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 \r
  25 import jalview.schemes.*;\r
  26 import java.awt.BorderLayout;\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 showSeqFeatures = 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   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 115   protected ButtonGroup colours = new ButtonGroup();\r
 116   JMenuItem vamsasStore = new JMenuItem();\r
 117   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
 118   public JMenuItem featureSettings = new JMenuItem();\r
 119   JMenuItem fetchSequence = new JMenuItem();\r
 120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 121   JMenuItem annotationColour = new JMenuItem();\r
 122   JMenuItem associatedData = new JMenuItem();\r
 123   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 124   JMenu addSequenceMenu = new JMenu();\r
 125   JMenuItem addFromFile = new JMenuItem();\r
 126   JMenuItem addFromText = new JMenuItem();\r
 127   JMenuItem addFromURL = new JMenuItem();\r
 128   JMenuItem exportAnnotations = new JMenuItem();\r
 129   JMenuItem exportFeatures = new JMenuItem();\r
 130   JMenuItem dbRefs = new JMenuItem();\r
 131   protected JPanel statusPanel = new JPanel();\r
 132   GridLayout gridLayout1 = new GridLayout();\r
 133   JMenu jMenu3 = new JMenu();\r
 134   JMenuItem defaultDASSource = new JMenuItem();\r
 135   JMenuItem modifyDASSource = new JMenuItem();\r
 136   public GAlignFrame()\r
 137   {\r
 138 \r
 139 \r
 140     try\r
 141     {\r
 142       jbInit();\r
 143       setJMenuBar(alignFrameMenuBar);\r
 144 \r
 145       // dynamically fill save as menu with available formats\r
 146       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 147       {\r
 148         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 149                              elementAt(\r
 150                                  i));\r
 151         item.addActionListener(new java.awt.event.ActionListener()\r
 152         {\r
 153           public void actionPerformed(ActionEvent e)\r
 154           {\r
 155             outputText_actionPerformed(e);\r
 156           }\r
 157         });\r
 158 \r
 159         outputTextboxMenu.add(item);\r
 160       }\r
 161     }\r
 162     catch (Exception e)\r
 163     {\r
 164     }\r
 165 \r
 166 \r
 167     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 168     {\r
 169       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 170           getUserColourSchemes().keys();\r
 171 \r
 172       while (userColours.hasMoreElements())\r
 173       {\r
 174         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 175             nextElement().toString());\r
 176         radioItem.setName("USER_DEFINED");\r
 177         radioItem.addMouseListener(new MouseAdapter()\r
 178             {\r
 179               public void mousePressed(MouseEvent evt)\r
 180               {\r
 181                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 182                 {\r
 183                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 184 \r
 185                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 186                       "Remove from default list?",\r
 187                       "Remove user defined colour",\r
 188                       JOptionPane.YES_NO_OPTION);\r
 189                   if(option == JOptionPane.YES_OPTION)\r
 190                   {\r
 191                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 192                     colourMenu.remove(radioItem);\r
 193                   }\r
 194                   else\r
 195                     radioItem.addActionListener(new ActionListener()\r
 196                     {\r
 197                       public void actionPerformed(ActionEvent evt)\r
 198                       {\r
 199                         userDefinedColour_actionPerformed(evt);\r
 200                       }\r
 201                     });\r
 202                 }\r
 203               }\r
 204             });\r
 205         radioItem.addActionListener(new ActionListener()\r
 206         {\r
 207           public void actionPerformed(ActionEvent evt)\r
 208           {\r
 209             userDefinedColour_actionPerformed(evt);\r
 210           }\r
 211         });\r
 212         colourMenu.insert(radioItem, 15);\r
 213         colours.add(radioItem);\r
 214       }\r
 215     }\r
 216     colours.add(noColourmenuItem);\r
 217     colours.add(clustalColour);\r
 218     colours.add(zappoColour);\r
 219     colours.add(taylorColour);\r
 220     colours.add(hydrophobicityColour);\r
 221     colours.add(helixColour);\r
 222     colours.add(strandColour);\r
 223     colours.add(turnColour);\r
 224     colours.add(buriedColour);\r
 225     colours.add(userDefinedColour);\r
 226     colours.add(PIDColour);\r
 227     colours.add(BLOSUM62Colour);\r
 228     colours.add(nucleotideColour);\r
 229 \r
 230     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 231 \r
 232 \r
 233   }\r
 234 \r
 235   public void setColourSelected(String defaultColour)\r
 236   {\r
 237 \r
 238     if (defaultColour != null)\r
 239     {\r
 240       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 241 \r
 242       switch (index)\r
 243       {\r
 244         case ColourSchemeProperty.NONE:\r
 245               noColourmenuItem.setSelected(true);\r
 246               break;\r
 247         case ColourSchemeProperty.CLUSTAL:\r
 248           clustalColour.setSelected(true);\r
 249 \r
 250           break;\r
 251 \r
 252         case ColourSchemeProperty.BLOSUM:\r
 253           BLOSUM62Colour.setSelected(true);\r
 254 \r
 255           break;\r
 256 \r
 257         case ColourSchemeProperty.PID:\r
 258           PIDColour.setSelected(true);\r
 259 \r
 260           break;\r
 261 \r
