNameMenuItem);\r
 711     fontMenu.add(fontSizeMenuItem);\r
 712     fontMenu.add(fontStyleMenuItem);\r
 713     viewMenu.add(wrapMenuItem);\r
 714     viewMenu.add(viewBoxesMenuItem);\r
 715     viewMenu.add(viewTextMenuItem);\r
 716     viewMenu.add(colourTextMenuItem);\r
 717     viewMenu.add(renderGapsMenuItem);\r
 718     viewMenu.add(consensusGraphMenuItem);\r
 719     viewMenu.add(overviewMenuItem);\r
 720     viewMenu.add(sequenceFeatures);\r
 721     colourMenu.add(noColourmenuItem);\r
 722     colourMenu.add(clustalColour);\r
 723     colourMenu.add(zappoColour);\r
 724     colourMenu.add(taylorColour);\r
 725     colourMenu.add(hydrophobicityColour);\r
 726     colourMenu.add(helixColour);\r
 727     colourMenu.add(strandColour);\r
 728     colourMenu.add(turnColour);\r
 729     colourMenu.add(buriedColour);\r
 730     colourMenu.add(nucleotideColour);\r
 731     colourMenu.add(userDefinedColour);\r
 732     colourMenu.add(PIDColour);\r
 733     colourMenu.add(BLOSUM62Colour);\r
 734     colourMenu.addSeparator();\r
 735     colourMenu.add(abovePIDThreshold);\r
 736     colourMenu.add(conservationMenuItem);\r
 737     calculateMenu.add(sortPairwiseMenuItem);\r
 738     calculateMenu.add(sortIDMenuItem);\r
 739     calculateMenu.add(sortGroupMenuItem);\r
 740     calculateMenu.add(sortTreeOrderMenuItem);\r
 741     calculateMenu.add(removeRedundancyMenuItem);\r
 742     calculateMenu.addSeparator();\r
 743     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 744     calculateMenu.add(PCAMenuItem);\r
 745     calculateMenu.addSeparator();\r
 746     calculateMenu.add(averageDistanceTreeMenuItem);\r
 747     calculateMenu.add(neighbourTreeMenuItem);\r
 748     calculateMenu.add(avDistanceTreeBlosumMenuItem);\r
 749     calculateMenu.add(njTreeBlosumMenuItem);\r
 750     alignMenu.add(clustalAlignMenuItem);\r
 751     alignMenu.add(pdbTest);\r
 752     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 753     jMenu1.add(pasteNew);\r
 754     jMenu1.add(pasteThis);\r
 755   }\r
 756 \r
 757   protected void saveAs_actionPerformed(ActionEvent e)\r
 758   {\r
 759 \r
 760   }\r
 761 \r
 762   protected void outputText_actionPerformed(ActionEvent e)\r
 763   {\r
 764 \r
 765   }\r
 766 \r
 767   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 768   {\r
 769 \r
 770   }\r
 771 \r
 772 \r
 773 \r
 774 \r
 775 \r
 776   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 777   {\r
 778 \r
 779   }\r
 780 \r
 781   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 782   {\r
 783 \r
 784   }\r
 785 \r
 786   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 787   {\r
 788 \r
 789   }\r
 790 \r
 791 \r
 792   protected void groupsMenuItem_actionPerformed(ActionEvent e)\r
 793   {\r
 794 \r
 795   }\r
 796 \r
 797 \r
 798   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 799   {\r
 800 \r
 801   }\r
 802 \r
 803   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 804   {\r
 805 \r
 806   }\r
 807 \r
 808   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 809   {\r
 810 \r
 811   }\r
 812 \r
 813 \r
 814   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 815   {\r
 816 \r
 817   }\r
 818 \r
 819   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 820   {\r
 821 \r
 822   }\r
 823 \r
 824   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 825   {\r
 826 \r
 827   }\r
 828 \r
 829   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831 \r
 832   }\r
 833 \r
 834   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 835   {\r
 836 \r
 837   }\r
 838 \r
 839   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 840   {\r
 841 \r
 842   }\r
 843 \r
 844 \r
 845   protected void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 846   {\r
 847 \r
 848   }\r
 849 \r
 850   protected void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 851   {\r
 852 \r
 853   }\r
 854 \r
 855   protected void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857 \r
 858   }\r
 859 \r
 860   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862 \r
 863   }\r
 864 \r
 865 \r
 866   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 867   {\r
 868 \r
 869   }\r
 870 \r
