src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.jbgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 \r
  26 import jalview.gui.*;\r
  27 import jalview.schemes.*;\r
  28 \r
  29 public class GAlignFrame\r
  30     extends JInternalFrame\r
  31 {\r
  32   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  33   protected JMenu fileMenu = new JMenu();\r
  34   protected JMenuItem closeMenuItem = new JMenuItem();\r
  35   protected JMenu editMenu = new JMenu();\r
  36   protected JMenu viewMenu = new JMenu();\r
  37   protected JMenu colourMenu = new JMenu();\r
  38   protected JMenu calculateMenu = new JMenu();\r
  39   protected JMenu webService = new JMenu();\r
  40   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  41   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  42   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  43   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  44   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  45   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  46   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  47   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  48   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  49   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  50   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  51   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  54   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  57   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  58   BorderLayout borderLayout1 = new BorderLayout();\r
  59   public JLabel statusBar = new JLabel();\r
  60   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  61   protected JMenu outputTextboxMenu = new JMenu();\r
  62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  66       JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  74   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  75   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  76   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  77   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  78   JMenuItem htmlMenuItem = new JMenuItem();\r
  79   JMenuItem overviewMenuItem = new JMenuItem();\r
  80   protected JMenuItem undoMenuItem = new JMenuItem();\r
  81   protected JMenuItem redoMenuItem = new JMenuItem();\r
  82   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  84   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   JMenu searchMenu = new JMenu();\r
  89   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  90   public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  91   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  92   JMenuItem deleteGroups = new JMenuItem();\r
  93   JMenuItem delete = new JMenuItem();\r
  94   JMenuItem copy = new JMenuItem();\r
  95   JMenuItem cut = new JMenuItem();\r
  96   JMenu jMenu1 = new JMenu();\r
  97   JMenuItem pasteNew = new JMenuItem();\r
  98   JMenuItem pasteThis = new JMenuItem();\r
  99   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 100   JMenuItem createPNG = new JMenuItem();\r
 101   protected JMenuItem font = new JMenuItem();\r
 102   public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
 103   JMenuItem epsFile = new JMenuItem();\r
 104   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 105   JMenuItem jnet = new JMenuItem();\r
 106   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 107   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 108   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 109   JMenuItem modifyPID = new JMenuItem();\r
 110   JMenuItem modifyConservation = new JMenuItem();\r
 111   protected JMenu sortByTreeMenu = new JMenu();\r
 112   protected JMenu sort = new JMenu();\r
 113   JMenu calculate = new JMenu();\r
 114   JMenuItem msaAlignMenuItem = new JMenuItem();\r
 115   JMenu jMenu2 = new JMenu();\r
 116   JMenuItem padGapsMenuitem = new JMenuItem();\r
 117   JMenuItem ClustalRealign = new JMenuItem();\r
 118 \r
 119   public GAlignFrame()\r
 120   {\r
 121     ButtonGroup colours = new ButtonGroup();\r
 122     colours.add(noColourmenuItem);\r
 123     colours.add(clustalColour);\r
 124     colours.add(zappoColour);\r
 125     colours.add(taylorColour);\r
 126     colours.add(hydrophobicityColour);\r
 127     colours.add(helixColour);\r
 128     colours.add(strandColour);\r
 129     colours.add(turnColour);\r
 130     colours.add(buriedColour);\r
 131     colours.add(userDefinedColour);\r
 132     colours.add(PIDColour);\r
 133     colours.add(BLOSUM62Colour);\r
 134     colours.add(nucleotideColour);\r
 135 \r
 136     noColourmenuItem.setSelected(true);\r
 137 \r
 138     String defaultColour = jalview.bin.Cache.getDefault("DEFAULT_COLOUR", null);\r
 139 \r
 140     if (defaultColour != null)\r
 141     {\r
 142       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 143 \r
 144       switch (index)\r
 145       {\r
 146         case ColourSchemeProperty.CLUSTAL:\r
 147           clustalColour.setSelected(true);\r
 148 \r
 149           break;\r
