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.schemes.*;\r
  27 \r
  28 public class GAlignFrame\r
  29     extends JInternalFrame\r
  30 {\r
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  32   protected JMenu fileMenu = new JMenu();\r
  33   protected JMenuItem closeMenuItem = new JMenuItem();\r
  34   protected JMenu editMenu = new JMenu();\r
  35   protected JMenu viewMenu = new JMenu();\r
  36   protected JMenu colourMenu = new JMenu();\r
  37   protected JMenu calculateMenu = new JMenu();\r
  38   protected JMenu webService = new JMenu();\r
  39   protected JMenuItem webServiceNoServices;\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 seqLimits = new JCheckBoxMenuItem();\r
 103   JMenuItem epsFile = new JMenuItem();\r
 104   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 105   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 106   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 107   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 108   protected JMenuItem modifyPID = new JMenuItem();\r
 109   protected JMenuItem modifyConservation = new JMenuItem();\r
 110   protected JMenu sortByTreeMenu = new JMenu();\r
 111   protected JMenu sort = new JMenu();\r
 112   JMenu calculate = new JMenu();\r
 113   JMenu jMenu2 = new JMenu();\r
 114   JMenuItem padGapsMenuitem = new JMenuItem();\r
 115   protected ButtonGroup colours = new ButtonGroup();\r
 116   JMenuItem vamsasStore = new JMenuItem();\r
 117   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
 118   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 119   protected JMenuItem featureSettings = new JMenuItem();\r
 120   public JCheckBoxMenuItem seqDBRef = new JCheckBoxMenuItem();\r
 121 \r
 122   public GAlignFrame()\r
 123   {\r
 124 \r
 125 \r
 126     try\r
 127     {\r
 128       jbInit();\r
 129       setJMenuBar(alignFrameMenuBar);\r
 130 \r
 131       // dynamically fill save as menu with available formats\r
 132       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 133       {\r
 134         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 135                              elementAt(\r
 136                                  i));\r
 137         item.addActionListener(new java.awt.event.ActionListener()\r
 138         {\r
 139           public void actionPerformed(ActionEvent e)\r
 140           {\r
 141             outputText_actionPerformed(e);\r
 142           }\r
 143         });\r
 144 \r
 145         outputTextboxMenu.add(item);\r
 146       }\r
 147     }\r
 148     catch (Exception e)\r
 149     {\r
 150     }\r
 151 \r
 152 \r
 153     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 154     {\r
 155       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 156           getUserColourSchemes().keys();\r
 157 \r
 158       while (userColours.hasMoreElements())\r
 159       {\r
 160         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 161             nextElement().toString());\r
 162         radioItem.setName("USER_DEFINED");\r
 163         radioItem.addMouseListener(new MouseAdapter()\r
 164             {\r
 165               public void mousePressed(MouseEvent evt)\r
 166               {\r
 167                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 168                 {\r
 169                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 170 \r
 171                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 172                       "Remove from default list?",\r
 173                       "Remove user defined colour",\r
 174                       JOptionPane.YES_NO_OPTION);\r
 175                   if(option == JOptionPane.YES_OPTION)\r
 176                   {\r
 177                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 178                     colourMenu.remove(radioItem);\r
 179                   }\r
 180                   else\r
 181                     radioItem.addActionListener(new ActionListener()\r
 182                     {\r
 183                       public void actionPerformed(ActionEvent evt)\r
 184                       {\r
 185                         userDefinedColour_actionPerformed(evt);\r
 186                       }\r
 187                     });\r
 188                 }\r
 189               }\r
 190             });\r
 191         radioItem.addActionListener(new ActionListener()\r
 192         {\r
 193           public void actionPerformed(ActionEvent evt)\r
 194           {\r
 195             userDefinedColour_actionPerformed(evt);\r
 196           }\r
 197         });\r
 198         colourMenu.insert(radioItem, 15);\r
 199         colours.add(radioItem);\r
 200       }\r
 201     }\r
 202     colours.add(noColourmenuItem);\r
 203     colours.add(clustalColour);\r
 204     colours.add(zappoColour);\r
 205     colours.add(taylorColour);\r
 206     colours.add(hydrophobicityColour);\r
 207     colours.add(helixColour);\r
 208     colours.add(strandColour);\r
 209     colours.add(turnColour);\r
 210     colours.add(buriedColour);\r
 211     colours.add(userDefinedColour);\r
 212     colours.add(PIDColour);\r
 213     colours.add(BLOSUM62Colour);\r
 214     colours.add(nucleotideColour);\r
 215 \r
 216     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 217 \r