 262         case ColourSchemeProperty.ZAPPO:\r
 263           zappoColour.setSelected(true);\r
 264 \r
 265           break;\r
 266 \r
 267         case ColourSchemeProperty.TAYLOR:\r
 268           taylorColour.setSelected(true);\r
 269           break;\r
 270 \r
 271         case ColourSchemeProperty.HYDROPHOBIC:\r
 272           hydrophobicityColour.setSelected(true);\r
 273 \r
 274           break;\r
 275 \r
 276         case ColourSchemeProperty.HELIX:\r
 277           helixColour.setSelected(true);\r
 278 \r
 279           break;\r
 280 \r
 281         case ColourSchemeProperty.STRAND:\r
 282           strandColour.setSelected(true);\r
 283 \r
 284           break;\r
 285 \r
 286         case ColourSchemeProperty.TURN:\r
 287           turnColour.setSelected(true);\r
 288 \r
 289           break;\r
 290 \r
 291         case ColourSchemeProperty.BURIED:\r
 292           buriedColour.setSelected(true);\r
 293 \r
 294           break;\r
 295 \r
 296         case ColourSchemeProperty.NUCLEOTIDE:\r
 297           nucleotideColour.setSelected(true);\r
 298 \r
 299           break;\r
 300 \r
 301         case ColourSchemeProperty.USER_DEFINED:\r
 302           userDefinedColour.setSelected(true);\r
 303 \r
 304           break;\r
 305       }\r
 306     }\r
 307 \r
 308   }\r
 309 \r
 310   private void jbInit()\r
 311       throws Exception\r
 312   {\r
 313     fileMenu.setMnemonic('F');\r
 314     fileMenu.setText("File");\r
 315     saveAlignmentMenu.setMnemonic('L');\r
 316     saveAlignmentMenu.setText("Save As");\r
 317     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 318         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 319     saveAlignmentMenu.addActionListener(new ActionListener()\r
 320     {\r
 321       public void actionPerformed(ActionEvent e)\r
 322       {\r
 323         saveAlignmentMenu_actionPerformed(e);\r
 324       }\r
 325     });\r
 326     closeMenuItem.setMnemonic('C');\r
 327     closeMenuItem.setText("Close");\r
 328     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 329     {\r
 330       public void actionPerformed(ActionEvent e)\r
 331       {\r
 332         closeMenuItem_actionPerformed(e);\r
 333       }\r
 334     });\r
 335     editMenu.setText("Edit");\r
 336     viewMenu.setText("View");\r
 337     colourMenu.setText("Colour");\r
 338     calculateMenu.setText("Calculate");\r
 339     webService.setText("Web Service");\r
 340     selectAllSequenceMenuItem.setText("Select all");\r
 341     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 342         java.awt.event.KeyEvent.VK_A,\r
 343         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 344     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 345                                                 ActionListener()\r
 346     {\r
 347       public void actionPerformed(ActionEvent e)\r
 348       {\r
 349         selectAllSequenceMenuItem_actionPerformed(e);\r
 350       }\r
 351     });\r
 352     deselectAllSequenceMenuItem.setText("Deselect All");\r
 353     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 354                                                getKeyStroke(\r
 355         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 356     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 357                                                   ActionListener()\r
 358     {\r
 359       public void actionPerformed(ActionEvent e)\r
 360       {\r
 361         deselectAllSequenceMenuItem_actionPerformed(e);\r
 362       }\r
 363     });\r
 364     invertSequenceMenuItem.setText("Invert Selection");\r
 365     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 366     {\r
 367       public void actionPerformed(ActionEvent e)\r
 368       {\r
 369         invertSequenceMenuItem_actionPerformed(e);\r
 370       }\r
 371     });\r
 372     remove2LeftMenuItem.setText("Remove Left");\r
 373     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 374     {\r
 375       public void actionPerformed(ActionEvent e)\r
 376       {\r
 377         remove2LeftMenuItem_actionPerformed(e);\r
 378       }\r
 379     });\r
 380     remove2RightMenuItem.setText("Remove Right");\r
 381     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 382     {\r
 383       public void actionPerformed(ActionEvent e)\r
 384       {\r
 385         remove2RightMenuItem_actionPerformed(e);\r
 386       }\r
 387     });\r
 388     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 389     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 390                                                  ActionListener()\r
 391     {\r
 392       public void actionPerformed(ActionEvent e)\r
 393       {\r
 394         removeGappedColumnMenuItem_actionPerformed(e);\r
 395       }\r
 396     });\r
 397     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 398     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 399     {\r
 400       public void actionPerformed(ActionEvent e)\r
 401       {\r
 402         removeAllGapsMenuItem_actionPerformed(e);\r
 403       }\r
 404     });\r
 405     viewBoxesMenuItem.setText("Boxes");\r
 406     viewBoxesMenuItem.setState(true);\r
 407     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 408     {\r
 409       public void actionPerformed(ActionEvent e)\r
 410       {\r
 411         viewBoxesMenuItem_actionPerformed(e);\r
 412       }\r
 413     });\r
 414     viewTextMenuItem.setText("Text");\r
 415     viewTextMenuItem.setState(true);\r
 416     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 417     {\r
 418       public void actionPerformed(ActionEvent e)\r
 419       {\r
 420         viewTextMenuItem_actionPerformed(e);\r
 421       }\r
 422     });\r
 423     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 424     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 425     {\r
