src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 import java.awt.BorderLayout;\r
  28 \r
  29 \r
  30 \r
  31 \r
  32 public class GAlignFrame\r
  33     extends JInternalFrame\r
  34 {\r
  35   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  36   protected JMenu fileMenu = new JMenu();\r
  37   protected JMenuItem closeMenuItem = new JMenuItem();\r
  38   protected JMenu editMenu = new JMenu();\r
  39   protected JMenu viewMenu = new JMenu();\r
  40   protected JMenu colourMenu = new JMenu();\r
  41   protected JMenu calculateMenu = new JMenu();\r
  42   protected JMenu webService = new JMenu();\r
  43   protected JMenuItem webServiceNoServices;\r
  44   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  45   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  46   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  47   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  48   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  50   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  51   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  52   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  53   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  54   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  55   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  56   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  57   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  58   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  59   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  60   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  61   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  62   BorderLayout borderLayout1 = new BorderLayout();\r
  63   public JLabel statusBar = new JLabel();\r
  64   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  65   protected JMenu outputTextboxMenu = new JMenu();\r
  66   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  70       JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  75   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  76   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  77   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  78   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  79   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  80   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  81   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  82   JMenuItem htmlMenuItem = new JMenuItem();\r
  83   JMenuItem overviewMenuItem = new JMenuItem();\r
  84   protected JMenuItem undoMenuItem = new JMenuItem();\r
  85   protected JMenuItem redoMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  87   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  88   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  89   JMenuItem printMenuItem = new JMenuItem();\r
  90   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  91   JMenuItem findMenuItem = new JMenuItem();\r
  92   JMenu searchMenu = new JMenu();\r
  93   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  94   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  95   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  96   JMenuItem deleteGroups = new JMenuItem();\r
  97   JMenuItem delete = new JMenuItem();\r
  98   JMenuItem copy = new JMenuItem();\r
  99   JMenuItem cut = new JMenuItem();\r
 100   JMenu jMenu1 = new JMenu();\r
 101   JMenuItem pasteNew = new JMenuItem();\r
 102   JMenuItem pasteThis = new JMenuItem();\r
 103   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 104   JMenuItem createPNG = new JMenuItem();\r
 105   protected JMenuItem font = new JMenuItem();\r
 106   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 107   JMenuItem epsFile = new JMenuItem();\r
 108   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 109   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 110   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 111   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 112   protected JMenuItem modifyPID = new JMenuItem();\r
 113   protected JMenuItem modifyConservation = new JMenuItem();\r
 114   protected JMenu sortByTreeMenu = new JMenu();\r
 115   protected JMenu sort = new JMenu();\r
 116   JMenu calculate = new JMenu();\r
 117   JMenu jMenu2 = new JMenu();\r
 118   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 119   protected ButtonGroup colours = new ButtonGroup();\r
 120   JMenuItem vamsasStore = new JMenuItem();\r
 121   protected JMenuItem showTranslation = new JMenuItem();\r
 122   public JMenuItem featureSettings = new JMenuItem();\r
 123   JMenuItem fetchSequence = new JMenuItem();\r
 124   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 125   JMenuItem annotationColour = new JMenuItem();\r
 126   JMenuItem associatedData = new JMenuItem();\r
 127   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 128   JMenu addSequenceMenu = new JMenu();\r
 129   JMenuItem addFromFile = new JMenuItem();\r
 130   JMenuItem addFromText = new JMenuItem();\r
 131   JMenuItem addFromURL = new JMenuItem();\r
 132   JMenuItem exportAnnotations = new JMenuItem();\r
 133   JMenuItem exportFeatures = new JMenuItem();\r
 134   protected JPanel statusPanel = new JPanel();\r
 135   GridLayout gridLayout1 = new GridLayout();\r
 136   JMenu jMenu3 = new JMenu();\r
 137   JMenuItem showAllSeqs = new JMenuItem();\r
 138   JMenuItem showAllColumns = new JMenuItem();\r
 139   JMenu hideMenu = new JMenu();\r
 140   JMenuItem hideSelSequences = new JMenuItem();\r
 141   JMenuItem hideSelColumns = new JMenuItem();\r
 142   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 143   JMenuItem invertColSel = new JMenuItem();\r
 144   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 145   public GAlignFrame()\r
 146   {\r
 147     try\r
 148     {\r
 149       jbInit();\r
 150       setJMenuBar(alignFrameMenuBar);\r
 151 \r
 152       // dynamically fill save as menu with available formats\r
 153       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 154       {\r
 155         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 156 \r
 157         item.addActionListener(new java.awt.event.ActionListener()\r
 158         {\r
 159           public void actionPerformed(ActionEvent e)\r
 160           {\r
 161             outputText_actionPerformed(e);\r
 162           }\r
 163         });\r
 164 \r
 165         outputTextboxMenu.add(item);\r
 166       }\r
 167     }\r
 168     catch (Exception e)\r
 169     {\r
 170     }\r
 171 \r
 172 \r
 173     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 174     {\r
 175       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 176           getUserColourSchemes().keys();\r
 177 \r
 178       while (userColours.hasMoreElements())\r
 179       {\r
 180         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 181             nextElement().toString());\r