 150 \r
 151         case ColourSchemeProperty.BLOSUM:\r
 152           BLOSUM62Colour.setSelected(true);\r
 153 \r
 154           break;\r
 155 \r
 156         case ColourSchemeProperty.PID:\r
 157           PIDColour.setSelected(true);\r
 158 \r
 159           break;\r
 160 \r
 161         case ColourSchemeProperty.ZAPPO:\r
 162           zappoColour.setSelected(true);\r
 163 \r
 164           break;\r
 165 \r
 166         case ColourSchemeProperty.HYDROPHOBIC:\r
 167           hydrophobicityColour.setSelected(true);\r
 168 \r
 169           break;\r
 170 \r
 171         case ColourSchemeProperty.HELIX:\r
 172           helixColour.setSelected(true);\r
 173 \r
 174           break;\r
 175 \r
 176         case ColourSchemeProperty.STRAND:\r
 177           strandColour.setSelected(true);\r
 178 \r
 179           break;\r
 180 \r
 181         case ColourSchemeProperty.TURN:\r
 182           turnColour.setSelected(true);\r
 183 \r
 184           break;\r
 185 \r
 186         case ColourSchemeProperty.BURIED:\r
 187           buriedColour.setSelected(true);\r
 188 \r
 189           break;\r
 190 \r
 191         case ColourSchemeProperty.NUCLEOTIDE:\r
 192           nucleotideColour.setSelected(true);\r
 193 \r
 194           break;\r
 195 \r
 196         case ColourSchemeProperty.USER_DEFINED:\r
 197           userDefinedColour.setSelected(true);\r
 198 \r
 199           break;\r
 200       }\r
 201     }\r
 202 \r
 203     try\r
 204     {\r
 205       jbInit();\r
 206       setJMenuBar(alignFrameMenuBar);\r
 207 \r
 208       JMenuItem item;\r
 209 \r
 210       // dynamically fill save as menu with available formats\r
 211       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 212       {\r
 213         item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 214                              elementAt(\r
 215                                  i));\r
 216         item.addActionListener(new java.awt.event.ActionListener()\r
 217         {\r
 218           public void actionPerformed(ActionEvent e)\r
 219           {\r
 220             outputText_actionPerformed(e);\r
 221           }\r
 222         });\r
 223 \r
 224         outputTextboxMenu.add(item);\r
 225       }\r
 226     }\r
 227     catch (Exception e)\r
 228     {\r
 229     }\r
 230 \r
 231   }\r
 232 \r
 233   private void jbInit()\r
 234       throws Exception\r
 235   {\r
 236     fileMenu.setMnemonic('F');\r
 237     fileMenu.setText("File");\r
 238     saveAlignmentMenu.setMnemonic('L');\r
 239     saveAlignmentMenu.setText("Save As");\r
 240     saveAlignmentMenu.addActionListener(new ActionListener()\r
 241     {\r
 242       public void actionPerformed(ActionEvent e)\r
 243       {\r
 244         saveAlignmentMenu_actionPerformed(e);\r
 245       }\r
 246     });\r
 247     closeMenuItem.setMnemonic('C');\r
 248     closeMenuItem.setText("Close");\r
 249     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 250     {\r
 251       public void actionPerformed(ActionEvent e)\r
 252       {\r
 253         closeMenuItem_actionPerformed(e);\r
 254       }\r
 255     });\r
 256     editMenu.setText("Edit");\r
 257     viewMenu.setText("View");\r
 258     colourMenu.setText("Colour");\r
 259     calculateMenu.setText("Calculate");\r
 260     webService.setText("Web Service");\r
 261     selectAllSequenceMenuItem.setText("Select all");\r
 262     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 263         java.awt.event.KeyEvent.VK_A,\r
 264         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 265     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 266                                                 ActionListener()\r
 267     {\r
 268       public void actionPerformed(ActionEvent e)\r
 269       {\r
 270         selectAllSequenceMenuItem_actionPerformed(e);\r
 271       }\r
 272     });\r
 273     deselectAllSequenceMenuItem.setText("Deselect All");\r
 274     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 275                                                getKeyStroke(\r
 276         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 277     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 278                                                   ActionListener()\r
 279     {\r
 280       public void actionPerformed(ActionEvent e)\r
 281       {\r
 282         deselectAllSequenceMenuItem_actionPerformed(e);\r
 283       }\r
 284     });\r
 285     invertSequenceMenuItem.setText("Invert Selection");\r
 286     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 287     {\r
 288       public void actionPerformed(ActionEvent e)\r
 289       {\r
 290         invertSequenceMenuItem_actionPerformed(e);\r
 291       }\r
 292     });\r
 293     remove2LeftMenuItem.setText("Remove Left");\r
 294     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 295     {\r
 296       public void actionPerformed(ActionEvent e)\r
 297       {\r
 298         remove2LeftMenuItem_actionPerformed(e);\r
 299       }\r
 300     });\r
 301     remove2RightMenuItem.setText("Remove Right");\r