 426       public void actionPerformed(ActionEvent e)\r
 427       {\r
 428         sortPairwiseMenuItem_actionPerformed(e);\r
 429       }\r
 430     });\r
 431     sortIDMenuItem.setText("by ID");\r
 432     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 433     {\r
 434       public void actionPerformed(ActionEvent e)\r
 435       {\r
 436         sortIDMenuItem_actionPerformed(e);\r
 437       }\r
 438     });\r
 439     sortGroupMenuItem.setText("by Group");\r
 440     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 441     {\r
 442       public void actionPerformed(ActionEvent e)\r
 443       {\r
 444         sortGroupMenuItem_actionPerformed(e);\r
 445       }\r
 446     });\r
 447     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 448     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 449                                                ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         removeRedundancyMenuItem_actionPerformed(e);\r
 454       }\r
 455     });\r
 456     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 457     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 458                                                 ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     PCAMenuItem.setText("Principal Component Analysis");\r
 466     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         PCAMenuItem_actionPerformed(e);\r
 471       }\r
 472     });\r
 473     averageDistanceTreeMenuItem.setText(\r
 474         "Average Distance Using % Identity");\r
 475     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 476                                                   ActionListener()\r
 477     {\r
 478       public void actionPerformed(ActionEvent e)\r
 479       {\r
 480         averageDistanceTreeMenuItem_actionPerformed(e);\r
 481       }\r
 482     });\r
 483     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 484     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 485     {\r
 486       public void actionPerformed(ActionEvent e)\r
 487       {\r
 488         neighbourTreeMenuItem_actionPerformed(e);\r
 489       }\r
 490     });\r
 491     this.getContentPane().setLayout(borderLayout1);\r
 492     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 493     statusBar.setBackground(Color.white);\r
 494     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 495     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 496     statusBar.setText("Status bar");\r
 497     outputTextboxMenu.setMnemonic('T');\r
 498     outputTextboxMenu.setText("Output to Textbox");\r
 499     clustalColour.setText("Clustalx");\r
 500 \r
 501     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         clustalColour_actionPerformed(e);\r
 506       }\r
 507     });\r
 508     zappoColour.setText("Zappo");\r
 509     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 510     {\r
 511       public void actionPerformed(ActionEvent e)\r
 512       {\r
 513         zappoColour_actionPerformed(e);\r
 514       }\r
 515     });\r
 516     taylorColour.setText("Taylor");\r
 517     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 518     {\r
 519       public void actionPerformed(ActionEvent e)\r
 520       {\r
 521         taylorColour_actionPerformed(e);\r
 522       }\r
 523     });\r
 524     hydrophobicityColour.setText("Hydrophobicity");\r
 525     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 526     {\r
 527       public void actionPerformed(ActionEvent e)\r
 528       {\r
 529         hydrophobicityColour_actionPerformed(e);\r
 530       }\r
 531     });\r
 532     helixColour.setText("Helix Propensity");\r
 533     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 534     {\r
 535       public void actionPerformed(ActionEvent e)\r
 536       {\r
 537         helixColour_actionPerformed(e);\r
 538       }\r
 539     });\r
 540     strandColour.setText("Strand Propensity");\r
 541     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 542     {\r
 543       public void actionPerformed(ActionEvent e)\r
 544       {\r
 545         strandColour_actionPerformed(e);\r
 546       }\r
 547     });\r
 548     turnColour.setText("Turn Propensity");\r
 549     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 550     {\r
 551       public void actionPerformed(ActionEvent e)\r
 552       {\r
 553         turnColour_actionPerformed(e);\r
 554       }\r
 555     });\r
 556     buriedColour.setText("Buried Index");\r
 557     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 558     {\r
 559       public void actionPerformed(ActionEvent e)\r
 560       {\r
 561         buriedColour_actionPerformed(e);\r
 562       }\r
 563     });\r
 564     userDefinedColour.setText("User Defined...");\r
 565     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 566     {\r
 567       public void actionPerformed(ActionEvent e)\r
 568       {\r
 569         userDefinedColour_actionPerformed(e);\r
 570       }\r
 571     });\r
 572     PIDColour.setText("Percentage Identity");\r
 573     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 574     {\r
 575       public void actionPerformed(ActionEvent e)\r
 576       {\r
 577         PIDColour_actionPerformed(e);\r
 578       }\r
 579     });\r
 580     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 581     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 582     {\r
 583       public void actionPerformed(ActionEvent e)\r
 584       {\r
 585         BLOSUM62Colour_actionPerformed(e);\r
 586       }\r
 587     });\r
 588     avDistanceTreeBlosumMenuItem.setText(\r
 589         "Average Distance Using BLOSUM62");\r
 590     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 591         ActionListener()\r