 182         radioItem.setName("USER_DEFINED");\r
 183         radioItem.addMouseListener(new MouseAdapter()\r
 184             {\r
 185               public void mousePressed(MouseEvent evt)\r
 186               {\r
 187                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 188                 {\r
 189                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 190 \r
 191                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 192                       "Remove from default list?",\r
 193                       "Remove user defined colour",\r
 194                       JOptionPane.YES_NO_OPTION);\r
 195                   if(option == JOptionPane.YES_OPTION)\r
 196                   {\r
 197                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 198                     colourMenu.remove(radioItem);\r
 199                   }\r
 200                   else\r
 201                     radioItem.addActionListener(new ActionListener()\r
 202                     {\r
 203                       public void actionPerformed(ActionEvent evt)\r
 204                       {\r
 205                         userDefinedColour_actionPerformed(evt);\r
 206                       }\r
 207                     });\r
 208                 }\r
 209               }\r
 210             });\r
 211         radioItem.addActionListener(new ActionListener()\r
 212         {\r
 213           public void actionPerformed(ActionEvent evt)\r
 214           {\r
 215             userDefinedColour_actionPerformed(evt);\r
 216           }\r
 217         });\r
 218         colourMenu.insert(radioItem, 15);\r
 219         colours.add(radioItem);\r
 220       }\r
 221     }\r
 222     colours.add(noColourmenuItem);\r
 223     colours.add(clustalColour);\r
 224     colours.add(zappoColour);\r
 225     colours.add(taylorColour);\r
 226     colours.add(hydrophobicityColour);\r
 227     colours.add(helixColour);\r
 228     colours.add(strandColour);\r
 229     colours.add(turnColour);\r
 230     colours.add(buriedColour);\r
 231     colours.add(userDefinedColour);\r
 232     colours.add(PIDColour);\r
 233     colours.add(BLOSUM62Colour);\r
 234     colours.add(nucleotideColour);\r
 235 \r
 236     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 237 \r
 238 \r
 239   }\r
 240 \r
 241   public void setColourSelected(String defaultColour)\r
 242   {\r
 243 \r
 244     if (defaultColour != null)\r
 245     {\r
 246       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 247 \r
 248       switch (index)\r
 249       {\r
 250         case ColourSchemeProperty.NONE:\r
 251               noColourmenuItem.setSelected(true);\r
 252               break;\r
 253         case ColourSchemeProperty.CLUSTAL:\r
 254           clustalColour.setSelected(true);\r
 255 \r
 256           break;\r
 257 \r
 258         case ColourSchemeProperty.BLOSUM:\r
 259           BLOSUM62Colour.setSelected(true);\r
 260 \r
 261           break;\r
 262 \r
 263         case ColourSchemeProperty.PID:\r
 264           PIDColour.setSelected(true);\r
 265 \r
 266           break;\r
 267 \r
 268         case ColourSchemeProperty.ZAPPO:\r
 269           zappoColour.setSelected(true);\r
 270 \r
 271           break;\r
 272 \r
 273         case ColourSchemeProperty.TAYLOR:\r
 274           taylorColour.setSelected(true);\r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.HYDROPHOBIC:\r
 278           hydrophobicityColour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.HELIX:\r
 283           helixColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.STRAND:\r
 288           strandColour.setSelected(true);\r
 289 \r
 290           break;\r
 291 \r
 292         case ColourSchemeProperty.TURN:\r
 293           turnColour.setSelected(true);\r
 294 \r
 295           break;\r
 296 \r
 297         case ColourSchemeProperty.BURIED:\r
 298           buriedColour.setSelected(true);\r
 299 \r
 300           break;\r
 301 \r
 302         case ColourSchemeProperty.NUCLEOTIDE:\r
 303           nucleotideColour.setSelected(true);\r
 304 \r
 305           break;\r
 306 \r
 307         case ColourSchemeProperty.USER_DEFINED:\r
 308           userDefinedColour.setSelected(true);\r
 309 \r
 310           break;\r
 311       }\r
 312     }\r
 313 \r
 314   }\r
 315 \r
 316   private void jbInit()\r
 317       throws Exception\r
 318   {\r
 319     fileMenu.setMnemonic('F');\r
 320     fileMenu.setText("File");\r
 321     saveAlignmentMenu.setMnemonic('L');\r
 322     saveAlignmentMenu.setText("Save As");\r
 323     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 324         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 325     saveAlignmentMenu.addActionListener(new ActionListener()\r
 326     {\r
 327       public void actionPerformed(ActionEvent e)\r
 328       {\r
 329         saveAlignmentMenu_actionPerformed(e);\r
 330       }\r
 331     });\r
 332     closeMenuItem.setMnemonic('C');\r
 333     closeMenuItem.setText("Close");\r
 334     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 335     {\r
 336       public void actionPerformed(ActionEvent e)\r
 337       {\r
 338         closeMenuItem_actionPerformed(e);\r
 339       }\r
 340     });\r
 341     editMenu.setText("Edit");\r
 342     viewMenu.setText("View");\r
 343     colourMenu.setText("Colour");\r
 344     calculateMenu.setText("Calculate");\r
 345     webService.setText("Web Service");\r
 346     selectAllSequenceMenuItem.setText("Select all");\r
 347     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 348         java.awt.event.KeyEvent.VK_A,\r
 349         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 350     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 351                                                 ActionListener()\r
 352     {\r
 353       public void actionPerformed(ActionEvent e)\r
 354       {\r
 355         selectAllSequenceMenuItem_actionPerformed(e);\r
 356       }\r
 357     });\r
 358     deselectAllSequenceMenuItem.setText("Deselect All");\r
 359     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 360                                                getKeyStroke(\r
 361         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 362     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 363                                                   ActionListener()\r
 364     {\r
 365       public void actionPerformed(ActionEvent e)\r
 366       {\r
 367         deselectAllSequenceMenuItem_actionPerformed(e);\r
 368       }\r
 369     });\r
 370     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 371     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 372         java.awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 373     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 374     {\r
 375       public void actionPerformed(ActionEvent e)\r
