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.addActionListener(new java.awt.event.ActionListener()\r
 372     {\r
 373       public void actionPerformed(ActionEvent e)\r
 374       {\r
 375         invertSequenceMenuItem_actionPerformed(e);\r
 376       }\r
 377     });\r
 378     remove2LeftMenuItem.setText("Remove Left");\r
 379     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 380     {\r
 381       public void actionPerformed(ActionEvent e)\r
 382       {\r
 383         remove2LeftMenuItem_actionPerformed(e);\r
 384       }\r
 385     });\r
 386     remove2RightMenuItem.setText("Remove Right");\r
 387     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 388     {\r
 389       public void actionPerformed(ActionEvent e)\r
 390       {\r
 391         remove2RightMenuItem_actionPerformed(e);\r
 392       }\r
 393     });\r
 394     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 395     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 396                                                  ActionListener()\r
 397     {\r
 398       public void actionPerformed(ActionEvent e)\r
 399       {\r
 400         removeGappedColumnMenuItem_actionPerformed(e);\r
 401       }\r
 402     });\r
 403     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 404     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 405     {\r
 406       public void actionPerformed(ActionEvent e)\r
 407       {\r
 408         removeAllGapsMenuItem_actionPerformed(e);\r
 409       }\r
 410     });\r
 411     viewBoxesMenuItem.setText("Boxes");\r
 412     viewBoxesMenuItem.setState(true);\r
 413     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 414     {\r
 415       public void actionPerformed(ActionEvent e)\r
 416       {\r
 417         viewBoxesMenuItem_actionPerformed(e);\r
 418       }\r
 419     });\r
 420     viewTextMenuItem.setText("Text");\r
 421     viewTextMenuItem.setState(true);\r
 422     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 423     {\r
 424       public void actionPerformed(ActionEvent e)\r
 425       {\r
 426         viewTextMenuItem_actionPerformed(e);\r
 427       }\r
 428     });\r
 429     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 430     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 431     {\r
 432       public void actionPerformed(ActionEvent e)\r
 433       {\r
 434         sortPairwiseMenuItem_actionPerformed(e);\r
 435       }\r
 436     });\r
 437     sortIDMenuItem.setText("by ID");\r
 438     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 439     {\r
 440       public void actionPerformed(ActionEvent e)\r
 441       {\r
 442         sortIDMenuItem_actionPerformed(e);\r
 443       }\r
 444     });\r
 445     sortGroupMenuItem.setText("by Group");\r
 446     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 447     {\r
 448       public void actionPerformed(ActionEvent e)\r
 449       {\r
 450         sortGroupMenuItem_actionPerformed(e);\r
 451       }\r
 452     });\r
 453     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 454     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 455                                                ActionListener()\r
 456     {\r
 457       public void actionPerformed(ActionEvent e)\r
 458       {\r
 459         removeRedundancyMenuItem_actionPerformed(e);\r
 460       }\r
 461     });\r
 462     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 463     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 464                                                 ActionListener()\r
 465     {\r
 466       public void actionPerformed(ActionEvent e)\r
 467       {\r
 468         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 469       }\r
 470     });\r
 471     PCAMenuItem.setText("Principal Component Analysis");\r
 472     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 473     {\r
 474       public void actionPerformed(ActionEvent e)\r
 475       {\r
 476         PCAMenuItem_actionPerformed(e);\r
 477       }\r
 478     });\r
 479     averageDistanceTreeMenuItem.setText(\r
 480         "Average Distance Using % Identity");\r
 481     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 482                                                   ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         averageDistanceTreeMenuItem_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 490     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         neighbourTreeMenuItem_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     this.getContentPane().setLayout(borderLayout1);\r
 498     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 499     statusBar.setBackground(Color.white);\r
 500     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 501     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 502     statusBar.setText("Status bar");\r
 503     outputTextboxMenu.setMnemonic('T');\r
 504     outputTextboxMenu.setText("Output to Textbox");\r
 505     clustalColour.setText("Clustalx");\r
 506 \r
 507     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 508     {\r
 509       public void actionPerformed(ActionEvent e)\r
 510       {\r
 511         clustalColour_actionPerformed(e);\r
 512       }\r
 513     });\r
 514     zappoColour.setText("Zappo");\r
 515     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 516     {\r
 517       public void actionPerformed(ActionEvent e)\r
 518       {\r
 519         zappoColour_actionPerformed(e);\r
 520       }\r
 521     });\r
 522     taylorColour.setText("Taylor");\r
 523     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 524     {\r