 592     {\r
 593       public void actionPerformed(ActionEvent e)\r
 594       {\r
 595         avTreeBlosumMenuItem_actionPerformed(e);\r
 596       }\r
 597     });\r
 598     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 599     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 600     {\r
 601       public void actionPerformed(ActionEvent e)\r
 602       {\r
 603         njTreeBlosumMenuItem_actionPerformed(e);\r
 604       }\r
 605     });\r
 606     annotationPanelMenuItem.setActionCommand("");\r
 607     annotationPanelMenuItem.setText("Show Annotations");\r
 608     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 609     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 610     {\r
 611       public void actionPerformed(ActionEvent e)\r
 612       {\r
 613         annotationPanelMenuItem_actionPerformed(e);\r
 614       }\r
 615     });\r
 616     colourTextMenuItem.setText("Colour Text");\r
 617     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 618     {\r
 619       public void actionPerformed(ActionEvent e)\r
 620       {\r
 621         colourTextMenuItem_actionPerformed(e);\r
 622       }\r
 623     });\r
 624     htmlMenuItem.setText("HTML");\r
 625     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 626     {\r
 627       public void actionPerformed(ActionEvent e)\r
 628       {\r
 629         htmlMenuItem_actionPerformed(e);\r
 630       }\r
 631     });\r
 632     overviewMenuItem.setText("Overview Window");\r
 633     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 634     {\r
 635       public void actionPerformed(ActionEvent e)\r
 636       {\r
 637         overviewMenuItem_actionPerformed(e);\r
 638       }\r
 639     });\r
 640     undoMenuItem.setEnabled(false);\r
 641     undoMenuItem.setMnemonic('Z');\r
 642     undoMenuItem.setText("Undo");\r
 643     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 644         java.awt.event.KeyEvent.VK_Z,\r
 645         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 646     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 647     {\r
 648       public void actionPerformed(ActionEvent e)\r
 649       {\r
 650         undoMenuItem_actionPerformed(e);\r
 651       }\r
 652     });\r
 653     redoMenuItem.setEnabled(false);\r
 654     redoMenuItem.setMnemonic('0');\r
 655     redoMenuItem.setText("Redo");\r
 656     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 657     {\r
 658       public void actionPerformed(ActionEvent e)\r
 659       {\r
 660         redoMenuItem_actionPerformed(e);\r
 661       }\r
 662     });\r
 663     conservationMenuItem.setText("By Conservation");\r
 664     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 665     {\r
 666       public void actionPerformed(ActionEvent e)\r
 667       {\r
 668         conservationMenuItem_actionPerformed(e);\r
 669       }\r
 670     });\r
 671     noColourmenuItem.setText("None");\r
 672     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 673     {\r
 674       public void actionPerformed(ActionEvent e)\r
 675       {\r
 676         noColourmenuItem_actionPerformed(e);\r
 677       }\r
 678     });\r
 679     wrapMenuItem.setText("Wrap");\r
 680     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 681     {\r
 682       public void actionPerformed(ActionEvent e)\r
 683       {\r
 684         wrapMenuItem_actionPerformed(e);\r
 685       }\r
 686     });\r
 687     printMenuItem.setText("Print");\r
 688     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 689     {\r
 690       public void actionPerformed(ActionEvent e)\r
 691       {\r
 692         printMenuItem_actionPerformed(e);\r
 693       }\r
 694     });\r
 695     renderGapsMenuItem.setText("Show Gaps");\r
 696     renderGapsMenuItem.setState(true);\r
 697     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 698     {\r
 699       public void actionPerformed(ActionEvent e)\r
 700       {\r
 701         renderGapsMenuItem_actionPerformed(e);\r
 702       }\r
 703     });\r
 704     findMenuItem.setText("Find...");\r
 705     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 706         java.awt.event.KeyEvent.VK_F,\r
 707         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 708     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 709     {\r
 710       public void actionPerformed(ActionEvent e)\r
 711       {\r
 712         findMenuItem_actionPerformed(e);\r
 713       }\r
 714     });\r
 715     searchMenu.setText("Search");\r
 716 \r
 717     abovePIDThreshold.setText("Above Identity Threshold");\r
 718     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 719     {\r
 720       public void actionPerformed(ActionEvent e)\r
 721       {\r
 722         abovePIDThreshold_actionPerformed(e);\r
 723       }\r
 724     });\r
 725     showSeqFeatures.setText("Show Sequence Features");\r
 726     showSeqFeatures.addActionListener(new ActionListener()\r
 727     {\r
 728       public void actionPerformed(ActionEvent actionEvent)\r
 729       {\r
 730         showSeqFeatures_actionPerformed(actionEvent);\r
 731       }\r
 732     });\r
 733     nucleotideColour.setText("Nucleotide");\r
 734     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 735     {\r
 736       public void actionPerformed(ActionEvent e)\r
 737       {\r
 738         nucleotideColour_actionPerformed(e);\r
 739       }\r
 740     });\r
 741     deleteGroups.setText("Undefine groups");\r
 742     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 743     {\r
 744       public void actionPerformed(ActionEvent e)\r
 745       {\r
 746         deleteGroups_actionPerformed(e);\r
 747       }\r
 748     });\r
 749     copy.setText("Copy");\r
 750     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 751         java.awt.event.KeyEvent.VK_C,\r