 376       {\r
 377         invertSequenceMenuItem_actionPerformed(e);\r
 378       }\r
 379     });\r
 380     remove2LeftMenuItem.setText("Remove Left");\r
 381     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 382         awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 383     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 384     {\r
 385       public void actionPerformed(ActionEvent e)\r
 386       {\r
 387         remove2LeftMenuItem_actionPerformed(e);\r
 388       }\r
 389     });\r
 390     remove2RightMenuItem.setText("Remove Right");\r
 391     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 392         awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 393     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 394     {\r
 395       public void actionPerformed(ActionEvent e)\r
 396       {\r
 397         remove2RightMenuItem_actionPerformed(e);\r
 398       }\r
 399     });\r
 400     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 401     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 402                                               getKeyStroke(java.awt.event.\r
 403         KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 404     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 405                                                  ActionListener()\r
 406     {\r
 407       public void actionPerformed(ActionEvent e)\r
 408       {\r
 409         removeGappedColumnMenuItem_actionPerformed(e);\r
 410       }\r
 411     });\r
 412     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 413     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 414         java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 415     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 416     {\r
 417       public void actionPerformed(ActionEvent e)\r
 418       {\r
 419         removeAllGapsMenuItem_actionPerformed(e);\r
 420       }\r
 421     });\r
 422     viewBoxesMenuItem.setText("Boxes");\r
 423     viewBoxesMenuItem.setState(true);\r
 424     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 425     {\r
 426       public void actionPerformed(ActionEvent e)\r
 427       {\r
 428         viewBoxesMenuItem_actionPerformed(e);\r
 429       }\r
 430     });\r
 431     viewTextMenuItem.setText("Text");\r
 432     viewTextMenuItem.setState(true);\r
 433     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 434     {\r
 435       public void actionPerformed(ActionEvent e)\r
 436       {\r
 437         viewTextMenuItem_actionPerformed(e);\r
 438       }\r
 439     });\r
 440     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 441     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 442     {\r
 443       public void actionPerformed(ActionEvent e)\r
 444       {\r
 445         sortPairwiseMenuItem_actionPerformed(e);\r
 446       }\r
 447     });\r
 448     sortIDMenuItem.setText("by ID");\r
 449     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         sortIDMenuItem_actionPerformed(e);\r
 454       }\r
 455     });\r
 456     sortGroupMenuItem.setText("by Group");\r
 457     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 458     {\r
 459       public void actionPerformed(ActionEvent e)\r
 460       {\r
 461         sortGroupMenuItem_actionPerformed(e);\r
 462       }\r
 463     });\r
 464     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 465     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 466         java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 467     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 468                                                ActionListener()\r
 469     {\r
 470       public void actionPerformed(ActionEvent e)\r
 471       {\r
 472         removeRedundancyMenuItem_actionPerformed(e);\r
 473       }\r
 474     });\r
 475     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 476     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 477                                                 ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     PCAMenuItem.setText("Principal Component Analysis");\r
 485     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 486     {\r
 487       public void actionPerformed(ActionEvent e)\r
 488       {\r
 489         PCAMenuItem_actionPerformed(e);\r
 490       }\r
 491     });\r
 492     averageDistanceTreeMenuItem.setText(\r
 493         "Average Distance Using % Identity");\r
 494     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 495                                                   ActionListener()\r
 496     {\r
 497       public void actionPerformed(ActionEvent e)\r
 498       {\r
 499         averageDistanceTreeMenuItem_actionPerformed(e);\r
 500       }\r
 501     });\r
 502     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 503     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 504     {\r
 505       public void actionPerformed(ActionEvent e)\r
 506       {\r
 507         neighbourTreeMenuItem_actionPerformed(e);\r
 508       }\r
 509     });\r
 510     this.getContentPane().setLayout(borderLayout1);\r
 511     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 512     statusBar.setBackground(Color.white);\r
 513     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 514     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 515     statusBar.setText("Status bar");\r
 516     outputTextboxMenu.setMnemonic('T');\r
 517     outputTextboxMenu.setText("Output to Textbox");\r
 518     clustalColour.setText("Clustalx");\r
 519 \r
 520     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 521     {\r
 522       public void actionPerformed(ActionEvent e)\r
 523       {\r
 524         clustalColour_actionPerformed(e);\r
 525       }\r
 526     });\r
 527     zappoColour.setText("Zappo");\r
 528     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 529     {\r
 530       public void actionPerformed(ActionEvent e)\r
 531       {\r
 532         zappoColour_actionPerformed(e);\r
 533       }\r
 534     });\r
 535     taylorColour.setText("Taylor");\r
 536     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 537     {\r
 538       public void actionPerformed(ActionEvent e)\r
 539       {\r
 540         taylorColour_actionPerformed(e);\r
 541       }\r
 542     });\r
 543     hydrophobicityColour.setText("Hydrophobicity");\r
 544     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 545     {\r
 546       public void actionPerformed(ActionEvent e)\r
 547       {\r
 548         hydrophobicityColour_actionPerformed(e);\r
 549       }\r
 550     });\r
 551     helixColour.setText("Helix Propensity");\r
 552     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 553     {\r
 554       public void actionPerformed(ActionEvent e)\r
 555       {\r
 556         helixColour_actionPerformed(e);\r
 557       }\r