 302     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 303     {\r
 304       public void actionPerformed(ActionEvent e)\r
 305       {\r
 306         remove2RightMenuItem_actionPerformed(e);\r
 307       }\r
 308     });\r
 309     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 310     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 311                                                  ActionListener()\r
 312     {\r
 313       public void actionPerformed(ActionEvent e)\r
 314       {\r
 315         removeGappedColumnMenuItem_actionPerformed(e);\r
 316       }\r
 317     });\r
 318     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 319     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 320     {\r
 321       public void actionPerformed(ActionEvent e)\r
 322       {\r
 323         removeAllGapsMenuItem_actionPerformed(e);\r
 324       }\r
 325     });\r
 326     viewBoxesMenuItem.setText("Boxes");\r
 327     viewBoxesMenuItem.setState(true);\r
 328     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 329     {\r
 330       public void actionPerformed(ActionEvent e)\r
 331       {\r
 332         viewBoxesMenuItem_actionPerformed(e);\r
 333       }\r
 334     });\r
 335     viewTextMenuItem.setText("Text");\r
 336     viewTextMenuItem.setState(true);\r
 337     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 338     {\r
 339       public void actionPerformed(ActionEvent e)\r
 340       {\r
 341         viewTextMenuItem_actionPerformed(e);\r
 342       }\r
 343     });\r
 344     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 345     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 346     {\r
 347       public void actionPerformed(ActionEvent e)\r
 348       {\r
 349         sortPairwiseMenuItem_actionPerformed(e);\r
 350       }\r
 351     });\r
 352     sortIDMenuItem.setText("by ID");\r
 353     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 354     {\r
 355       public void actionPerformed(ActionEvent e)\r
 356       {\r
 357         sortIDMenuItem_actionPerformed(e);\r
 358       }\r
 359     });\r
 360     sortGroupMenuItem.setText("by Group");\r
 361     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 362     {\r
 363       public void actionPerformed(ActionEvent e)\r
 364       {\r
 365         sortGroupMenuItem_actionPerformed(e);\r
 366       }\r
 367     });\r
 368     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 369     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 370                                                ActionListener()\r
 371     {\r
 372       public void actionPerformed(ActionEvent e)\r
 373       {\r
 374         removeRedundancyMenuItem_actionPerformed(e);\r
 375       }\r
 376     });\r
 377     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 378     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 379                                                 ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     PCAMenuItem.setText("Principal Component Analysis");\r
 387     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         PCAMenuItem_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     averageDistanceTreeMenuItem.setText(\r
 395         "Average Distance Using % Identity");\r
 396     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 397                                                   ActionListener()\r
 398     {\r
 399       public void actionPerformed(ActionEvent e)\r
 400       {\r
 401         averageDistanceTreeMenuItem_actionPerformed(e);\r
 402       }\r
 403     });\r
 404     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 405     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 406     {\r
 407       public void actionPerformed(ActionEvent e)\r
 408       {\r
 409         neighbourTreeMenuItem_actionPerformed(e);\r
 410       }\r
 411     });\r
 412     clustalAlignMenuItem.setText("Clustal Alignment");\r
 413     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 414     {\r
 415       public void actionPerformed(ActionEvent e)\r
 416       {\r
 417         clustalAlignMenuItem_actionPerformed(e);\r
 418       }\r
 419     });\r
 420     this.getContentPane().setLayout(borderLayout1);\r
 421     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 422     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
 423     {\r
 424       public void ancestorAdded(AncestorEvent event)\r
 425       {\r
 426         alignFrameMenuBar_ancestorAdded(event);\r
 427       }\r
 428 \r
 429       public void ancestorRemoved(AncestorEvent event)\r
 430       {\r
 431       }\r
 432 \r
 433       public void ancestorMoved(AncestorEvent event)\r
 434       {\r
 435       }\r
 436     });\r
 437     statusBar.setBackground(Color.white);\r
 438     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 439     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 440     statusBar.setText("Status bar");\r
 441     outputTextboxMenu.setMnemonic('T');\r
 442     outputTextboxMenu.setText("Output to Textbox");\r