 752         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 753     copy.setMnemonic(KeyEvent.VK_C);\r
 754 \r
 755     copy.addActionListener(new java.awt.event.ActionListener()\r
 756     {\r
 757       public void actionPerformed(ActionEvent e)\r
 758       {\r
 759         copy_actionPerformed(e);\r
 760       }\r
 761     });\r
 762     cut.setText("Cut");\r
 763     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 764         java.awt.event.KeyEvent.VK_X,\r
 765         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 766     cut.setMnemonic(KeyEvent.VK_X);\r
 767     cut.addActionListener(new java.awt.event.ActionListener()\r
 768     {\r
 769       public void actionPerformed(ActionEvent e)\r
 770       {\r
 771         cut_actionPerformed(e);\r
 772       }\r
 773     });\r
 774     delete.setText("Delete");\r
 775     delete.addActionListener(new java.awt.event.ActionListener()\r
 776     {\r
 777       public void actionPerformed(ActionEvent e)\r
 778       {\r
 779         delete_actionPerformed(e);\r
 780       }\r
 781     });\r
 782     jMenu1.setMnemonic('V');\r
 783     jMenu1.setText("Paste");\r
 784     pasteNew.setText("To New Alignment");\r
 785     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 786         java.awt.event.KeyEvent.VK_V,\r
 787         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 788     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 789     {\r
 790       public void actionPerformed(ActionEvent e)\r
 791       {\r
 792         pasteNew_actionPerformed(e);\r
 793       }\r
 794     });\r
 795     pasteThis.setText("Add To This Alignment");\r
 796     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 797     {\r
 798       public void actionPerformed(ActionEvent e)\r
 799       {\r
 800         pasteThis_actionPerformed(e);\r
 801       }\r
 802     });\r
 803     applyToAllGroups.setText("Apply Colour To All Groups");\r
 804     applyToAllGroups.setState(true);\r
 805     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 806     {\r
 807       public void actionPerformed(ActionEvent e)\r
 808       {\r
 809         applyToAllGroups_actionPerformed(e);\r
 810       }\r
 811     });\r
 812     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 813     {\r
 814       public void actionPerformed(ActionEvent e)\r
 815       {\r
 816         createPNG(null);\r
 817       }\r
 818     });\r
 819     createPNG.setActionCommand("Save As PNG Image");\r
 820     createPNG.setText("PNG");\r
 821     font.setText("Font...");\r
 822     font.addActionListener(new java.awt.event.ActionListener()\r
 823     {\r
 824       public void actionPerformed(ActionEvent e)\r
 825       {\r
 826         font_actionPerformed(e);\r
 827       }\r
 828     });\r
 829 \r
 830     seqLimits.setText("Show Sequence Limits");\r
 831     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 832     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 833     {\r
 834       public void actionPerformed(ActionEvent e)\r
 835       {\r
 836         seqLimit_actionPerformed(e);\r
 837       }\r
 838     });\r
 839     epsFile.setText("EPS");\r
 840     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 841     {\r
 842       public void actionPerformed(ActionEvent e)\r
 843       {\r
 844         createEPS(null);\r
 845       }\r
 846     });\r
 847     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 848     LoadtreeMenuItem.setText("Load Associated Tree");\r
 849     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 850     {\r
 851       public void actionPerformed(ActionEvent e)\r
 852       {\r
 853         LoadtreeMenuItem_actionPerformed(e);\r
 854       }\r
 855     });\r
 856     scaleAbove.setVisible(false);\r
 857     scaleAbove.setText("Scale Above");\r
 858     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 859     {\r
 860       public void actionPerformed(ActionEvent e)\r
 861       {\r
 862         scaleAbove_actionPerformed(e);\r
 863       }\r
 864     });\r
 865     scaleLeft.setVisible(false);\r
 866     scaleLeft.setSelected(true);\r
 867     scaleLeft.setText("Scale Left");\r
 868     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 869     {\r
 870       public void actionPerformed(ActionEvent e)\r
 871       {\r
 872         scaleLeft_actionPerformed(e);\r
 873       }\r
 874     });\r
 875     scaleRight.setVisible(false);\r
 876     scaleRight.setSelected(true);\r
 877     scaleRight.setText("Scale Right");\r
 878     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 879     {\r
 880       public void actionPerformed(ActionEvent e)\r
 881       {\r
 882         scaleRight_actionPerformed(e);\r
 883       }\r
 884     });\r
 885     modifyPID.setText("Modify Identity Threshold...");\r
 886     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 887     {\r
 888       public void actionPerformed(ActionEvent e)\r
 889       {\r
 890         modifyPID_actionPerformed(e);\r
 891       }\r
 892     });\r
 893     modifyConservation.setText("Modify Conservation Threshold...");\r
 894     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 895     {\r
 896       public void actionPerformed(ActionEvent e)\r
 897       {\r
 898         modifyConservation_actionPerformed(e);\r
 899       }\r
 900     });\r
 901     sortByTreeMenu.setText("By Tree Order");\r
 902     sort.setText("Sort");\r
 903     calculate.setText("Calculate Tree");\r
 904 \r
 905     jMenu2.setText("Export");\r
 906     padGapsMenuitem.setText("Pad Gaps");\r
 907     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\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.setVisible(false);\r
 916     vamsasStore.setText("VAMSAS store");\r
 917     vamsasStore.addActionListener(new ActionListener()\r