 558     });\r
 559     strandColour.setText("Strand Propensity");\r
 560     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 561     {\r
 562       public void actionPerformed(ActionEvent e)\r
 563       {\r
 564         strandColour_actionPerformed(e);\r
 565       }\r
 566     });\r
 567     turnColour.setText("Turn Propensity");\r
 568     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 569     {\r
 570       public void actionPerformed(ActionEvent e)\r
 571       {\r
 572         turnColour_actionPerformed(e);\r
 573       }\r
 574     });\r
 575     buriedColour.setText("Buried Index");\r
 576     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 577     {\r
 578       public void actionPerformed(ActionEvent e)\r
 579       {\r
 580         buriedColour_actionPerformed(e);\r
 581       }\r
 582     });\r
 583     userDefinedColour.setText("User Defined...");\r
 584     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 585     {\r
 586       public void actionPerformed(ActionEvent e)\r
 587       {\r
 588         userDefinedColour_actionPerformed(e);\r
 589       }\r
 590     });\r
 591     PIDColour.setText("Percentage Identity");\r
 592     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 593     {\r
 594       public void actionPerformed(ActionEvent e)\r
 595       {\r
 596         PIDColour_actionPerformed(e);\r
 597       }\r
 598     });\r
 599     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 600     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 601     {\r
 602       public void actionPerformed(ActionEvent e)\r
 603       {\r
 604         BLOSUM62Colour_actionPerformed(e);\r
 605       }\r
 606     });\r
 607     avDistanceTreeBlosumMenuItem.setText(\r
 608         "Average Distance Using BLOSUM62");\r
 609     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 610         ActionListener()\r
 611     {\r
 612       public void actionPerformed(ActionEvent e)\r
 613       {\r
 614         avTreeBlosumMenuItem_actionPerformed(e);\r
 615       }\r
 616     });\r
 617     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 618     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 619     {\r
 620       public void actionPerformed(ActionEvent e)\r
 621       {\r
 622         njTreeBlosumMenuItem_actionPerformed(e);\r
 623       }\r
 624     });\r
 625     annotationPanelMenuItem.setActionCommand("");\r
 626     annotationPanelMenuItem.setText("Show Annotations");\r
 627     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 628     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 629     {\r
 630       public void actionPerformed(ActionEvent e)\r
 631       {\r
 632         annotationPanelMenuItem_actionPerformed(e);\r
 633       }\r
 634     });\r
 635     colourTextMenuItem.setText("Colour Text");\r
 636     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 637     {\r
 638       public void actionPerformed(ActionEvent e)\r
 639       {\r
 640         colourTextMenuItem_actionPerformed(e);\r
 641       }\r
 642     });\r
 643     htmlMenuItem.setText("HTML");\r
 644     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 645     {\r
 646       public void actionPerformed(ActionEvent e)\r
 647       {\r
 648         htmlMenuItem_actionPerformed(e);\r
 649       }\r
 650     });\r
 651     overviewMenuItem.setText("Overview Window");\r
 652     overviewMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 653         event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 654     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 655     {\r
 656       public void actionPerformed(ActionEvent e)\r
 657       {\r
 658         overviewMenuItem_actionPerformed(e);\r
 659       }\r
 660     });\r
 661     undoMenuItem.setEnabled(false);\r
 662     undoMenuItem.setMnemonic('Z');\r
 663     undoMenuItem.setText("Undo");\r
 664     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 665         java.awt.event.KeyEvent.VK_Z,\r
 666         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 667     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 668     {\r
 669       public void actionPerformed(ActionEvent e)\r
 670       {\r
 671         undoMenuItem_actionPerformed(e);\r
 672       }\r
 673     });\r
 674     redoMenuItem.setEnabled(false);\r
 675     redoMenuItem.setMnemonic('0');\r
 676     redoMenuItem.setText("Redo");\r
 677     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 678         event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 679     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 680     {\r
 681       public void actionPerformed(ActionEvent e)\r
 682       {\r
 683         redoMenuItem_actionPerformed(e);\r
 684       }\r
 685     });\r
 686     conservationMenuItem.setText("By Conservation");\r
 687     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 688     {\r
 689       public void actionPerformed(ActionEvent e)\r
 690       {\r
 691         conservationMenuItem_actionPerformed(e);\r
 692       }\r
 693     });\r
 694     noColourmenuItem.setText("None");\r
 695     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 696     {\r
 697       public void actionPerformed(ActionEvent e)\r
 698       {\r
 699         noColourmenuItem_actionPerformed(e);\r
 700       }\r
 701     });\r
 702     wrapMenuItem.setText("Wrap");\r
 703     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 704     {\r
 705       public void actionPerformed(ActionEvent e)\r
 706       {\r
 707         wrapMenuItem_actionPerformed(e);\r
 708       }\r
 709     });\r
 710     printMenuItem.setText("Print");\r
 711     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 712     {\r
 713       public void actionPerformed(ActionEvent e)\r
 714       {\r
 715         printMenuItem_actionPerformed(e);\r
 716       }\r
 717     });\r
 718     renderGapsMenuItem.setText("Show Gaps");\r
 719     renderGapsMenuItem.setState(true);\r
 720     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 721     {\r
 722       public void actionPerformed(ActionEvent e)\r
 723       {\r
 724         renderGapsMenuItem_actionPerformed(e);\r
 725       }\r
 726     });\r
 727     findMenuItem.setText("Find...");\r
 728     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 729         java.awt.event.KeyEvent.VK_F,\r
 730         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 731     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 732     {\r
 733       public void actionPerformed(ActionEvent e)\r
 734       {\r
 735         findMenuItem_actionPerformed(e);\r
 736       }\r
 737     });\r
 738     searchMenu.setText("Search");\r
 739 \r
 740     abovePIDThreshold.setText("Above Identity Threshold");\r
 741     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 742     {\r
 743       public void actionPerformed(ActionEvent e)\r
 744       {\r