 443     clustalColour.setText("Clustalx");\r
 444 \r
 445     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 446     {\r
 447       public void actionPerformed(ActionEvent e)\r
 448       {\r
 449         clustalColour_actionPerformed(e);\r
 450       }\r
 451     });\r
 452     zappoColour.setText("Zappo");\r
 453     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 454     {\r
 455       public void actionPerformed(ActionEvent e)\r
 456       {\r
 457         zappoColour_actionPerformed(e);\r
 458       }\r
 459     });\r
 460     taylorColour.setText("Taylor");\r
 461     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 462     {\r
 463       public void actionPerformed(ActionEvent e)\r
 464       {\r
 465         taylorColour_actionPerformed(e);\r
 466       }\r
 467     });\r
 468     hydrophobicityColour.setText("Hydrophobicity");\r
 469     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         hydrophobicityColour_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     helixColour.setText("Helix Propensity");\r
 477     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         helixColour_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     strandColour.setText("Strand Propensity");\r
 485     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         strandColour_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     turnColour.setText("Turn Propensity");\r
 493     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         turnColour_actionPerformed(e);\r
 498       }\r
 499     });\r
 500     buriedColour.setText("Buried Index");\r
 501     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         buriedColour_actionPerformed(e);\r
 506       }\r
 507     });\r
 508     userDefinedColour.setText("User Defined...");\r
 509     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 510     {\r
 511       public void actionPerformed(ActionEvent e)\r
 512       {\r
 513         userDefinedColour_actionPerformed(e);\r
 514       }\r
 515     });\r
 516     PIDColour.setText("Percentage Identity");\r
 517     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 518     {\r
 519       public void actionPerformed(ActionEvent e)\r
 520       {\r
 521         PIDColour_actionPerformed(e);\r
 522       }\r
 523     });\r
 524     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 525     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 526     {\r
 527       public void actionPerformed(ActionEvent e)\r
 528       {\r
 529         BLOSUM62Colour_actionPerformed(e);\r
 530       }\r
 531     });\r
 532     avDistanceTreeBlosumMenuItem.setText(\r
 533         "Average Distance Using BLOSUM62");\r
 534     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 535         ActionListener()\r
 536     {\r
 537       public void actionPerformed(ActionEvent e)\r
 538       {\r
 539         avTreeBlosumMenuItem_actionPerformed(e);\r
 540       }\r
 541     });\r
 542     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 543     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 544     {\r
 545       public void actionPerformed(ActionEvent e)\r
 546       {\r
 547         njTreeBlosumMenuItem_actionPerformed(e);\r
 548       }\r
 549     });\r
 550     annotationPanelMenuItem.setActionCommand("");\r
 551     annotationPanelMenuItem.setText("Show Annotations");\r
 552     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 553     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         annotationPanelMenuItem_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     colourTextMenuItem.setText("Colour Text");\r
 561     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         colourTextMenuItem_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     htmlMenuItem.setText("HTML");\r
 569     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         htmlMenuItem_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     overviewMenuItem.setText("Overview Window");\r
 577     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 578     {\r
 579       public void actionPerformed(ActionEvent e)\r
 580       {\r
 581         overviewMenuItem_actionPerformed(e);\r
 582       }\r
 583     });\r
 584     undoMenuItem.setEnabled(false);\r
 585     undoMenuItem.setMnemonic('Z');\r
 586     undoMenuItem.setText("Undo");\r
 587     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 588         java.awt.event.KeyEvent.VK_Z,\r
 589         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 590     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 591     {\r
 592       public void actionPerformed(ActionEvent e)\r
 593       {\r
 594         undoMenuItem_actionPerformed(e);\r
 595       }\r
 596     });\r
 597     redoMenuItem.setEnabled(false);\r
 598     redoMenuItem.setMnemonic('0');\r
 599     redoMenuItem.setText("Redo");\r
 600     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 601     {\r
 602       public void actionPerformed(ActionEvent e)\r
 603       {\r
 604         redoMenuItem_actionPerformed(e);\r
 605       }\r