 218 \r
 219   }\r
 220 \r
 221   public void setColourSelected(String defaultColour)\r
 222   {\r
 223 \r
 224     if (defaultColour != null)\r
 225     {\r
 226       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 227 \r
 228       switch (index)\r
 229       {\r
 230         case ColourSchemeProperty.NONE:\r
 231               noColourmenuItem.setSelected(true);\r
 232               break;\r
 233         case ColourSchemeProperty.CLUSTAL:\r
 234           clustalColour.setSelected(true);\r
 235 \r
 236           break;\r
 237 \r
 238         case ColourSchemeProperty.BLOSUM:\r
 239           BLOSUM62Colour.setSelected(true);\r
 240 \r
 241           break;\r
 242 \r
 243         case ColourSchemeProperty.PID:\r
 244           PIDColour.setSelected(true);\r
 245 \r
 246           break;\r
 247 \r
 248         case ColourSchemeProperty.ZAPPO:\r
 249           zappoColour.setSelected(true);\r
 250 \r
 251           break;\r
 252 \r
 253         case ColourSchemeProperty.TAYLOR:\r
 254           taylorColour.setSelected(true);\r
 255           break;\r
 256 \r
 257         case ColourSchemeProperty.HYDROPHOBIC:\r
 258           hydrophobicityColour.setSelected(true);\r
 259 \r
 260           break;\r
 261 \r
 262         case ColourSchemeProperty.HELIX:\r
 263           helixColour.setSelected(true);\r
 264 \r
 265           break;\r
 266 \r
 267         case ColourSchemeProperty.STRAND:\r
 268           strandColour.setSelected(true);\r
 269 \r
 270           break;\r
 271 \r
 272         case ColourSchemeProperty.TURN:\r
 273           turnColour.setSelected(true);\r
 274 \r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.BURIED:\r
 278           buriedColour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.NUCLEOTIDE:\r
 283           nucleotideColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.USER_DEFINED:\r
 288           userDefinedColour.setSelected(true);\r
 289 \r
 290           break;\r
 291       }\r
 292     }\r
 293 \r
 294   }\r
 295 \r
 296   private void jbInit()\r
 297       throws Exception\r
 298   {\r
 299     fileMenu.setMnemonic('F');\r
 300     fileMenu.setText("File");\r
 301     saveAlignmentMenu.setMnemonic('L');\r
 302     saveAlignmentMenu.setText("Save As");\r
 303     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 304         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 305     saveAlignmentMenu.addActionListener(new ActionListener()\r
 306     {\r
 307       public void actionPerformed(ActionEvent e)\r
 308       {\r
 309         saveAlignmentMenu_actionPerformed(e);\r
 310       }\r
 311     });\r
 312     closeMenuItem.setMnemonic('C');\r
 313     closeMenuItem.setText("Close");\r
 314     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 315     {\r
 316       public void actionPerformed(ActionEvent e)\r
 317       {\r
 318         closeMenuItem_actionPerformed(e);\r
 319       }\r
 320     });\r
 321     editMenu.setText("Edit");\r
 322     viewMenu.setText("View");\r
 323     colourMenu.setText("Colour");\r
 324     calculateMenu.setText("Calculate");\r
 325     webService.setText("Web Service");\r
 326     selectAllSequenceMenuItem.setText("Select all");\r
 327     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 328         java.awt.event.KeyEvent.VK_A,\r
 329         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 330     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 331                                                 ActionListener()\r
 332     {\r
 333       public void actionPerformed(ActionEvent e)\r
 334       {\r
 335         selectAllSequenceMenuItem_actionPerformed(e);\r
 336       }\r
 337     });\r
 338     deselectAllSequenceMenuItem.setText("Deselect All");\r
 339     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 340                                                getKeyStroke(\r
 341         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 342     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 343                                                   ActionListener()\r
 344     {\r
 345       public void actionPerformed(ActionEvent e)\r
 346       {\r
 347         deselectAllSequenceMenuItem_actionPerformed(e);\r
 348       }\r
 349     });\r
 350     invertSequenceMenuItem.setText("Invert Selection");\r
 351     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 352     {\r
 353       public void actionPerformed(ActionEvent e)\r
 354       {\r
 355         invertSequenceMenuItem_actionPerformed(e);\r
 356       }\r
 357     });\r
 358     remove2LeftMenuItem.setText("Remove Left");\r
 359     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 360     {\r
 361       public void actionPerformed(ActionEvent e)\r
 362       {\r
 363         remove2LeftMenuItem_actionPerformed(e);\r
 364       }\r
 365     });\r
 366     remove2RightMenuItem.setText("Remove Right");\r
 367     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 368     {\r
 369       public void actionPerformed(ActionEvent e)\r
 370       {\r
 371         remove2RightMenuItem_actionPerformed(e);\r
 372       }\r
 373     });\r