 745         abovePIDThreshold_actionPerformed(e);\r
 746       }\r
 747     });\r
 748     showSeqFeatures.setText("Show Sequence Features");\r
 749     showSeqFeatures.addActionListener(new ActionListener()\r
 750     {\r
 751       public void actionPerformed(ActionEvent actionEvent)\r
 752       {\r
 753         showSeqFeatures_actionPerformed(actionEvent);\r
 754       }\r
 755     });\r
 756     nucleotideColour.setText("Nucleotide");\r
 757     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 758     {\r
 759       public void actionPerformed(ActionEvent e)\r
 760       {\r
 761         nucleotideColour_actionPerformed(e);\r
 762       }\r
 763     });\r
 764     deleteGroups.setText("Undefine groups");\r
 765     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 766         event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 767     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 768     {\r
 769       public void actionPerformed(ActionEvent e)\r
 770       {\r
 771         deleteGroups_actionPerformed(e);\r
 772       }\r
 773     });\r
 774     copy.setText("Copy");\r
 775     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 776         java.awt.event.KeyEvent.VK_C,\r
 777         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 778     copy.setMnemonic(KeyEvent.VK_C);\r
 779 \r
 780     copy.addActionListener(new java.awt.event.ActionListener()\r
 781     {\r
 782       public void actionPerformed(ActionEvent e)\r
 783       {\r
 784         copy_actionPerformed(e);\r
 785       }\r
 786     });\r
 787     cut.setText("Cut");\r
 788     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 789         java.awt.event.KeyEvent.VK_X,\r
 790         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 791     cut.setMnemonic(KeyEvent.VK_X);\r
 792     cut.addActionListener(new java.awt.event.ActionListener()\r
 793     {\r
 794       public void actionPerformed(ActionEvent e)\r
 795       {\r
 796         cut_actionPerformed(e);\r
 797       }\r
 798     });\r
 799     delete.setText("Delete");\r
 800     delete.addActionListener(new java.awt.event.ActionListener()\r
 801     {\r
 802       public void actionPerformed(ActionEvent e)\r
 803       {\r
 804         delete_actionPerformed(e);\r
 805       }\r
 806     });\r
 807     jMenu1.setMnemonic('V');\r
 808     jMenu1.setText("Paste");\r
 809     pasteNew.setText("To New Alignment");\r
 810     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 811         java.awt.event.KeyEvent.VK_V,\r
 812         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 813     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 814     {\r
 815       public void actionPerformed(ActionEvent e)\r
 816       {\r
 817         pasteNew_actionPerformed(e);\r
 818       }\r
 819     });\r
 820     pasteThis.setText("Add To This Alignment");\r
 821     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 822     {\r
 823       public void actionPerformed(ActionEvent e)\r
 824       {\r
 825         pasteThis_actionPerformed(e);\r
 826       }\r
 827     });\r
 828     applyToAllGroups.setText("Apply Colour To All Groups");\r
 829     applyToAllGroups.setState(true);\r
 830     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 831     {\r
 832       public void actionPerformed(ActionEvent e)\r
 833       {\r
 834         applyToAllGroups_actionPerformed(e);\r
 835       }\r
 836     });\r
 837     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 838     {\r
 839       public void actionPerformed(ActionEvent e)\r
 840       {\r
 841         createPNG(null);\r
 842       }\r
 843     });\r
 844     createPNG.setActionCommand("Save As PNG Image");\r
 845     createPNG.setText("PNG");\r
 846     font.setText("Font...");\r
 847     font.addActionListener(new java.awt.event.ActionListener()\r
 848     {\r
 849       public void actionPerformed(ActionEvent e)\r
 850       {\r
 851         font_actionPerformed(e);\r
 852       }\r
 853     });\r
 854 \r
 855     seqLimits.setText("Show Sequence Limits");\r
 856     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 857     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 858     {\r
 859       public void actionPerformed(ActionEvent e)\r
 860       {\r
 861         seqLimit_actionPerformed(e);\r
 862       }\r
 863     });\r
 864     epsFile.setText("EPS");\r
 865     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 866     {\r
 867       public void actionPerformed(ActionEvent e)\r
 868       {\r
 869         createEPS(null);\r
 870       }\r
 871     });\r
 872     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 873     LoadtreeMenuItem.setText("Load Associated Tree");\r
 874     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 875     {\r
 876       public void actionPerformed(ActionEvent e)\r
 877       {\r
 878         LoadtreeMenuItem_actionPerformed(e);\r
 879       }\r
 880     });\r
 881     scaleAbove.setVisible(false);\r
 882     scaleAbove.setText("Scale Above");\r
 883     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 884     {\r
 885       public void actionPerformed(ActionEvent e)\r
 886       {\r
 887         scaleAbove_actionPerformed(e);\r
 888       }\r
 889     });\r
 890     scaleLeft.setVisible(false);\r
 891     scaleLeft.setSelected(true);\r
 892     scaleLeft.setText("Scale Left");\r
 893     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 894     {\r
 895       public void actionPerformed(ActionEvent e)\r
 896       {\r
 897         scaleLeft_actionPerformed(e);\r
 898       }\r
 899     });\r
 900     scaleRight.setVisible(false);\r
 901     scaleRight.setSelected(true);\r
 902     scaleRight.setText("Scale Right");\r
 903     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 904     {\r
 905       public void actionPerformed(ActionEvent e)\r
 906       {\r
 907         scaleRight_actionPerformed(e);\r
 908       }\r
 909     });\r
 910     modifyPID.setText("Modify Identity Threshold...");\r
 911     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 912     {\r
 913       public void actionPerformed(ActionEvent e)\r
 914       {\r
 915         modifyPID_actionPerformed(e);\r
 916       }\r
 917     });\r
 918     modifyConservation.setText("Modify Conservation Threshold...");\r
 919     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 920     {\r
 921       public void actionPerformed(ActionEvent e)\r
 922       {\r
 923         modifyConservation_actionPerformed(e);\r
 924       }\r
 925     });\r
 926     sortByTreeMenu.setText("By Tree Order");\r
 927     sort.setText("Sort");\r
 928     calculate.setText("Calculate Tree");\r
 929 \r
 930     jMenu2.setText("Export");\r
 931     padGapsMenuitem.setText("Pad Gaps");\r
 932     padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 933         event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 934     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 935     padGapsMenuitem.addActionListener(new ActionListener()\r