 871   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 872   {\r
 873 \r
 874   }\r
 875 \r
 876 \r
 877   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 878   {\r
 879 \r
 880   }\r
 881 \r
 882 \r
 883 \r
 884   protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886 \r
 887   }\r
 888 \r
 889   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
 890   {\r
 891 \r
 892   }\r
 893 \r
 894   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896 \r
 897   }\r
 898 \r
 899   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901 \r
 902   }\r
 903 \r
 904   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 905   {\r
 906 \r
 907   }\r
 908 \r
 909   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912   }\r
 913 \r
 914   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916 \r
 917   }\r
 918 \r
 919   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921 \r
 922   }\r
 923 \r
 924   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
 925   {\r
 926 \r
 927   }\r
 928 \r
 929   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 930   {\r
 931 \r
 932   }\r
 933 \r
 934   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 935   {\r
 936 \r
 937   }\r
 938 \r
 939 \r
 940   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 941   {\r
 942 \r
 943   }\r
 944 \r
 945   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 946   {\r
 947 \r
 948   }\r
 949 \r
 950 \r
 951 \r
 952   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 953   {\r
 954 \r
 955   }\r
 956 \r
 957 \r
 958 \r
 959 \r
 960   protected void clustalColour_actionPerformed(ActionEvent e)\r
 961   {\r
 962 \r
 963   }\r
 964 \r
 965   protected void zappoColour_actionPerformed(ActionEvent e)\r
 966   {\r
 967 \r
 968   }\r
 969 \r
 970   protected void taylorColour_actionPerformed(ActionEvent e)\r
 971   {\r
 972 \r
 973   }\r
 974 \r
 975 \r
 976   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 977   {\r
 978 \r
 979   }\r
 980 \r
 981   protected void helixColour_actionPerformed(ActionEvent e)\r
 982   {\r
 983 \r
 984   }\r
 985 \r
 986   protected void strandColour_actionPerformed(ActionEvent e)\r
 987   {\r
 988 \r
 989   }\r
 990 \r
 991   protected void turnColour_actionPerformed(ActionEvent e)\r
 992   {\r
 993 \r
 994   }\r
 995 \r
 996   protected void buriedColour_actionPerformed(ActionEvent e)\r
 997   {\r
 998 \r
 999   }\r
1000 \r
1001 \r
1002 \r
1003   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1004   {\r
1005 \r
1006   }\r
1007 \r
1008   protected void PIDColour_actionPerformed(ActionEvent e)\r
1009   {\r
1010 \r
1011   }\r
1012 \r
1013   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1014   {\r
1015 \r
1016   }\r
1017 \r
1018 \r
1019   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1020   {\r
1021 \r
1022   }\r
1023 \r
1024   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
1025   {\r
1026 \r
1027   }\r
1028 \r
1029   protected void pdbTest_actionPerformed(ActionEvent e)\r
1030   {\r
1031 \r
1032   }\r
1033 \r
1034   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1035   {\r
1036 \r
1037   }\r
1038 \r
1039   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1040   {\r
1041 \r
1042   }\r
1043 \r
1044   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046 \r
1047   }\r
1048 \r
1049 \r
1050   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
1051 \r
1052   }\r
1053 \r
1054   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1055   {\r
1056 \r
1057   }\r
1058 \r
1059   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1060   {\r
1061 \r
1062   }\r
1063 \r
1064   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1065   {\r
1066 \r
1067   }\r
1068 \r
1069  protected void copy_actionPerformed(ActionEvent e)\r
1070   {\r
1071 \r
1072   }\r
1073 \r
1074 \r
1075   protected void cut_actionPerformed(ActionEvent e)\r
1076   {\r
1077 \r
1078   }\r
1079 \r
1080   protected void delete_actionPerformed(ActionEvent e)\r
1081   {\r
1082 \r
1083   }\r
1084 \r
1085   protected void pasteNew_actionPerformed(ActionEvent e)\r
1086   {\r
1087 \r
1088   }\r
1089 \r
1090   protected void pasteThis_actionPerformed(ActionEvent e)\r
1091   {\r
1092 \r
1093   }\r
1094 \r
1095 \r
1096 \r
1097 }\r