 374     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 375     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 376                                                  ActionListener()\r
 377     {\r
 378       public void actionPerformed(ActionEvent e)\r
 379       {\r
 380         removeGappedColumnMenuItem_actionPerformed(e);\r
 381       }\r
 382     });\r
 383     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 384     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 385     {\r
 386       public void actionPerformed(ActionEvent e)\r
 387       {\r
 388         removeAllGapsMenuItem_actionPerformed(e);\r
 389       }\r
 390     });\r
 391     viewBoxesMenuItem.setText("Boxes");\r
 392     viewBoxesMenuItem.setState(true);\r
 393     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 394     {\r
 395       public void actionPerformed(ActionEvent e)\r
 396       {\r
 397         viewBoxesMenuItem_actionPerformed(e);\r
 398       }\r
 399     });\r
 400     viewTextMenuItem.setText("Text");\r
 401     viewTextMenuItem.setState(true);\r
 402     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 403     {\r
 404       public void actionPerformed(ActionEvent e)\r
 405       {\r
 406         viewTextMenuItem_actionPerformed(e);\r
 407       }\r
 408     });\r
 409     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 410     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 411     {\r
 412       public void actionPerformed(ActionEvent e)\r
 413       {\r
 414         sortPairwiseMenuItem_actionPerformed(e);\r
 415       }\r
 416     });\r
 417     sortIDMenuItem.setText("by ID");\r
 418     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 419     {\r
 420       public void actionPerformed(ActionEvent e)\r
 421       {\r
 422         sortIDMenuItem_actionPerformed(e);\r
 423       }\r
 424     });\r
 425     sortGroupMenuItem.setText("by Group");\r
 426     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 427     {\r
 428       public void actionPerformed(ActionEvent e)\r
 429       {\r
 430         sortGroupMenuItem_actionPerformed(e);\r
 431       }\r
 432     });\r
 433     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 434     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 435                                                ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         removeRedundancyMenuItem_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 443     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 444                                                 ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     PCAMenuItem.setText("Principal Component Analysis");\r
 452     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 453     {\r
 454       public void actionPerformed(ActionEvent e)\r
 455       {\r
 456         PCAMenuItem_actionPerformed(e);\r
 457       }\r
 458     });\r
 459     averageDistanceTreeMenuItem.setText(\r
 460         "Average Distance Using % Identity");\r
 461     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 462                                                   ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         averageDistanceTreeMenuItem_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 470     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 471     {\r
 472       public void actionPerformed(ActionEvent e)\r
 473       {\r
 474         neighbourTreeMenuItem_actionPerformed(e);\r
 475       }\r
 476     });\r
 477     this.getContentPane().setLayout(borderLayout1);\r
 478     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 479     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
 480     {\r
 481       public void ancestorAdded(AncestorEvent event)\r
 482       {\r
 483         alignFrameMenuBar_ancestorAdded(event);\r
 484       }\r
 485 \r
 486       public void ancestorRemoved(AncestorEvent event)\r
 487       {\r
 488       }\r
 489 \r
 490       public void ancestorMoved(AncestorEvent event)\r
 491       {\r
 492       }\r
 493     });\r
 494     statusBar.setBackground(Color.white);\r
 495     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 496     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 497     statusBar.setText("Status bar");\r
 498     outputTextboxMenu.setMnemonic('T');\r
 499     outputTextboxMenu.setText("Output to Textbox");\r
 500     clustalColour.setText("Clustalx");\r
 501 \r
 502     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 503     {\r
 504       public void actionPerformed(ActionEvent e)\r
 505       {\r
 506         clustalColour_actionPerformed(e);\r
 507       }\r
 508     });\r
 509     zappoColour.setText("Zappo");\r
 510     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 511     {\r
 512       public void actionPerformed(ActionEvent e)\r
 513       {\r
 514         zappoColour_actionPerformed(e);\r
 515       }\r
 516     });\r
 517     taylorColour.setText("Taylor");\r
 518     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         taylorColour_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     hydrophobicityColour.setText("Hydrophobicity");\r
 526     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 527     {\r
 528       public void actionPerformed(ActionEvent e)\r
 529       {\r