 606     });\r
 607     conservationMenuItem.setText("By Conservation");\r
 608     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 609     {\r
 610       public void actionPerformed(ActionEvent e)\r
 611       {\r
 612         conservationMenuItem_actionPerformed(e);\r
 613       }\r
 614     });\r
 615     noColourmenuItem.setText("None");\r
 616     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 617     {\r
 618       public void actionPerformed(ActionEvent e)\r
 619       {\r
 620         noColourmenuItem_actionPerformed(e);\r
 621       }\r
 622     });\r
 623     wrapMenuItem.setText("Wrap");\r
 624     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 625     {\r
 626       public void actionPerformed(ActionEvent e)\r
 627       {\r
 628         wrapMenuItem_actionPerformed(e);\r
 629       }\r
 630     });\r
 631     printMenuItem.setText("Print");\r
 632     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 633     {\r
 634       public void actionPerformed(ActionEvent e)\r
 635       {\r
 636         printMenuItem_actionPerformed(e);\r
 637       }\r
 638     });\r
 639     renderGapsMenuItem.setText("Show Gaps");\r
 640     renderGapsMenuItem.setState(true);\r
 641     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 642     {\r
 643       public void actionPerformed(ActionEvent e)\r
 644       {\r
 645         renderGapsMenuItem_actionPerformed(e);\r
 646       }\r
 647     });\r
 648     findMenuItem.setText("Find...");\r
 649     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 650         java.awt.event.KeyEvent.VK_F,\r
 651         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 652     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 653     {\r
 654       public void actionPerformed(ActionEvent e)\r
 655       {\r
 656         findMenuItem_actionPerformed(e);\r
 657       }\r
 658     });\r
 659     searchMenu.setText("Search");\r
 660 \r
 661     abovePIDThreshold.setText("Above Identity Threshold");\r
 662     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 663     {\r
 664       public void actionPerformed(ActionEvent e)\r
 665       {\r
 666         abovePIDThreshold_actionPerformed(e);\r
 667       }\r
 668     });\r
 669     sequenceFeatures.setText("Sequence Features");\r
 670     sequenceFeatures.addActionListener(new ActionListener()\r
 671     {\r
 672       public void actionPerformed(ActionEvent actionEvent)\r
 673       {\r
 674         sequenceFeatures_actionPerformed(actionEvent);\r
 675       }\r
 676     });\r
 677     nucleotideColour.setText("Nucleotide");\r
 678     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 679     {\r
 680       public void actionPerformed(ActionEvent e)\r
 681       {\r
 682         nucleotideColour_actionPerformed(e);\r
 683       }\r
 684     });\r
 685     deleteGroups.setText("Undefine groups");\r
 686     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 687     {\r
 688       public void actionPerformed(ActionEvent e)\r
 689       {\r
 690         deleteGroups_actionPerformed(e);\r
 691       }\r
 692     });\r
 693     copy.setText("Copy");\r
 694     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 695         java.awt.event.KeyEvent.VK_C,\r
 696         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 697     copy.setMnemonic(KeyEvent.VK_C);\r
 698 \r
 699     copy.addActionListener(new java.awt.event.ActionListener()\r
 700     {\r
 701       public void actionPerformed(ActionEvent e)\r
 702       {\r
 703         copy_actionPerformed(e);\r
 704       }\r
 705     });\r
 706     cut.setText("Cut");\r
 707     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 708         java.awt.event.KeyEvent.VK_X,\r
 709         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 710     cut.setMnemonic(KeyEvent.VK_X);\r
 711     cut.addActionListener(new java.awt.event.ActionListener()\r
 712     {\r
 713       public void actionPerformed(ActionEvent e)\r
 714       {\r
 715         cut_actionPerformed(e);\r
 716       }\r
 717     });\r
 718     delete.setText("Delete");\r
 719     delete.addActionListener(new java.awt.event.ActionListener()\r
 720     {\r
 721       public void actionPerformed(ActionEvent e)\r
 722       {\r
 723         delete_actionPerformed(e);\r
 724       }\r
 725     });\r
 726     jMenu1.setMnemonic('V');\r
 727     jMenu1.setText("Paste");\r
 728     pasteNew.setText("To New Alignment");\r
 729     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 730         java.awt.event.KeyEvent.VK_V,\r
 731         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 732     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 733     {\r
 734       public void actionPerformed(ActionEvent e)\r
 735       {\r
 736         pasteNew_actionPerformed(e);\r
 737       }\r
 738     });\r
 739     pasteThis.setText("Add To This Alignment");\r
 740     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 741     {\r
 742       public void actionPerformed(ActionEvent e)\r
 743       {\r
 744         pasteThis_actionPerformed(e);\r