 525       public void actionPerformed(ActionEvent e)\r
 526       {\r
 527         taylorColour_actionPerformed(e);\r
 528       }\r
 529     });\r
 530     hydrophobicityColour.setText("Hydrophobicity");\r
 531     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 532     {\r
 533       public void actionPerformed(ActionEvent e)\r
 534       {\r
 535         hydrophobicityColour_actionPerformed(e);\r
 536       }\r
 537     });\r
 538     helixColour.setText("Helix Propensity");\r
 539     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 540     {\r
 541       public void actionPerformed(ActionEvent e)\r
 542       {\r
 543         helixColour_actionPerformed(e);\r
 544       }\r
 545     });\r
 546     strandColour.setText("Strand Propensity");\r
 547     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 548     {\r
 549       public void actionPerformed(ActionEvent e)\r
 550       {\r
 551         strandColour_actionPerformed(e);\r
 552       }\r
 553     });\r
 554     turnColour.setText("Turn Propensity");\r
 555     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 556     {\r
 557       public void actionPerformed(ActionEvent e)\r
 558       {\r
 559         turnColour_actionPerformed(e);\r
 560       }\r
 561     });\r
 562     buriedColour.setText("Buried Index");\r
 563     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 564     {\r
 565       public void actionPerformed(ActionEvent e)\r
 566       {\r
 567         buriedColour_actionPerformed(e);\r
 568       }\r
 569     });\r
 570     userDefinedColour.setText("User Defined...");\r
 571     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 572     {\r
 573       public void actionPerformed(ActionEvent e)\r
 574       {\r
 575         userDefinedColour_actionPerformed(e);\r
 576       }\r
 577     });\r
 578     PIDColour.setText("Percentage Identity");\r
 579     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent e)\r
 582       {\r
 583         PIDColour_actionPerformed(e);\r
 584       }\r
 585     });\r
 586     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 587     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent e)\r
 590       {\r
 591         BLOSUM62Colour_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     avDistanceTreeBlosumMenuItem.setText(\r
 595         "Average Distance Using BLOSUM62");\r
 596     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 597         ActionListener()\r
 598     {\r
 599       public void actionPerformed(ActionEvent e)\r
 600       {\r
 601         avTreeBlosumMenuItem_actionPerformed(e);\r
 602       }\r
 603     });\r
 604     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 605     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 606     {\r
 607       public void actionPerformed(ActionEvent e)\r
 608       {\r
 609         njTreeBlosumMenuItem_actionPerformed(e);\r
 610       }\r
 611     });\r
 612     annotationPanelMenuItem.setActionCommand("");\r
 613     annotationPanelMenuItem.setText("Show Annotations");\r
 614     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 615     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 616     {\r
 617       public void actionPerformed(ActionEvent e)\r
 618       {\r
 619         annotationPanelMenuItem_actionPerformed(e);\r
 620       }\r
 621     });\r
 622     colourTextMenuItem.setText("Colour Text");\r
 623     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 624     {\r
 625       public void actionPerformed(ActionEvent e)\r
 626       {\r
 627         colourTextMenuItem_actionPerformed(e);\r
 628       }\r
 629     });\r
 630     htmlMenuItem.setText("HTML");\r
 631     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 632     {\r
 633       public void actionPerformed(ActionEvent e)\r
 634       {\r
 635         htmlMenuItem_actionPerformed(e);\r
 636       }\r
 637     });\r
 638     overviewMenuItem.setText("Overview Window");\r
 639     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 640     {\r
 641       public void actionPerformed(ActionEvent e)\r
 642       {\r
 643         overviewMenuItem_actionPerformed(e);\r
 644       }\r
 645     });\r
 646     undoMenuItem.setEnabled(false);\r
 647     undoMenuItem.setMnemonic('Z');\r
 648     undoMenuItem.setText("Undo");\r
 649     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 650         java.awt.event.KeyEvent.VK_Z,\r
 651         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 652     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 653     {\r
 654       public void actionPerformed(ActionEvent e)\r
 655       {\r
 656         undoMenuItem_actionPerformed(e);\r
 657       }\r
 658     });\r
 659     redoMenuItem.setEnabled(false);\r
 660     redoMenuItem.setMnemonic('0');\r
 661     redoMenuItem.setText("Redo");\r
 662     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 663     {\r
 664       public void actionPerformed(ActionEvent e)\r
 665       {\r
 666         redoMenuItem_actionPerformed(e);\r
 667       }\r
 668     });\r
 669     conservationMenuItem.setText("By Conservation");\r
 670     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 671     {\r
 672       public void actionPerformed(ActionEvent e)\r
 673       {\r
 674         conservationMenuItem_actionPerformed(e);\r
 675       }\r
 676     });\r
 677     noColourmenuItem.setText("None");\r
 678     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 679     {\r
 680       public void actionPerformed(ActionEvent e)\r
 681       {\r
 682         noColourmenuItem_actionPerformed(e);\r
 683       }\r
 684     });\r
 685     wrapMenuItem.setText("Wrap");\r