 530         hydrophobicityColour_actionPerformed(e);\r
 531       }\r
 532     });\r
 533     helixColour.setText("Helix Propensity");\r
 534     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 535     {\r
 536       public void actionPerformed(ActionEvent e)\r
 537       {\r
 538         helixColour_actionPerformed(e);\r
 539       }\r
 540     });\r
 541     strandColour.setText("Strand Propensity");\r
 542     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 543     {\r
 544       public void actionPerformed(ActionEvent e)\r
 545       {\r
 546         strandColour_actionPerformed(e);\r
 547       }\r
 548     });\r
 549     turnColour.setText("Turn Propensity");\r
 550     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 551     {\r
 552       public void actionPerformed(ActionEvent e)\r
 553       {\r
 554         turnColour_actionPerformed(e);\r
 555       }\r
 556     });\r
 557     buriedColour.setText("Buried Index");\r
 558     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 559     {\r
 560       public void actionPerformed(ActionEvent e)\r
 561       {\r
 562         buriedColour_actionPerformed(e);\r
 563       }\r
 564     });\r
 565     userDefinedColour.setText("User Defined...");\r
 566     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 567     {\r
 568       public void actionPerformed(ActionEvent e)\r
 569       {\r
 570         userDefinedColour_actionPerformed(e);\r
 571       }\r
 572     });\r
 573     PIDColour.setText("Percentage Identity");\r
 574     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         PIDColour_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 582     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 583     {\r
 584       public void actionPerformed(ActionEvent e)\r
 585       {\r
 586         BLOSUM62Colour_actionPerformed(e);\r
 587       }\r
 588     });\r
 589     avDistanceTreeBlosumMenuItem.setText(\r
 590         "Average Distance Using BLOSUM62");\r
 591     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 592         ActionListener()\r
 593     {\r
 594       public void actionPerformed(ActionEvent e)\r
 595       {\r
 596         avTreeBlosumMenuItem_actionPerformed(e);\r
 597       }\r
 598     });\r
 599     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 600     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 601     {\r
 602       public void actionPerformed(ActionEvent e)\r
 603       {\r
 604         njTreeBlosumMenuItem_actionPerformed(e);\r
 605       }\r
 606     });\r
 607     annotationPanelMenuItem.setActionCommand("");\r
 608     annotationPanelMenuItem.setText("Show Annotations");\r
 609     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 610     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 611     {\r
 612       public void actionPerformed(ActionEvent e)\r
 613       {\r
 614         annotationPanelMenuItem_actionPerformed(e);\r
 615       }\r
 616     });\r
 617     colourTextMenuItem.setText("Colour Text");\r
 618     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 619     {\r
 620       public void actionPerformed(ActionEvent e)\r
 621       {\r
 622         colourTextMenuItem_actionPerformed(e);\r
 623       }\r
 624     });\r
 625     htmlMenuItem.setText("HTML");\r
 626     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         htmlMenuItem_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     overviewMenuItem.setText("Overview Window");\r
 634     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         overviewMenuItem_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     undoMenuItem.setEnabled(false);\r
 642     undoMenuItem.setMnemonic('Z');\r
 643     undoMenuItem.setText("Undo");\r
 644     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 645         java.awt.event.KeyEvent.VK_Z,\r
 646         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 647     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 648     {\r
 649       public void actionPerformed(ActionEvent e)\r
 650       {\r
 651         undoMenuItem_actionPerformed(e);\r
 652       }\r
 653     });\r
 654     redoMenuItem.setEnabled(false);\r
 655     redoMenuItem.setMnemonic('0');\r
 656     redoMenuItem.setText("Redo");\r
 657     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 658     {\r
 659       public void actionPerformed(ActionEvent e)\r
 660       {\r
 661         redoMenuItem_actionPerformed(e);\r
 662       }\r
 663     });\r
 664     conservationMenuItem.setText("By Conservation");\r
 665     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 666     {\r
 667       public void actionPerformed(ActionEvent e)\r
 668       {\r
 669         conservationMenuItem_actionPerformed(e);\r
 670       }\r
 671     });\r
 672     noColourmenuItem.setText("None");\r
 673     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 674     {\r
 675       public void actionPerformed(ActionEvent e)\r
 676       {\r
 677         noColourmenuItem_actionPerformed(e);\r
 678       }\r
 679     });\r
 680     wrapMenuItem.setText("Wrap");\r
 681     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 682     {\r
 683       public void actionPerformed(ActionEvent e)\r
 684       {\r
 685         wrapMenuItem_actionPerformed(e);\r