 745       }\r
 746     });\r
 747     applyToAllGroups.setText("Apply Colour To All Groups");\r
 748     applyToAllGroups.setState(true);\r
 749     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 750     {\r
 751       public void actionPerformed(ActionEvent e)\r
 752       {\r
 753         applyToAllGroups_actionPerformed(e);\r
 754       }\r
 755     });\r
 756     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 757     {\r
 758       public void actionPerformed(ActionEvent e)\r
 759       {\r
 760         createPNG(null);\r
 761       }\r
 762     });\r
 763     createPNG.setActionCommand("Save As PNG Image");\r
 764     createPNG.setText("PNG");\r
 765     font.setText("Font...");\r
 766     font.addActionListener(new java.awt.event.ActionListener()\r
 767     {\r
 768       public void actionPerformed(ActionEvent e)\r
 769       {\r
 770         font_actionPerformed(e);\r
 771       }\r
 772     });\r
 773     fullSeqId.setText("Show Full Sequence ID");\r
 774     fullSeqId.setState(true);\r
 775     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
 776     {\r
 777       public void actionPerformed(ActionEvent e)\r
 778       {\r
 779         fullSeqId_actionPerformed(e);\r
 780       }\r
 781     });\r
 782     epsFile.setText("EPS");\r
 783     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 784     {\r
 785       public void actionPerformed(ActionEvent e)\r
 786       {\r
 787         createEPS(null);\r
 788       }\r
 789     });\r
 790     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 791     LoadtreeMenuItem.setText("Load Assocated Tree");\r
 792     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 793     {\r
 794       public void actionPerformed(ActionEvent e)\r
 795       {\r
 796         LoadtreeMenuItem_actionPerformed(e);\r
 797       }\r
 798     });\r
 799     jnet.setText("JNet");\r
 800     jnet.addActionListener(new java.awt.event.ActionListener()\r
 801     {\r
 802       public void actionPerformed(ActionEvent e)\r
 803       {\r
 804         jpred_actionPerformed(e);\r
 805       }\r
 806     });\r
 807     scaleAbove.setVisible(false);\r
 808     scaleAbove.setText("Scale Above");\r
 809     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 810     {\r
 811       public void actionPerformed(ActionEvent e)\r
 812       {\r
 813         scaleAbove_actionPerformed(e);\r
 814       }\r
 815     });\r
 816     scaleLeft.setVisible(false);\r
 817     scaleLeft.setSelected(true);\r
 818     scaleLeft.setText("Scale Left");\r
 819     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 820     {\r
 821       public void actionPerformed(ActionEvent e)\r
 822       {\r
 823         scaleLeft_actionPerformed(e);\r
 824       }\r
 825     });\r
 826     scaleRight.setVisible(false);\r
 827     scaleRight.setSelected(true);\r
 828     scaleRight.setText("Scale Right");\r
 829     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 830     {\r
 831       public void actionPerformed(ActionEvent e)\r
 832       {\r
 833         scaleRight_actionPerformed(e);\r
 834       }\r
 835     });\r
 836     modifyPID.setText("Modify Identity Threshold...");\r
 837     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 838     {\r
 839       public void actionPerformed(ActionEvent e)\r
 840       {\r
 841         modifyPID_actionPerformed(e);\r
 842       }\r
 843     });\r
 844     modifyConservation.setText("Modify Conservation Threshold...");\r
 845     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 846     {\r
 847       public void actionPerformed(ActionEvent e)\r
 848       {\r
 849         modifyConservation_actionPerformed(e);\r
 850       }\r
 851     });\r
 852     sortByTreeMenu.setText("By Tree Order");\r
 853     sort.setText("Sort");\r
 854     calculate.setText("Calculate Tree");\r
 855     msaAlignMenuItem.setText("Muscle Alignment");\r
 856     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 857     {\r
 858       public void actionPerformed(ActionEvent e)\r
 859       {\r
 860         msaAlignMenuItem_actionPerformed(e);\r
 861       }\r
 862     });\r
 863     jMenu2.setText("Export");\r
 864     padGapsMenuitem.setText("Pad Gaps");\r
 865     padGapsMenuitem.addActionListener(new ActionListener()\r
 866     {\r
 867       public void actionPerformed(ActionEvent e)\r
 868       {\r
 869         padGapsMenuitem_actionPerformed(e);\r
 870       }\r
 871     });\r
 872     ClustalRealign.setText("Clustal Realign");\r
 873     ClustalRealign.addActionListener(new ActionListener()\r
 874     {\r
 875       public void actionPerformed(ActionEvent e)\r
 876       {\r
 877         ClustalRealign_actionPerformed(e);\r
 878       }\r
 879     });\r
 880     alignFrameMenuBar.add(fileMenu);\r
 881     alignFrameMenuBar.add(editMenu);\r
 882     alignFrameMenuBar.add(searchMenu);\r
 883     alignFrameMenuBar.add(viewMenu);\r
 884     alignFrameMenuBar.add(colourMenu);\r
 885     alignFrameMenuBar.add(calculateMenu);\r
 886     fileMenu.add(saveAlignmentMenu);\r
 887     fileMenu.add(jMenu2);\r