 918     {\r
 919       public void actionPerformed(ActionEvent e)\r
 920       {\r
 921         vamsasStore_actionPerformed(e);\r
 922       }\r
 923     });\r
 924     showTranslation.setText("Translate cDNA");\r
 925     showTranslation.addActionListener(new ActionListener()\r
 926     {\r
 927       public void actionPerformed(ActionEvent e)\r
 928       {\r
 929         showTranslation_actionPerformed(e);\r
 930       }\r
 931     });\r
 932 \r
 933    /* tabbedPane.addChangeListener(new ChangeListener()\r
 934         {\r
 935           public void stateChanged(ChangeEvent ece)\r
 936           {\r
 937 \r
 938             tabSelected();\r
 939           }\r
 940         });*/\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     fetchSequence.setText("Fetch Sequence(s)...");\r
 950     fetchSequence.addActionListener(new ActionListener()\r
 951     {\r
 952       public void actionPerformed(ActionEvent e)\r
 953       {\r
 954         fetchSequence_actionPerformed(e);\r
 955       }\r
 956     });\r
 957     smoothFont.setText("Smooth Fonts");\r
 958     smoothFont.addActionListener(new ActionListener()\r
 959     {\r
 960       public void actionPerformed(ActionEvent e)\r
 961       {\r
 962         smoothFont_actionPerformed(e);\r
 963       }\r
 964     });\r
 965     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 966     annotationColour.setText("By Annotation...");\r
 967     annotationColour.addActionListener(new ActionListener()\r
 968     {\r
 969       public void actionPerformed(ActionEvent e)\r
 970       {\r
 971         annotationColour_actionPerformed(e);\r
 972       }\r
 973     });\r
 974     associatedData.setText("Load Features / Annotations");\r
 975     associatedData.addActionListener(new ActionListener()\r
 976     {\r
 977       public void actionPerformed(ActionEvent e)\r
 978       {\r
 979         associatedData_actionPerformed(e);\r
 980       }\r
 981     });\r
 982     autoCalculate.setText("Autocalculate Consensus");\r
 983     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 984     autoCalculate.addActionListener(new ActionListener()\r
 985     {\r
 986       public void actionPerformed(ActionEvent e)\r
 987       {\r
 988         autoCalculate_actionPerformed(e);\r
 989       }\r
 990     });\r
 991     addSequenceMenu.setText("Add Sequences");\r
 992     addFromFile.setText("From File");\r
 993     addFromFile.addActionListener(new ActionListener()\r
 994     {\r
 995       public void actionPerformed(ActionEvent e)\r
 996       {\r
 997         addFromFile_actionPerformed(e);\r
 998       }\r
 999     });\r
1000     addFromText.setText("From Textbox");\r
1001     addFromText.addActionListener(new ActionListener()\r
1002     {\r
1003       public void actionPerformed(ActionEvent e)\r
1004       {\r
1005         addFromText_actionPerformed(e);\r
1006       }\r
1007     });\r
1008     addFromURL.setText("From URL");\r
1009     addFromURL.addActionListener(new ActionListener()\r
1010     {\r
1011       public void actionPerformed(ActionEvent e)\r
1012       {\r
1013         addFromURL_actionPerformed(e);\r
1014       }\r
1015     });\r
1016     exportFeatures.setText("Export Features...");\r
1017     exportFeatures.addActionListener(new ActionListener()\r
1018     {\r
1019       public void actionPerformed(ActionEvent e)\r
1020       {\r
1021         exportFeatures_actionPerformed(e);\r
1022       }\r
1023     });\r
1024     exportAnnotations.setText("Export Annotations...");\r
1025     exportAnnotations.addActionListener(new ActionListener()\r
1026     {\r
1027       public void actionPerformed(ActionEvent e)\r
1028       {\r
1029         exportAnnotations_actionPerformed(e);\r
1030       }\r
1031     });\r
1032     dbRefs.setText("Fetch DB Refs");\r
1033     dbRefs.addActionListener(new ActionListener()\r
1034     {\r
1035       public void actionPerformed(ActionEvent e)\r
1036       {\r
1037         dbRefs_actionPerformed(e);\r
1038       }\r
1039     });\r
1040     statusPanel.setLayout(gridLayout1);\r
1041     jMenu3.setText("Fetch Sequence Features");\r
1042     defaultDASSource.setText("Use Default DAS Source");\r
1043     defaultDASSource.addActionListener(new ActionListener()\r
1044     {\r
1045       public void actionPerformed(ActionEvent e)\r
1046       {\r
1047         defaultDASSource_actionPerformed(e);\r
1048       }\r
1049     });\r
1050     modifyDASSource.setText("Modify DAS Source...");\r
1051     modifyDASSource.addActionListener(new ActionListener()\r
1052     {\r
1053       public void actionPerformed(ActionEvent e)\r
1054       {\r
1055         modifyDASSource_actionPerformed(e);\r
1056       }\r
1057     });\r
1058     alignFrameMenuBar.add(fileMenu);\r
1059     alignFrameMenuBar.add(editMenu);\r
1060     alignFrameMenuBar.add(searchMenu);\r
1061     alignFrameMenuBar.add(viewMenu);\r
1062     alignFrameMenuBar.add(colourMenu);\r
1063     alignFrameMenuBar.add(calculateMenu);\r
1064     alignFrameMenuBar.add(webService);\r
1065     fileMenu.add(addSequenceMenu);\r
1066     fileMenu.add(fetchSequence);\r
1067     fileMenu.addSeparator();\r
1068     fileMenu.add(vamsasStore);\r
1069     fileMenu.add(saveAlignmentMenu);\r
1070     fileMenu.add(jMenu2);\r
1071     fileMenu.add(outputTextboxMenu);\r
1072     fileMenu.add(printMenuItem);\r
1073     fileMenu.addSeparator();\r
1074     fileMenu.add(exportFeatures);\r
1075     fileMenu.add(exportAnnotations);\r
1076     fileMenu.add(LoadtreeMenuItem);\r
1077     fileMenu.add(associatedData);\r
1078     fileMenu.addSeparator();\r
1079     fileMenu.add(closeMenuItem);\r
1080     editMenu.add(undoMenuItem);\r
1081     editMenu.add(redoMenuItem);\r
1082     editMenu.add(cut);\r
1083     editMenu.add(copy);\r
1084     editMenu.add(jMenu1);\r
1085     editMenu.add(delete);\r