 686       }\r
 687     });\r
 688     printMenuItem.setText("Print");\r
 689     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 690     {\r
 691       public void actionPerformed(ActionEvent e)\r
 692       {\r
 693         printMenuItem_actionPerformed(e);\r
 694       }\r
 695     });\r
 696     renderGapsMenuItem.setText("Show Gaps");\r
 697     renderGapsMenuItem.setState(true);\r
 698     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 699     {\r
 700       public void actionPerformed(ActionEvent e)\r
 701       {\r
 702         renderGapsMenuItem_actionPerformed(e);\r
 703       }\r
 704     });\r
 705     findMenuItem.setText("Find...");\r
 706     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 707         java.awt.event.KeyEvent.VK_F,\r
 708         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 709     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 710     {\r
 711       public void actionPerformed(ActionEvent e)\r
 712       {\r
 713         findMenuItem_actionPerformed(e);\r
 714       }\r
 715     });\r
 716     searchMenu.setText("Search");\r
 717 \r
 718     abovePIDThreshold.setText("Above Identity Threshold");\r
 719     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 720     {\r
 721       public void actionPerformed(ActionEvent e)\r
 722       {\r
 723         abovePIDThreshold_actionPerformed(e);\r
 724       }\r
 725     });\r
 726     sequenceFeatures.setText("Sequence Features");\r
 727     sequenceFeatures.addActionListener(new ActionListener()\r
 728     {\r
 729       public void actionPerformed(ActionEvent actionEvent)\r
 730       {\r
 731         sequenceFeatures_actionPerformed(actionEvent);\r
 732       }\r
 733     });\r
 734     nucleotideColour.setText("Nucleotide");\r
 735     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 736     {\r
 737       public void actionPerformed(ActionEvent e)\r
 738       {\r
 739         nucleotideColour_actionPerformed(e);\r
 740       }\r
 741     });\r
 742     deleteGroups.setText("Undefine groups");\r
 743     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 744     {\r
 745       public void actionPerformed(ActionEvent e)\r
 746       {\r
 747         deleteGroups_actionPerformed(e);\r
 748       }\r
 749     });\r
 750     copy.setText("Copy");\r
 751     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 752         java.awt.event.KeyEvent.VK_C,\r
 753         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 754     copy.setMnemonic(KeyEvent.VK_C);\r
 755 \r
 756     copy.addActionListener(new java.awt.event.ActionListener()\r
 757     {\r
 758       public void actionPerformed(ActionEvent e)\r
 759       {\r
 760         copy_actionPerformed(e);\r
 761       }\r
 762     });\r
 763     cut.setText("Cut");\r
 764     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 765         java.awt.event.KeyEvent.VK_X,\r
 766         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 767     cut.setMnemonic(KeyEvent.VK_X);\r
 768     cut.addActionListener(new java.awt.event.ActionListener()\r
 769     {\r
 770       public void actionPerformed(ActionEvent e)\r
 771       {\r
 772         cut_actionPerformed(e);\r
 773       }\r
 774     });\r
 775     delete.setText("Delete");\r
 776     delete.addActionListener(new java.awt.event.ActionListener()\r
 777     {\r
 778       public void actionPerformed(ActionEvent e)\r
 779       {\r
 780         delete_actionPerformed(e);\r
 781       }\r
 782     });\r
 783     jMenu1.setMnemonic('V');\r
 784     jMenu1.setText("Paste");\r
 785     pasteNew.setText("To New Alignment");\r
 786     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 787         java.awt.event.KeyEvent.VK_V,\r
 788         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 789     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 790     {\r
 791       public void actionPerformed(ActionEvent e)\r
 792       {\r
 793         pasteNew_actionPerformed(e);\r
 794       }\r
 795     });\r
 796     pasteThis.setText("Add To This Alignment");\r
 797     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 798     {\r
 799       public void actionPerformed(ActionEvent e)\r
 800       {\r
 801         pasteThis_actionPerformed(e);\r
 802       }\r
 803     });\r
 804     applyToAllGroups.setText("Apply Colour To All Groups");\r
 805     applyToAllGroups.setState(true);\r
 806     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 807     {\r
 808       public void actionPerformed(ActionEvent e)\r
 809       {\r
 810         applyToAllGroups_actionPerformed(e);\r
 811       }\r
 812     });\r
 813     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 814     {\r
 815       public void actionPerformed(ActionEvent e)\r
 816       {\r
 817         createPNG(null);\r
 818       }\r
 819     });\r
 820     createPNG.setActionCommand("Save As PNG Image");\r
 821     createPNG.setText("PNG");\r
 822     font.setText("Font...");\r
 823     font.addActionListener(new java.awt.event.ActionListener()\r
 824     {\r
 825       public void actionPerformed(ActionEvent e)\r
 826       {\r
 827         font_actionPerformed(e);\r
 828       }\r
 829     });\r
 830 \r
 831     seqLimits.setText("Show Sequence Limits");\r