 888     fileMenu.add(outputTextboxMenu);\r
 889     fileMenu.add(printMenuItem);\r
 890     fileMenu.addSeparator();\r
 891     fileMenu.add(LoadtreeMenuItem);\r
 892     fileMenu.addSeparator();\r
 893     fileMenu.add(closeMenuItem);\r
 894     editMenu.add(undoMenuItem);\r
 895     editMenu.add(redoMenuItem);\r
 896     editMenu.add(cut);\r
 897     editMenu.add(copy);\r
 898     editMenu.add(jMenu1);\r
 899     editMenu.add(delete);\r
 900     editMenu.addSeparator();\r
 901     editMenu.add(selectAllSequenceMenuItem);\r
 902     editMenu.add(deselectAllSequenceMenuItem);\r
 903     editMenu.add(invertSequenceMenuItem);\r
 904     editMenu.add(deleteGroups);\r
 905     editMenu.addSeparator();\r
 906     editMenu.add(remove2LeftMenuItem);\r
 907     editMenu.add(remove2RightMenuItem);\r
 908     editMenu.add(removeGappedColumnMenuItem);\r
 909     editMenu.add(removeAllGapsMenuItem);\r
 910     editMenu.add(removeRedundancyMenuItem);\r
 911     editMenu.addSeparator();\r
 912     editMenu.add(padGapsMenuitem);\r
 913     searchMenu.add(findMenuItem);\r
 914     viewMenu.add(font);\r
 915     viewMenu.addSeparator();\r
 916     viewMenu.add(wrapMenuItem);\r
 917     viewMenu.add(fullSeqId);\r
 918     viewMenu.add(scaleAbove);\r
 919     viewMenu.add(scaleLeft);\r
 920     viewMenu.add(scaleRight);\r
 921     viewMenu.add(viewBoxesMenuItem);\r
 922     viewMenu.add(viewTextMenuItem);\r
 923     viewMenu.add(colourTextMenuItem);\r
 924     viewMenu.add(renderGapsMenuItem);\r
 925     viewMenu.add(annotationPanelMenuItem);\r
 926     viewMenu.add(sequenceFeatures);\r
 927     viewMenu.addSeparator();\r
 928     viewMenu.add(overviewMenuItem);\r
 929     colourMenu.add(applyToAllGroups);\r
 930     colourMenu.addSeparator();\r
 931     colourMenu.add(noColourmenuItem);\r
 932     colourMenu.add(clustalColour);\r
 933     colourMenu.add(BLOSUM62Colour);\r
 934     colourMenu.add(PIDColour);\r
 935     colourMenu.add(zappoColour);\r
 936     colourMenu.add(taylorColour);\r
 937     colourMenu.add(hydrophobicityColour);\r
 938     colourMenu.add(helixColour);\r
 939     colourMenu.add(strandColour);\r
 940     colourMenu.add(turnColour);\r
 941     colourMenu.add(buriedColour);\r
 942     colourMenu.add(nucleotideColour);\r
 943     colourMenu.add(userDefinedColour);\r
 944     colourMenu.addSeparator();\r
 945     colourMenu.add(conservationMenuItem);\r
 946     colourMenu.add(modifyConservation);\r
 947     colourMenu.add(abovePIDThreshold);\r
 948     colourMenu.add(modifyPID);\r
 949     calculateMenu.add(sort);\r
 950     calculateMenu.add(calculate);\r
 951     calculateMenu.addSeparator();\r
 952     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 953     calculateMenu.add(PCAMenuItem);\r
 954     calculateMenu.addSeparator();\r
 955     calculateMenu.add(webService);\r
 956     webService.add(clustalAlignMenuItem);\r
 957     webService.add(msaAlignMenuItem);\r
 958     webService.add(jnet);\r
 959     webService.add(ClustalRealign);\r
 960     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 961     jMenu1.add(pasteNew);\r
 962     jMenu1.add(pasteThis);\r
 963     sort.add(sortIDMenuItem);\r
 964     sort.add(sortGroupMenuItem);\r
 965     sort.add(sortPairwiseMenuItem);\r
 966     calculate.add(averageDistanceTreeMenuItem);\r
 967     calculate.add(neighbourTreeMenuItem);\r
 968     calculate.add(avDistanceTreeBlosumMenuItem);\r
 969     calculate.add(njTreeBlosumMenuItem);\r
 970     jMenu2.add(htmlMenuItem);\r
 971     jMenu2.add(epsFile);\r
 972     jMenu2.add(createPNG);\r
 973   }\r
 974 \r
 975   protected void outputText_actionPerformed(ActionEvent e)\r
 976   {\r
 977   }\r
 978 \r
 979   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 980   {\r
 981   }\r
 982 \r
 983   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 984   {\r
 985   }\r
 986 \r
 987   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 988   {\r
 989   }\r
 990 \r
 991   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 992   {\r
 993   }\r
 994 \r
 995   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 996   {\r
 997   }\r
 998 \r
 999   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1000   {\r
1001   }\r
1002 \r
1003   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1004   {\r
1005   }\r
1006 \r
1007   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1008   {\r
1009   }\r
1010 \r
1011   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1012   {\r
1013   }\r
1014 \r
1015   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1016   {\r
1017   }\r
1018 \r
1019   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1020   {\r
1021   }\r
1022 \r
1023   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1024   {\r
1025   }\r
1026 \r
1027   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1028   {\r
1029   }\r
1030 \r
1031   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1032   {\r
1033   }\r
1034 \r
1035   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1036   {\r
1037   }\r
1038 \r
1039   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1040   {\r