1086     editMenu.addSeparator();\r
1087     editMenu.add(selectAllSequenceMenuItem);\r
1088     editMenu.add(deselectAllSequenceMenuItem);\r
1089     editMenu.add(invertSequenceMenuItem);\r
1090     editMenu.add(deleteGroups);\r
1091     editMenu.addSeparator();\r
1092     editMenu.add(remove2LeftMenuItem);\r
1093     editMenu.add(remove2RightMenuItem);\r
1094     editMenu.add(removeGappedColumnMenuItem);\r
1095     editMenu.add(removeAllGapsMenuItem);\r
1096     editMenu.add(removeRedundancyMenuItem);\r
1097     editMenu.addSeparator();\r
1098     editMenu.add(padGapsMenuitem);\r
1099     searchMenu.add(findMenuItem);\r
1100     viewMenu.add(font);\r
1101     viewMenu.add(smoothFont);\r
1102     viewMenu.addSeparator();\r
1103     viewMenu.add(wrapMenuItem);\r
1104     viewMenu.add(seqLimits);\r
1105     viewMenu.add(scaleAbove);\r
1106     viewMenu.add(scaleLeft);\r
1107     viewMenu.add(scaleRight);\r
1108     viewMenu.add(viewBoxesMenuItem);\r
1109     viewMenu.add(viewTextMenuItem);\r
1110     viewMenu.add(colourTextMenuItem);\r
1111     viewMenu.add(renderGapsMenuItem);\r
1112     viewMenu.add(annotationPanelMenuItem);\r
1113     viewMenu.addSeparator();\r
1114     viewMenu.add(dbRefs);\r
1115     viewMenu.add(jMenu3);\r
1116     viewMenu.add(showSeqFeatures);\r
1117     viewMenu.add(featureSettings);\r
1118     viewMenu.addSeparator();\r
1119     viewMenu.add(overviewMenuItem);\r
1120     colourMenu.add(applyToAllGroups);\r
1121     colourMenu.addSeparator();\r
1122     colourMenu.add(noColourmenuItem);\r
1123     colourMenu.add(clustalColour);\r
1124     colourMenu.add(BLOSUM62Colour);\r
1125     colourMenu.add(PIDColour);\r
1126     colourMenu.add(zappoColour);\r
1127     colourMenu.add(taylorColour);\r
1128     colourMenu.add(hydrophobicityColour);\r
1129     colourMenu.add(helixColour);\r
1130     colourMenu.add(strandColour);\r
1131     colourMenu.add(turnColour);\r
1132     colourMenu.add(buriedColour);\r
1133     colourMenu.add(nucleotideColour);\r
1134     colourMenu.add(userDefinedColour);\r
1135     colourMenu.addSeparator();\r
1136     colourMenu.add(conservationMenuItem);\r
1137     colourMenu.add(modifyConservation);\r
1138     colourMenu.add(abovePIDThreshold);\r
1139     colourMenu.add(modifyPID);\r
1140     colourMenu.add(annotationColour);\r
1141     calculateMenu.add(sort);\r
1142     calculateMenu.add(calculate);\r
1143     calculateMenu.addSeparator();\r
1144     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1145     calculateMenu.add(PCAMenuItem);\r
1146     calculateMenu.addSeparator();\r
1147     calculateMenu.add(showTranslation);\r
1148     calculateMenu.add(autoCalculate);\r
1149     webServiceNoServices=new JMenuItem("<No Services>");\r
1150     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1151     jMenu1.add(pasteThis);\r
1152     sort.add(sortIDMenuItem);\r
1153     sort.add(sortGroupMenuItem);\r
1154     sort.add(sortPairwiseMenuItem);\r
1155     calculate.add(averageDistanceTreeMenuItem);\r
1156     calculate.add(neighbourTreeMenuItem);\r
1157     calculate.add(avDistanceTreeBlosumMenuItem);\r
1158     calculate.add(njTreeBlosumMenuItem);\r
1159     jMenu2.add(htmlMenuItem);\r
1160     jMenu2.add(epsFile);\r
1161     jMenu2.add(createPNG);\r
1162     addSequenceMenu.add(addFromFile);\r
1163     addSequenceMenu.add(addFromText);\r
1164     addSequenceMenu.add(addFromURL);\r
1165     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1166     statusPanel.add(statusBar, null);\r
1167     jMenu3.add(defaultDASSource);\r
1168     jMenu3.add(modifyDASSource);\r
1169   }\r
1170 \r
1171   protected void outputText_actionPerformed(ActionEvent e)\r
1172   {\r
1173   }\r
1174 \r
1175   public void addFromFile_actionPerformed(ActionEvent e)\r
1176   {\r
1177 \r
1178   }\r
1179 \r
1180   public void addFromText_actionPerformed(ActionEvent e)\r
1181   {\r
1182 \r
1183   }\r
1184 \r
1185   public void addFromURL_actionPerformed(ActionEvent e)\r
1186   {\r
1187 \r
1188   }\r
1189 \r
1190   public void exportFeatures_actionPerformed(ActionEvent e)\r
1191   {\r
1192 \r
1193   }\r
1194 \r
1195   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1196   {\r
1197 \r
1198   }\r
1199 \r
1200   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1201   {\r
1202   }\r
1203 \r
1204   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1205   {\r
1206   }\r
1207 \r
1208   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1209   {\r
1210   }\r
1211 \r
1212   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1213   {\r
1214   }\r
1215 \r
1216   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1217   {\r
1218   }\r
1219 \r
1220   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1221   {\r
1222   }\r
1223 \r
1224   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1225   {\r
1226   }\r
1227 \r
1228   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1229   {\r
1230   }\r
1231 \r
1232   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1233   {\r
1234   }\r
1235 \r
1236   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1237   {\r
1238   }\r
1239 \r
1240   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1241   {\r
1242   }\r
1243 \r
1244   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1245   {\r
1246   }\r
1247 \r
1248   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1249   {\r
1250   }\r
1251 \r
1252   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1253   {\r
1254   }\r
1255 \r
1256   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1257   {\r
1258   }\r
1259 \r
1260   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1261   {\r
1262   }\r
1263 \r
1264   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1265   {\r
1266   }\r
1267 \r
1268   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1269   {\r