 832     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 833     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 834     {\r
 835       public void actionPerformed(ActionEvent e)\r
 836       {\r
 837         seqLimit_actionPerformed(e);\r
 838       }\r
 839     });\r
 840     epsFile.setText("EPS");\r
 841     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 842     {\r
 843       public void actionPerformed(ActionEvent e)\r
 844       {\r
 845         createEPS(null);\r
 846       }\r
 847     });\r
 848     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 849     LoadtreeMenuItem.setText("Load Assocated Tree");\r
 850     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 851     {\r
 852       public void actionPerformed(ActionEvent e)\r
 853       {\r
 854         LoadtreeMenuItem_actionPerformed(e);\r
 855       }\r
 856     });\r
 857     scaleAbove.setVisible(false);\r
 858     scaleAbove.setText("Scale Above");\r
 859     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 860     {\r
 861       public void actionPerformed(ActionEvent e)\r
 862       {\r
 863         scaleAbove_actionPerformed(e);\r
 864       }\r
 865     });\r
 866     scaleLeft.setVisible(false);\r
 867     scaleLeft.setSelected(true);\r
 868     scaleLeft.setText("Scale Left");\r
 869     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 870     {\r
 871       public void actionPerformed(ActionEvent e)\r
 872       {\r
 873         scaleLeft_actionPerformed(e);\r
 874       }\r
 875     });\r
 876     scaleRight.setVisible(false);\r
 877     scaleRight.setSelected(true);\r
 878     scaleRight.setText("Scale Right");\r
 879     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 880     {\r
 881       public void actionPerformed(ActionEvent e)\r
 882       {\r
 883         scaleRight_actionPerformed(e);\r
 884       }\r
 885     });\r
 886     modifyPID.setText("Modify Identity Threshold...");\r
 887     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 888     {\r
 889       public void actionPerformed(ActionEvent e)\r
 890       {\r
 891         modifyPID_actionPerformed(e);\r
 892       }\r
 893     });\r
 894     modifyConservation.setText("Modify Conservation Threshold...");\r
 895     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 896     {\r
 897       public void actionPerformed(ActionEvent e)\r
 898       {\r
 899         modifyConservation_actionPerformed(e);\r
 900       }\r
 901     });\r
 902     sortByTreeMenu.setText("By Tree Order");\r
 903     sort.setText("Sort");\r
 904     calculate.setText("Calculate Tree");\r
 905 \r
 906     jMenu2.setText("Export");\r
 907     padGapsMenuitem.setText("Pad Gaps");\r
 908     padGapsMenuitem.addActionListener(new ActionListener()\r
 909     {\r
 910       public void actionPerformed(ActionEvent e)\r
 911       {\r
 912         padGapsMenuitem_actionPerformed(e);\r
 913       }\r
 914     });\r
 915     vamsasStore.setText("VAMSAS store");\r
 916     vamsasStore.addActionListener(new ActionListener()\r
 917     {\r
 918       public void actionPerformed(ActionEvent e)\r
 919       {\r
 920         vamsasStore_actionPerformed(e);\r
 921       }\r
 922     });\r
 923     showTranslation.setText("Translate cDNA");\r
 924     showTranslation.addActionListener(new ActionListener()\r
 925     {\r
 926       public void actionPerformed(ActionEvent e)\r
 927       {\r
 928         showTranslation_actionPerformed(e);\r
 929       }\r
 930     });\r
 931 \r
 932     tabbedPane.addChangeListener(new ChangeListener()\r
 933         {\r
 934           public void stateChanged(ChangeEvent ece)\r
 935           {\r
 936 \r
 937             tabSelected();\r
 938           }\r
 939         });\r
 940     featureSettings.setEnabled(false);\r
 941     featureSettings.setText("Feature Settings...");\r
 942     featureSettings.addActionListener(new ActionListener()\r
 943     {\r
 944       public void actionPerformed(ActionEvent e)\r
 945       {\r
 946         featureSettings_actionPerformed(e);\r
 947       }\r
 948     });\r
 949     seqDBRef.setState( jalview.bin.Cache.getDefault("SHOW_DBPREFIX",true));\r
 950     seqDBRef.setText("Show Sequence DB Refs");\r
 951     seqDBRef.addActionListener(new ActionListener()\r
 952     {\r
 953       public void actionPerformed(ActionEvent e)\r
 954       {\r
 955         seqDBRef_actionPerformed(e);\r
 956       }\r
 957     });\r
 958     alignFrameMenuBar.add(fileMenu);\r
 959     alignFrameMenuBar.add(editMenu);\r
 960     alignFrameMenuBar.add(searchMenu);\r
 961     alignFrameMenuBar.add(viewMenu);\r
 962     alignFrameMenuBar.add(colourMenu);\r
 963     alignFrameMenuBar.add(calculateMenu);\r
 964     alignFrameMenuBar.add(webService);\r
 965     fileMenu.add(vamsasStore);\r
 966     fileMenu.add(saveAlignmentMenu);\r
 967     fileMenu.add(jMenu2);\r
 968     fileMenu.add(outputTextboxMenu);\r
 969     fileMenu.add(printMenuItem);\r
 970     fileMenu.addSeparator();\r
 971     fileMenu.add(LoadtreeMenuItem);\r
 972     fileMenu.addSeparator();\r
 973     fileMenu.add(closeMenuItem);\r
 974     editMenu.add(undoMenuItem);\r
 975     editMenu.add(redoMenuItem);\r
 976     editMenu.add(cut);\r
 977     editMenu.add(copy);\r