 936     {\r
 937       public void actionPerformed(ActionEvent e)\r
 938       {\r
 939         padGapsMenuitem_actionPerformed(e);\r
 940       }\r
 941     });\r
 942     vamsasStore.setVisible(false);\r
 943     vamsasStore.setText("VAMSAS store");\r
 944     vamsasStore.addActionListener(new ActionListener()\r
 945     {\r
 946       public void actionPerformed(ActionEvent e)\r
 947       {\r
 948         vamsasStore_actionPerformed(e);\r
 949       }\r
 950     });\r
 951     showTranslation.setText("Translate cDNA");\r
 952     showTranslation.addActionListener(new ActionListener()\r
 953     {\r
 954       public void actionPerformed(ActionEvent e)\r
 955       {\r
 956         showTranslation_actionPerformed(e);\r
 957       }\r
 958     });\r
 959 \r
 960    /* tabbedPane.addChangeListener(new ChangeListener()\r
 961         {\r
 962           public void stateChanged(ChangeEvent ece)\r
 963           {\r
 964 \r
 965             tabSelected();\r
 966           }\r
 967         });*/\r
 968     featureSettings.setText("Feature Settings...");\r
 969     featureSettings.addActionListener(new ActionListener()\r
 970     {\r
 971       public void actionPerformed(ActionEvent e)\r
 972       {\r
 973         featureSettings_actionPerformed(e);\r
 974       }\r
 975     });\r
 976     fetchSequence.setText("Fetch Sequence(s)...");\r
 977     fetchSequence.addActionListener(new ActionListener()\r
 978     {\r
 979       public void actionPerformed(ActionEvent e)\r
 980       {\r
 981         fetchSequence_actionPerformed(e);\r
 982       }\r
 983     });\r
 984     smoothFont.setText("Smooth Fonts");\r
 985     smoothFont.addActionListener(new ActionListener()\r
 986     {\r
 987       public void actionPerformed(ActionEvent e)\r
 988       {\r
 989         smoothFont_actionPerformed(e);\r
 990       }\r
 991     });\r
 992     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 993     annotationColour.setText("By Annotation...");\r
 994     annotationColour.addActionListener(new ActionListener()\r
 995     {\r
 996       public void actionPerformed(ActionEvent e)\r
 997       {\r
 998         annotationColour_actionPerformed(e);\r
 999       }\r
1000     });\r
1001     associatedData.setText("Load Features / Annotations");\r
1002     associatedData.addActionListener(new ActionListener()\r
1003     {\r
1004       public void actionPerformed(ActionEvent e)\r
1005       {\r
1006         associatedData_actionPerformed(e);\r
1007       }\r
1008     });\r
1009     autoCalculate.setText("Autocalculate Consensus");\r
1010     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1011     autoCalculate.addActionListener(new ActionListener()\r
1012     {\r
1013       public void actionPerformed(ActionEvent e)\r
1014       {\r
1015         autoCalculate_actionPerformed(e);\r
1016       }\r
1017     });\r
1018     addSequenceMenu.setText("Add Sequences");\r
1019     addFromFile.setText("From File");\r
1020     addFromFile.addActionListener(new ActionListener()\r
1021     {\r
1022       public void actionPerformed(ActionEvent e)\r
1023       {\r
1024         addFromFile_actionPerformed(e);\r
1025       }\r
1026     });\r
1027     addFromText.setText("From Textbox");\r
1028     addFromText.addActionListener(new ActionListener()\r
1029     {\r
1030       public void actionPerformed(ActionEvent e)\r
1031       {\r
1032         addFromText_actionPerformed(e);\r
1033       }\r
1034     });\r
1035     addFromURL.setText("From URL");\r
1036     addFromURL.addActionListener(new ActionListener()\r
1037     {\r
1038       public void actionPerformed(ActionEvent e)\r
1039       {\r
1040         addFromURL_actionPerformed(e);\r
1041       }\r
1042     });\r
1043     exportFeatures.setText("Export Features...");\r
1044     exportFeatures.addActionListener(new ActionListener()\r
1045     {\r
1046       public void actionPerformed(ActionEvent e)\r
1047       {\r
1048         exportFeatures_actionPerformed(e);\r
1049       }\r
1050     });\r
1051     exportAnnotations.setText("Export Annotations...");\r
1052     exportAnnotations.addActionListener(new ActionListener()\r
1053     {\r
1054       public void actionPerformed(ActionEvent e)\r
1055       {\r
1056         exportAnnotations_actionPerformed(e);\r
1057       }\r
1058     });\r
1059     statusPanel.setLayout(gridLayout1);\r
1060     jMenu3.setText("Show");\r
1061     showAllSeqs.setText("All Sequences");\r
1062     showAllSeqs.addActionListener(new ActionListener()\r
1063     {\r
1064       public void actionPerformed(ActionEvent e)\r
1065       {\r
1066         showAllSeqs_actionPerformed(e);\r
1067       }\r
1068     });\r
1069     showAllColumns.setText("All Columns");\r
1070     showAllColumns.addActionListener(new ActionListener()\r
1071     {\r
1072       public void actionPerformed(ActionEvent e)\r
1073       {\r
1074         showAllColumns_actionPerformed(e);\r
1075       }\r
1076     });\r
1077     hideMenu.setText("Hide");\r
1078     hideSelSequences.setText("Selected Sequences");\r
1079     hideSelSequences.addActionListener(new ActionListener()\r
1080     {\r
1081       public void actionPerformed(ActionEvent e)\r
1082       {\r
1083         hideSelSequences_actionPerformed(e);\r
1084       }\r
1085     });\r
1086     hideSelColumns.setText("Selected Columns");\r
1087     hideSelColumns.addActionListener(new ActionListener()\r
1088     {\r
1089       public void actionPerformed(ActionEvent e)\r
1090       {\r
1091         hideSelColumns_actionPerformed(e);\r
1092       }\r
1093     });\r
1094     hiddenMarkers.setText("Hidden Markers");\r
1095     hiddenMarkers.setState(true);\r
1096     hiddenMarkers.addActionListener(new ActionListener()\r
1097     {\r
1098       public void actionPerformed(ActionEvent e)\r
1099       {\r
1100         hiddenMarkers_actionPerformed(e);\r
1101       }\r
1102     });\r
1103     invertColSel.setText("Invert Column Selection");\r
1104     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1105         event.KeyEvent.VK_C, java.awt.event.KeyEvent.SHIFT_MASK, false));\r
1106     invertColSel.addActionListener(new ActionListener()\r
1107     {\r
1108       public void actionPerformed(ActionEvent e)\r
1109       {\r
1110         invertColSel_actionPerformed(e);\r
1111       }\r
1112     });\r
1113     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1114     {\r
1115         public void stateChanged(ChangeEvent evt)\r
1116         {\r
1117             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1118             int sel = pane.getSelectedIndex();\r
1119             tabSelectionChanged(sel);\r
1120         }\r
1121     });\r
1122     tabbedPane.addMouseListener(new MouseAdapter()\r
1123     {\r
1124       public void mousePressed(MouseEvent e)\r
1125       {\r
1126         tabbedPane_mousePressed(e);\r