1270   }\r
1271 \r
1272   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1273   {\r
1274   }\r
1275 \r
1276   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1277   {\r
1278   }\r
1279 \r
1280   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1281   {\r
1282   }\r
1283 \r
1284   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1285   {\r
1286   }\r
1287 \r
1288   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1289   {\r
1290   }\r
1291 \r
1292   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1293   {\r
1294   }\r
1295 \r
1296   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1297   {\r
1298   }\r
1299 \r
1300   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1301   {\r
1302   }\r
1303 \r
1304   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1305   {\r
1306   }\r
1307 \r
1308   protected void clustalColour_actionPerformed(ActionEvent e)\r
1309   {\r
1310   }\r
1311 \r
1312   protected void zappoColour_actionPerformed(ActionEvent e)\r
1313   {\r
1314   }\r
1315 \r
1316   protected void taylorColour_actionPerformed(ActionEvent e)\r
1317   {\r
1318   }\r
1319 \r
1320   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1321   {\r
1322   }\r
1323 \r
1324   protected void helixColour_actionPerformed(ActionEvent e)\r
1325   {\r
1326   }\r
1327 \r
1328   protected void strandColour_actionPerformed(ActionEvent e)\r
1329   {\r
1330   }\r
1331 \r
1332   protected void turnColour_actionPerformed(ActionEvent e)\r
1333   {\r
1334   }\r
1335 \r
1336   protected void buriedColour_actionPerformed(ActionEvent e)\r
1337   {\r
1338   }\r
1339 \r
1340   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1341   {\r
1342   }\r
1343 \r
1344   protected void PIDColour_actionPerformed(ActionEvent e)\r
1345   {\r
1346   }\r
1347 \r
1348   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1349   {\r
1350   }\r
1351 \r
1352   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1353   {\r
1354   }\r
1355 \r
1356   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1357   {\r
1358   }\r
1359 \r
1360   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1361   {\r
1362   }\r
1363 \r
1364   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1365   {\r
1366   }\r
1367 \r
1368   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1369   {\r
1370   }\r
1371 \r
1372   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1373   {\r
1374   }\r
1375 \r
1376   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1377   {\r
1378   }\r
1379 \r
1380   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1381   {\r
1382   }\r
1383 \r
1384   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1385   {\r
1386   }\r
1387 \r
1388   protected void copy_actionPerformed(ActionEvent e)\r
1389   {\r
1390   }\r
1391 \r
1392   protected void cut_actionPerformed(ActionEvent e)\r
1393   {\r
1394   }\r
1395 \r
1396   protected void delete_actionPerformed(ActionEvent e)\r
1397   {\r
1398   }\r
1399 \r
1400   protected void pasteNew_actionPerformed(ActionEvent e)\r
1401   {\r
1402   }\r
1403 \r
1404   protected void pasteThis_actionPerformed(ActionEvent e)\r
1405   {\r
1406   }\r
1407 \r
1408   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1409   {\r
1410   }\r
1411 \r
1412   public void createPNG(java.io.File f)\r
1413   {\r
1414   }\r
1415 \r
1416   protected void font_actionPerformed(ActionEvent e)\r
1417   {\r
1418   }\r
1419 \r
1420   protected void seqLimit_actionPerformed(ActionEvent e)\r
1421   {\r
1422   }\r
1423 \r
1424   public void seqDBRef_actionPerformed(ActionEvent e)\r
1425   {\r
1426 \r
1427   }\r
1428 \r
1429 \r
1430   public void createEPS(java.io.File f)\r
1431   {\r
1432   }\r
1433 \r
1434   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1435   {\r
1436   }\r
1437 \r
1438   protected void jpred_actionPerformed(ActionEvent e)\r
1439   {\r
1440   }\r
1441 \r
1442   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1443   {\r
1444   }\r
1445 \r
1446   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1447   {\r
1448   }\r
1449 \r
1450   protected void scaleRight_actionPerformed(ActionEvent e)\r
1451   {\r
1452   }\r
1453 \r
1454   protected void modifyPID_actionPerformed(ActionEvent e)\r
1455   {\r
1456   }\r
1457 \r
1458   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1459   {\r
1460   }\r
1461 \r
1462 \r
1463 \r
1464   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1465   {\r
1466   }\r
1467 \r
1468   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1469   {\r
1470   }\r
1471 \r
1472 \r
1473   public void vamsasStore_actionPerformed(ActionEvent e)\r
1474   {\r
1475 \r
1476   }\r
1477 \r
1478   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1479   {\r
1480 \r
1481   }\r
1482 \r
1483   public void showTranslation_actionPerformed(ActionEvent e)\r
1484   {\r
1485 \r
1486   }\r
1487 \r
1488   public void featureSettings_actionPerformed(ActionEvent e)\r
1489   {\r
1490 \r
1491   }\r
1492 \r
1493   public void fetchSequence_actionPerformed(ActionEvent e)\r
1494   {\r
1495 \r
1496   }\r
1497 \r
1498   public void smoothFont_actionPerformed(ActionEvent e)\r
1499   {\r
1500 \r
1501   }\r
1502 \r
1503   public void annotationColour_actionPerformed(ActionEvent e)\r
1504   {\r
1505 \r
1506   }\r
1507 \r
1508 \r
1509   public void associatedData_actionPerformed(ActionEvent e)\r
1510   {\r
1511 \r
1512   }\r
1513 \r
1514   public void autoCalculate_actionPerformed(ActionEvent e)\r
1515   {\r
1516 \r
1517   }\r
1518 \r
1519   public void dbRefs_actionPerformed(ActionEvent e)\r
1520   {\r
1521 \r
1522   }\r
1523 \r
1524   public void defaultDASSource_actionPerformed(ActionEvent e)\r
1525   {\r
1526 \r
1527   }\r
1528 \r
1529   public void modifyDASSource_actionPerformed(ActionEvent e)\r
1530   {\r
1531 \r
1532   }\r
1533 \r
1534 \r
1535 }\r