 978     editMenu.add(jMenu1);\r
 979     editMenu.add(delete);\r
 980     editMenu.addSeparator();\r
 981     editMenu.add(selectAllSequenceMenuItem);\r
 982     editMenu.add(deselectAllSequenceMenuItem);\r
 983     editMenu.add(invertSequenceMenuItem);\r
 984     editMenu.add(deleteGroups);\r
 985     editMenu.addSeparator();\r
 986     editMenu.add(remove2LeftMenuItem);\r
 987     editMenu.add(remove2RightMenuItem);\r
 988     editMenu.add(removeGappedColumnMenuItem);\r
 989     editMenu.add(removeAllGapsMenuItem);\r
 990     editMenu.add(removeRedundancyMenuItem);\r
 991     editMenu.addSeparator();\r
 992     editMenu.add(padGapsMenuitem);\r
 993     searchMenu.add(findMenuItem);\r
 994     viewMenu.add(font);\r
 995     viewMenu.addSeparator();\r
 996     viewMenu.add(wrapMenuItem);\r
 997     viewMenu.add(seqDBRef);\r
 998     viewMenu.add(seqLimits);\r
 999     viewMenu.add(scaleAbove);\r
1000     viewMenu.add(scaleLeft);\r
1001     viewMenu.add(scaleRight);\r
1002     viewMenu.add(viewBoxesMenuItem);\r
1003     viewMenu.add(viewTextMenuItem);\r
1004     viewMenu.add(colourTextMenuItem);\r
1005     viewMenu.add(renderGapsMenuItem);\r
1006     viewMenu.add(annotationPanelMenuItem);\r
1007     viewMenu.addSeparator();\r
1008     viewMenu.add(sequenceFeatures);\r
1009     viewMenu.add(featureSettings);\r
1010     viewMenu.addSeparator();\r
1011     viewMenu.add(overviewMenuItem);\r
1012     colourMenu.add(applyToAllGroups);\r
1013     colourMenu.addSeparator();\r
1014     colourMenu.add(noColourmenuItem);\r
1015     colourMenu.add(clustalColour);\r
1016     colourMenu.add(BLOSUM62Colour);\r
1017     colourMenu.add(PIDColour);\r
1018     colourMenu.add(zappoColour);\r
1019     colourMenu.add(taylorColour);\r
1020     colourMenu.add(hydrophobicityColour);\r
1021     colourMenu.add(helixColour);\r
1022     colourMenu.add(strandColour);\r
1023     colourMenu.add(turnColour);\r
1024     colourMenu.add(buriedColour);\r
1025     colourMenu.add(nucleotideColour);\r
1026     colourMenu.add(userDefinedColour);\r
1027     colourMenu.addSeparator();\r
1028     colourMenu.add(conservationMenuItem);\r
1029     colourMenu.add(modifyConservation);\r
1030     colourMenu.add(abovePIDThreshold);\r
1031     colourMenu.add(modifyPID);\r
1032     calculateMenu.add(sort);\r
1033     calculateMenu.add(calculate);\r
1034     calculateMenu.addSeparator();\r
1035     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1036     calculateMenu.add(PCAMenuItem);\r
1037     calculateMenu.addSeparator();\r
1038     calculateMenu.add(showTranslation);\r
1039     webServiceNoServices=new JMenuItem("<No Services>");\r
1040     webService.add(webServiceNoServices);\r
1041     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
1042     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1043     jMenu1.add(pasteNew);\r
1044     jMenu1.add(pasteThis);\r
1045     sort.add(sortIDMenuItem);\r
1046     sort.add(sortGroupMenuItem);\r
1047     sort.add(sortPairwiseMenuItem);\r
1048     calculate.add(averageDistanceTreeMenuItem);\r
1049     calculate.add(neighbourTreeMenuItem);\r
1050     calculate.add(avDistanceTreeBlosumMenuItem);\r
1051     calculate.add(njTreeBlosumMenuItem);\r
1052     jMenu2.add(htmlMenuItem);\r
1053     jMenu2.add(epsFile);\r
1054     jMenu2.add(createPNG);\r
1055   }\r
1056 \r
1057   protected void outputText_actionPerformed(ActionEvent e)\r
1058   {\r
1059   }\r
1060 \r
1061   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1062   {\r
1063   }\r
1064 \r
1065   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1066   {\r
1067   }\r
1068 \r
1069   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1070   {\r
1071   }\r
1072 \r
1073   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1074   {\r
1075   }\r
1076 \r
1077   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1078   {\r
1079   }\r
1080 \r
1081   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1082   {\r
1083   }\r
1084 \r
1085   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1086   {\r
1087   }\r
1088 \r
1089   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1090   {\r
1091   }\r
1092 \r
1093   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1094   {\r
1095   }\r
1096 \r
1097   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1098   {\r
1099   }\r
1100 \r
1101   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1102   {\r
1103   }\r
1104 \r
1105   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1106   {\r
1107   }\r
1108 \r
1109   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1110   {\r
1111   }\r
1112 \r
1113   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1114   {\r
1115   }\r
1116 \r
1117   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1118   {\r
1119   }\r
1120 \r
1121   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1122   {\r
1123   }\r
1124 \r
1125   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1126   {\r
1127   }\r
1128 \r
1129   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1130   {\r
1131   }\r
1132 \r
1133   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1134   {\r
1135   }\r
1136 \r
1137   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1138   {\r
1139   }\r
1140 \r