1127       }\r
1128     });\r
1129 \r
1130     alignFrameMenuBar.add(fileMenu);\r
1131     alignFrameMenuBar.add(editMenu);\r
1132     alignFrameMenuBar.add(searchMenu);\r
1133     alignFrameMenuBar.add(viewMenu);\r
1134     alignFrameMenuBar.add(colourMenu);\r
1135     alignFrameMenuBar.add(calculateMenu);\r
1136     alignFrameMenuBar.add(webService);\r
1137     fileMenu.add(addSequenceMenu);\r
1138     fileMenu.add(fetchSequence);\r
1139     fileMenu.addSeparator();\r
1140     fileMenu.add(vamsasStore);\r
1141     fileMenu.add(saveAlignmentMenu);\r
1142     fileMenu.add(jMenu2);\r
1143     fileMenu.add(outputTextboxMenu);\r
1144     fileMenu.add(printMenuItem);\r
1145     fileMenu.addSeparator();\r
1146     fileMenu.add(exportFeatures);\r
1147     fileMenu.add(exportAnnotations);\r
1148     fileMenu.add(LoadtreeMenuItem);\r
1149     fileMenu.add(associatedData);\r
1150     fileMenu.addSeparator();\r
1151     fileMenu.add(closeMenuItem);\r
1152     editMenu.add(undoMenuItem);\r
1153     editMenu.add(redoMenuItem);\r
1154     editMenu.add(cut);\r
1155     editMenu.add(copy);\r
1156     editMenu.add(jMenu1);\r
1157     editMenu.add(delete);\r
1158     editMenu.addSeparator();\r
1159     editMenu.add(selectAllSequenceMenuItem);\r
1160     editMenu.add(deselectAllSequenceMenuItem);\r
1161     editMenu.add(invertSequenceMenuItem);\r
1162     editMenu.add(invertColSel);\r
1163     editMenu.add(deleteGroups);\r
1164     editMenu.addSeparator();\r
1165     editMenu.add(remove2LeftMenuItem);\r
1166     editMenu.add(remove2RightMenuItem);\r
1167     editMenu.add(removeGappedColumnMenuItem);\r
1168     editMenu.add(removeAllGapsMenuItem);\r
1169     editMenu.add(removeRedundancyMenuItem);\r
1170     editMenu.addSeparator();\r
1171     editMenu.add(padGapsMenuitem);\r
1172     searchMenu.add(findMenuItem);\r
1173     viewMenu.add(font);\r
1174     viewMenu.add(smoothFont);\r
1175     viewMenu.addSeparator();\r
1176     viewMenu.add(jMenu3);\r
1177     viewMenu.add(hideMenu);\r
1178     viewMenu.add(hiddenMarkers);\r
1179     viewMenu.addSeparator();\r
1180     viewMenu.add(wrapMenuItem);\r
1181     viewMenu.add(seqLimits);\r
1182     viewMenu.add(scaleAbove);\r
1183     viewMenu.add(scaleLeft);\r
1184     viewMenu.add(scaleRight);\r
1185     viewMenu.add(viewBoxesMenuItem);\r
1186     viewMenu.add(viewTextMenuItem);\r
1187     viewMenu.add(colourTextMenuItem);\r
1188     viewMenu.add(renderGapsMenuItem);\r
1189     viewMenu.add(annotationPanelMenuItem);\r
1190     viewMenu.addSeparator();\r
1191     viewMenu.add(showSeqFeatures);\r
1192     viewMenu.add(featureSettings);\r
1193     viewMenu.addSeparator();\r
1194     viewMenu.add(overviewMenuItem);\r
1195     colourMenu.add(applyToAllGroups);\r
1196     colourMenu.addSeparator();\r
1197     colourMenu.add(noColourmenuItem);\r
1198     colourMenu.add(clustalColour);\r
1199     colourMenu.add(BLOSUM62Colour);\r
1200     colourMenu.add(PIDColour);\r
1201     colourMenu.add(zappoColour);\r
1202     colourMenu.add(taylorColour);\r
1203     colourMenu.add(hydrophobicityColour);\r
1204     colourMenu.add(helixColour);\r
1205     colourMenu.add(strandColour);\r
1206     colourMenu.add(turnColour);\r
1207     colourMenu.add(buriedColour);\r
1208     colourMenu.add(nucleotideColour);\r
1209     colourMenu.add(userDefinedColour);\r
1210     colourMenu.addSeparator();\r
1211     colourMenu.add(conservationMenuItem);\r
1212     colourMenu.add(modifyConservation);\r
1213     colourMenu.add(abovePIDThreshold);\r
1214     colourMenu.add(modifyPID);\r
1215     colourMenu.add(annotationColour);\r
1216     calculateMenu.add(sort);\r
1217     calculateMenu.add(calculate);\r
1218     calculateMenu.addSeparator();\r
1219     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1220     calculateMenu.add(PCAMenuItem);\r
1221     calculateMenu.addSeparator();\r
1222     calculateMenu.add(showTranslation);\r
1223     calculateMenu.add(autoCalculate);\r
1224     webServiceNoServices=new JMenuItem("<No Services>");\r
1225     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1226     jMenu1.add(pasteThis);\r
1227     sort.add(sortIDMenuItem);\r
1228     sort.add(sortGroupMenuItem);\r
1229     sort.add(sortPairwiseMenuItem);\r
1230     calculate.add(averageDistanceTreeMenuItem);\r
1231     calculate.add(neighbourTreeMenuItem);\r
1232     calculate.add(avDistanceTreeBlosumMenuItem);\r
1233     calculate.add(njTreeBlosumMenuItem);\r
1234     jMenu2.add(htmlMenuItem);\r
1235     jMenu2.add(epsFile);\r
1236     jMenu2.add(createPNG);\r
1237     addSequenceMenu.add(addFromFile);\r
1238     addSequenceMenu.add(addFromText);\r
1239     addSequenceMenu.add(addFromURL);\r
1240     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1241     statusPanel.add(statusBar, null);\r
1242     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1243     jMenu3.add(showAllColumns);\r
1244     jMenu3.add(showAllSeqs);\r
1245     hideMenu.add(hideSelColumns);\r
1246     hideMenu.add(hideSelSequences);\r
1247   }\r
1248 \r
1249   protected void outputText_actionPerformed(ActionEvent e)\r
1250   {\r
1251   }\r
1252 \r
1253   public void addFromFile_actionPerformed(ActionEvent e)\r
1254   {\r
1255 \r
1256   }\r
1257 \r
1258   public void addFromText_actionPerformed(ActionEvent e)\r
1259   {\r
1260 \r
1261   }\r
1262 \r
1263   public void addFromURL_actionPerformed(ActionEvent e)\r
1264   {\r
1265 \r
1266   }\r
1267 \r
1268   public void exportFeatures_actionPerformed(ActionEvent e)\r
1269   {\r
1270 \r
1271   }\r
1272 \r
1273   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1274   {\r
1275 \r
1276   }\r
1277 \r
1278   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1279   {\r
1280   }\r
1281 \r
1282   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1283   {\r
1284   }\r
1285 \r
1286   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1287   {\r
1288   }\r
1289 \r
1290   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1291   {\r
1292   }\r
1293 \r
1294   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1295   {\r
1296   }\r
1297 \r
1298   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1299   {\r
1300   }\r
1301 \r
1302   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1303   {\r
1304   }\r
1305 \r
1306   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1307   {\r
1308   }\r
1309 \r
1310   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1311   {\r
1312   }\r
1313 \r
1314   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1315   {\r
1316   }\r
1317 \r
1318   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1319   {\r
1320   }\r
1321 \r
1322   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1323   {\r
1324   }\r
1325 \r
1326   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1327   {\r
1328   }\r
1329 \r
1330   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1331   {\r
1332   }\r
1333 \r