1041   }\r
1042 \r
1043   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1044   {\r
1045   }\r
1046 \r
1047   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1048   {\r
1049   }\r
1050 \r
1051   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1052   {\r
1053   }\r
1054 \r
1055   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1056   {\r
1057   }\r
1058 \r
1059   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1060   {\r
1061   }\r
1062 \r
1063   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1064   {\r
1065   }\r
1066 \r
1067   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1068   {\r
1069   }\r
1070 \r
1071   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1072   {\r
1073   }\r
1074 \r
1075   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1076   {\r
1077   }\r
1078 \r
1079   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1080   {\r
1081   }\r
1082 \r
1083   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1084   {\r
1085   }\r
1086 \r
1087   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1088   {\r
1089   }\r
1090 \r
1091   protected void clustalColour_actionPerformed(ActionEvent e)\r
1092   {\r
1093   }\r
1094 \r
1095   protected void zappoColour_actionPerformed(ActionEvent e)\r
1096   {\r
1097   }\r
1098 \r
1099   protected void taylorColour_actionPerformed(ActionEvent e)\r
1100   {\r
1101   }\r
1102 \r
1103   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1104   {\r
1105   }\r
1106 \r
1107   protected void helixColour_actionPerformed(ActionEvent e)\r
1108   {\r
1109   }\r
1110 \r
1111   protected void strandColour_actionPerformed(ActionEvent e)\r
1112   {\r
1113   }\r
1114 \r
1115   protected void turnColour_actionPerformed(ActionEvent e)\r
1116   {\r
1117   }\r
1118 \r
1119   protected void buriedColour_actionPerformed(ActionEvent e)\r
1120   {\r
1121   }\r
1122 \r
1123   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1124   {\r
1125   }\r
1126 \r
1127   protected void PIDColour_actionPerformed(ActionEvent e)\r
1128   {\r
1129   }\r
1130 \r
1131   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1132   {\r
1133   }\r
1134 \r
1135   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1136   {\r
1137   }\r
1138 \r
1139   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1140   {\r
1141   }\r
1142 \r
1143   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1144   {\r
1145   }\r
1146 \r
1147   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1148   {\r
1149   }\r
1150 \r
1151   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1152   {\r
1153   }\r
1154 \r
1155   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1156   {\r
1157   }\r
1158 \r
1159   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1160   {\r
1161   }\r
1162 \r
1163   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1164   {\r
1165   }\r
1166 \r
1167   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1168   {\r
1169   }\r
1170 \r
1171   protected void copy_actionPerformed(ActionEvent e)\r
1172   {\r
1173   }\r
1174 \r
1175   protected void cut_actionPerformed(ActionEvent e)\r
1176   {\r
1177   }\r
1178 \r
1179   protected void delete_actionPerformed(ActionEvent e)\r
1180   {\r
1181   }\r
1182 \r
1183   protected void pasteNew_actionPerformed(ActionEvent e)\r
1184   {\r
1185   }\r
1186 \r
1187   protected void pasteThis_actionPerformed(ActionEvent e)\r
1188   {\r
1189   }\r
1190 \r
1191   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1192   {\r
1193   }\r
1194 \r
1195   public void createPNG(java.io.File f)\r
1196   {\r
1197   }\r
1198 \r
1199   protected void font_actionPerformed(ActionEvent e)\r
1200   {\r
1201   }\r
1202 \r
1203   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1204   {\r
1205   }\r
1206 \r
1207   public void createEPS(java.io.File f)\r
1208   {\r
1209   }\r
1210 \r
1211   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1212   {\r
1213   }\r
1214 \r
1215   protected void jpred_actionPerformed(ActionEvent e)\r
1216   {\r
1217   }\r
1218 \r
1219   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1220   {\r
1221   }\r
1222 \r
1223   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1224   {\r
1225   }\r
1226 \r
1227   protected void scaleRight_actionPerformed(ActionEvent e)\r
1228   {\r
1229   }\r
1230 \r
1231   protected void modifyPID_actionPerformed(ActionEvent e)\r
1232   {\r
1233   }\r
1234 \r
1235   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1236   {\r
1237   }\r
1238 \r
1239   protected void preferences_actionPerformed(ActionEvent e)\r
1240   {\r
1241   }\r
1242 \r
1243   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1244   {\r
1245   }\r
1246 \r
1247   protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
1248   {\r
1249   }\r
1250 \r
1251   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1252   {\r
1253   }\r
1254 \r
1255   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1256   {\r
1257   }\r
1258 \r
1259   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
1260   {\r
1261   }\r
1262 }\r