1141   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1142   {\r
1143   }\r
1144 \r
1145   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1146   {\r
1147   }\r
1148 \r
1149   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1150   {\r
1151   }\r
1152 \r
1153   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1154   {\r
1155   }\r
1156 \r
1157   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1158   {\r
1159   }\r
1160 \r
1161   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1162   {\r
1163   }\r
1164 \r
1165   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1166   {\r
1167   }\r
1168 \r
1169   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1170   {\r
1171   }\r
1172 \r
1173   protected void clustalColour_actionPerformed(ActionEvent e)\r
1174   {\r
1175   }\r
1176 \r
1177   protected void zappoColour_actionPerformed(ActionEvent e)\r
1178   {\r
1179   }\r
1180 \r
1181   protected void taylorColour_actionPerformed(ActionEvent e)\r
1182   {\r
1183   }\r
1184 \r
1185   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1186   {\r
1187   }\r
1188 \r
1189   protected void helixColour_actionPerformed(ActionEvent e)\r
1190   {\r
1191   }\r
1192 \r
1193   protected void strandColour_actionPerformed(ActionEvent e)\r
1194   {\r
1195   }\r
1196 \r
1197   protected void turnColour_actionPerformed(ActionEvent e)\r
1198   {\r
1199   }\r
1200 \r
1201   protected void buriedColour_actionPerformed(ActionEvent e)\r
1202   {\r
1203   }\r
1204 \r
1205   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1206   {\r
1207   }\r
1208 \r
1209   protected void PIDColour_actionPerformed(ActionEvent e)\r
1210   {\r
1211   }\r
1212 \r
1213   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1214   {\r
1215   }\r
1216 \r
1217   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1218   {\r
1219   }\r
1220 \r
1221   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1222   {\r
1223   }\r
1224 \r
1225   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1226   {\r
1227   }\r
1228 \r
1229   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1230   {\r
1231   }\r
1232 \r
1233   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1234   {\r
1235   }\r
1236 \r
1237   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1238   {\r
1239   }\r
1240 \r
1241   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1242   {\r
1243   }\r
1244 \r
1245   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1246   {\r
1247   }\r
1248 \r
1249   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1250   {\r
1251   }\r
1252 \r
1253   protected void copy_actionPerformed(ActionEvent e)\r
1254   {\r
1255   }\r
1256 \r
1257   protected void cut_actionPerformed(ActionEvent e)\r
1258   {\r
1259   }\r
1260 \r
1261   protected void delete_actionPerformed(ActionEvent e)\r
1262   {\r
1263   }\r
1264 \r
1265   protected void pasteNew_actionPerformed(ActionEvent e)\r
1266   {\r
1267   }\r
1268 \r
1269   protected void pasteThis_actionPerformed(ActionEvent e)\r
1270   {\r
1271   }\r
1272 \r
1273   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1274   {\r
1275   }\r
1276 \r
1277   public void createPNG(java.io.File f)\r
1278   {\r
1279   }\r
1280 \r
1281   protected void font_actionPerformed(ActionEvent e)\r
1282   {\r
1283   }\r
1284 \r
1285   protected void seqLimit_actionPerformed(ActionEvent e)\r
1286   {\r
1287   }\r
1288 \r
1289   public void seqDBRef_actionPerformed(ActionEvent e)\r
1290   {\r
1291 \r
1292   }\r
1293 \r
1294 \r
1295   public void createEPS(java.io.File f)\r
1296   {\r
1297   }\r
1298 \r
1299   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1300   {\r
1301   }\r
1302 \r
1303   protected void jpred_actionPerformed(ActionEvent e)\r
1304   {\r
1305   }\r
1306 \r
1307   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1308   {\r
1309   }\r
1310 \r
1311   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1312   {\r
1313   }\r
1314 \r
1315   protected void scaleRight_actionPerformed(ActionEvent e)\r
1316   {\r
1317   }\r
1318 \r
1319   protected void modifyPID_actionPerformed(ActionEvent e)\r
1320   {\r
1321   }\r
1322 \r
1323   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1324   {\r
1325   }\r
1326 \r
1327   protected void preferences_actionPerformed(ActionEvent e)\r
1328   {\r
1329   }\r
1330 \r
1331   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1332   {\r
1333   }\r
1334 \r
1335   protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
1336   {\r
1337   }\r
1338 \r
1339   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1340   {\r
1341   }\r
1342 \r
1343   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1344   {\r
1345   }\r
1346 \r
1347   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
1348   {\r
1349   }\r
1350 \r
1351   public void vamsasStore_actionPerformed(ActionEvent e)\r
1352   {\r
1353 \r
1354   }\r
1355 \r
1356   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1357   {\r
1358 \r
1359   }\r
1360 \r
1361   public void showTranslation_actionPerformed(ActionEvent e)\r
1362   {\r
1363 \r
1364   }\r
1365 \r
1366   public void tabSelected()\r
1367   {\r
1368 \r
1369   }\r
1370 \r
1371   public void featureSettings_actionPerformed(ActionEvent e)\r
1372   {\r
1373 \r
1374   }\r
1375 \r
1376 }\r