1334   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1335   {\r
1336   }\r
1337 \r
1338   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1339   {\r
1340   }\r
1341 \r
1342   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1343   {\r
1344   }\r
1345 \r
1346   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1347   {\r
1348   }\r
1349 \r
1350   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1351   {\r
1352   }\r
1353 \r
1354   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1355   {\r
1356   }\r
1357 \r
1358   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1359   {\r
1360   }\r
1361 \r
1362   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1363   {\r
1364   }\r
1365 \r
1366   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1367   {\r
1368   }\r
1369 \r
1370   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1371   {\r
1372   }\r
1373 \r
1374   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1375   {\r
1376   }\r
1377 \r
1378   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1379   {\r
1380   }\r
1381 \r
1382   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1383   {\r
1384   }\r
1385 \r
1386   protected void clustalColour_actionPerformed(ActionEvent e)\r
1387   {\r
1388   }\r
1389 \r
1390   protected void zappoColour_actionPerformed(ActionEvent e)\r
1391   {\r
1392   }\r
1393 \r
1394   protected void taylorColour_actionPerformed(ActionEvent e)\r
1395   {\r
1396   }\r
1397 \r
1398   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1399   {\r
1400   }\r
1401 \r
1402   protected void helixColour_actionPerformed(ActionEvent e)\r
1403   {\r
1404   }\r
1405 \r
1406   protected void strandColour_actionPerformed(ActionEvent e)\r
1407   {\r
1408   }\r
1409 \r
1410   protected void turnColour_actionPerformed(ActionEvent e)\r
1411   {\r
1412   }\r
1413 \r
1414   protected void buriedColour_actionPerformed(ActionEvent e)\r
1415   {\r
1416   }\r
1417 \r
1418   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1419   {\r
1420   }\r
1421 \r
1422   protected void PIDColour_actionPerformed(ActionEvent e)\r
1423   {\r
1424   }\r
1425 \r
1426   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1427   {\r
1428   }\r
1429 \r
1430   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1431   {\r
1432   }\r
1433 \r
1434   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1435   {\r
1436   }\r
1437 \r
1438   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1439   {\r
1440   }\r
1441 \r
1442   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1443   {\r
1444   }\r
1445 \r
1446   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1447   {\r
1448   }\r
1449 \r
1450   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1451   {\r
1452   }\r
1453 \r
1454   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1455   {\r
1456   }\r
1457 \r
1458   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1459   {\r
1460   }\r
1461 \r
1462   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1463   {\r
1464   }\r
1465 \r
1466   protected void copy_actionPerformed(ActionEvent e)\r
1467   {\r
1468   }\r
1469 \r
1470   protected void cut_actionPerformed(ActionEvent e)\r
1471   {\r
1472   }\r
1473 \r
1474   protected void delete_actionPerformed(ActionEvent e)\r
1475   {\r
1476   }\r
1477 \r
1478   protected void pasteNew_actionPerformed(ActionEvent e)\r
1479   {\r
1480   }\r
1481 \r
1482   protected void pasteThis_actionPerformed(ActionEvent e)\r
1483   {\r
1484   }\r
1485 \r
1486   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1487   {\r
1488   }\r
1489 \r
1490   public void createPNG(java.io.File f)\r
1491   {\r
1492   }\r
1493 \r
1494   protected void font_actionPerformed(ActionEvent e)\r
1495   {\r
1496   }\r
1497 \r
1498   protected void seqLimit_actionPerformed(ActionEvent e)\r
1499   {\r
1500   }\r
1501 \r
1502   public void seqDBRef_actionPerformed(ActionEvent e)\r
1503   {\r
1504 \r
1505   }\r
1506 \r
1507 \r
1508   public void createEPS(java.io.File f)\r
1509   {\r
1510   }\r
1511 \r
1512   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1513   {\r
1514   }\r
1515 \r
1516   protected void jpred_actionPerformed(ActionEvent e)\r
1517   {\r
1518   }\r
1519 \r
1520   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1521   {\r
1522   }\r
1523 \r
1524   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1525   {\r
1526   }\r
1527 \r
1528   protected void scaleRight_actionPerformed(ActionEvent e)\r
1529   {\r
1530   }\r
1531 \r
1532   protected void modifyPID_actionPerformed(ActionEvent e)\r
1533   {\r
1534   }\r
1535 \r
1536   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1537   {\r
1538   }\r
1539 \r
1540 \r
1541 \r
1542   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1543   {\r
1544   }\r
1545 \r
1546   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1547   {\r
1548   }\r
1549 \r
1550 \r
1551   public void vamsasStore_actionPerformed(ActionEvent e)\r
1552   {\r
1553 \r
1554   }\r
1555 \r
1556   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1557   {\r
1558 \r
1559   }\r
1560 \r
1561   public void showTranslation_actionPerformed(ActionEvent e)\r
1562   {\r
1563 \r
1564   }\r
1565 \r
1566   public void featureSettings_actionPerformed(ActionEvent e)\r
1567   {\r
1568 \r
1569   }\r
1570 \r
1571   public void fetchSequence_actionPerformed(ActionEvent e)\r
1572   {\r
1573 \r
1574   }\r
1575 \r
1576   public void smoothFont_actionPerformed(ActionEvent e)\r
1577   {\r
1578 \r
1579   }\r
1580 \r
1581   public void annotationColour_actionPerformed(ActionEvent e)\r
1582   {\r
1583 \r
1584   }\r
1585 \r
1586 \r
1587   public void associatedData_actionPerformed(ActionEvent e)\r
1588   {\r
1589 \r
1590   }\r
1591 \r
1592   public void autoCalculate_actionPerformed(ActionEvent e)\r
1593   {\r
1594 \r
1595   }\r
1596 \r
1597   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1598   {\r
1599 \r
1600   }\r
1601 \r
1602   public void showAllColumns_actionPerformed(ActionEvent e)\r
1603   {\r
1604 \r
1605   }\r
1606 \r
1607   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1608   {\r
1609 \r
1610   }\r
1611 \r
1612   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1613   {\r
1614 \r
1615   }\r
1616 \r
1617   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1618   {\r
1619 \r
1620   }\r
1621 \r
1622   public void findPdbId_actionPerformed(ActionEvent e)\r
1623   {\r
1624 \r
1625   }\r
1626 \r
1627   public void enterPdbId_actionPerformed(ActionEvent e)\r
1628   {\r
1629 \r
1630   }\r
1631 \r
1632   public void pdbFile_actionPerformed(ActionEvent e)\r
1633   {\r
1634 \r
1635   }\r
1636 \r
1637   public void invertColSel_actionPerformed(ActionEvent e)\r
1638   {\r
1639 \r
1640   }\r
1641 \r
1642   public void tabSelectionChanged(int sel)\r
1643   {\r
1644 \r
1645   }\r
1646 \r
1647   public void tabbedPane_mousePressed(MouseEvent e)\r
1648   {\r
1649 \r
1650   }\r
1651 }\r