 686     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 687     {\r
 688       public void actionPerformed(ActionEvent e)\r
 689       {\r
 690         wrapMenuItem_actionPerformed(e);\r
 691       }\r
 692     });\r
 693     printMenuItem.setText("Print");\r
 694     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 695     {\r
 696       public void actionPerformed(ActionEvent e)\r
 697       {\r
 698         printMenuItem_actionPerformed(e);\r
 699       }\r
 700     });\r
 701     renderGapsMenuItem.setText("Show Gaps");\r
 702     renderGapsMenuItem.setState(true);\r
 703     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 704     {\r
 705       public void actionPerformed(ActionEvent e)\r
 706       {\r
 707         renderGapsMenuItem_actionPerformed(e);\r
 708       }\r
 709     });\r
 710     findMenuItem.setText("Find...");\r
 711     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 712         java.awt.event.KeyEvent.VK_F,\r
 713         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 714     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 715     {\r
 716       public void actionPerformed(ActionEvent e)\r
 717       {\r
 718         findMenuItem_actionPerformed(e);\r
 719       }\r
 720     });\r
 721     searchMenu.setText("Search");\r
 722 \r
 723     abovePIDThreshold.setText("Above Identity Threshold");\r
 724     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 725     {\r
 726       public void actionPerformed(ActionEvent e)\r
 727       {\r
 728         abovePIDThreshold_actionPerformed(e);\r
 729       }\r
 730     });\r
 731     showSeqFeatures.setText("Show Sequence Features");\r
 732     showSeqFeatures.addActionListener(new ActionListener()\r
 733     {\r
 734       public void actionPerformed(ActionEvent actionEvent)\r
 735       {\r
 736         showSeqFeatures_actionPerformed(actionEvent);\r
 737       }\r
 738     });\r
 739     nucleotideColour.setText("Nucleotide");\r
 740     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 741     {\r
 742       public void actionPerformed(ActionEvent e)\r
 743       {\r
 744         nucleotideColour_actionPerformed(e);\r
 745       }\r
 746     });\r
 747     deleteGroups.setText("Undefine groups");\r
 748     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 749     {\r
 750       public void actionPerformed(ActionEvent e)\r
 751       {\r
 752         deleteGroups_actionPerformed(e);\r
 753       }\r
 754     });\r
 755     copy.setText("Copy");\r
 756     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 757         java.awt.event.KeyEvent.VK_C,\r
 758         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 759     copy.setMnemonic(KeyEvent.VK_C);\r
 760 \r
 761     copy.addActionListener(new java.awt.event.ActionListener()\r
 762     {\r
 763       public void actionPerformed(ActionEvent e)\r
 764       {\r
 765         copy_actionPerformed(e);\r
 766       }\r
 767     });\r
 768     cut.setText("Cut");\r
 769     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 770         java.awt.event.KeyEvent.VK_X,\r
 771         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 772     cut.setMnemonic(KeyEvent.VK_X);\r
 773     cut.addActionListener(new java.awt.event.ActionListener()\r
 774     {\r
 775       public void actionPerformed(ActionEvent e)\r
 776       {\r
 777         cut_actionPerformed(e);\r
 778       }\r
 779     });\r
 780     delete.setText("Delete");\r
 781     delete.addActionListener(new java.awt.event.ActionListener()\r
 782     {\r
 783       public void actionPerformed(ActionEvent e)\r
 784       {\r
 785         delete_actionPerformed(e);\r
 786       }\r
 787     });\r
 788     jMenu1.setMnemonic('V');\r
 789     jMenu1.setText("Paste");\r
 790     pasteNew.setText("To New Alignment");\r
 791     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 792         java.awt.event.KeyEvent.VK_V,\r
 793         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 794     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 795     {\r
 796       public void actionPerformed(ActionEvent e)\r
 797       {\r
 798         pasteNew_actionPerformed(e);\r
 799       }\r
 800     });\r
 801     pasteThis.setText("Add To This Alignment");\r
 802     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 803     {\r
 804       public void actionPerformed(ActionEvent e)\r
 805       {\r
 806         pasteThis_actionPerformed(e);\r
 807       }\r
 808     });\r
 809     applyToAllGroups.setText("Apply Colour To All Groups");\r
 810     applyToAllGroups.setState(true);\r
 811     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 812     {\r
 813       public void actionPerformed(ActionEvent e)\r
 814       {\r
 815         applyToAllGroups_actionPerformed(e);\r
 816       }\r
 817     });\r
 818     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 819     {\r
 820       public void actionPerformed(ActionEvent e)\r
 821       {\r
 822         createPNG(null);\r
 823       }\r
 824     });\r
 825     createPNG.setActionCommand("Save As PNG Image");\r
 826     createPNG.setText("PNG");\r
 827     font.setText("Font...");\r
 828     font.addActionListener(new java.awt.event.ActionListener()\r
 829     {\r
 830       public void actionPerformed(ActionEvent e)\r
 831       {\r
 832         font_actionPerformed(e);\r
 833       }\r
 834     });\r
 835 \r
 836     seqLimits.setText("Show Sequence Limits");\r
 837     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 838     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 839     {\r
 840       public void actionPerformed(ActionEvent e)\r
 841       {\r
 842         seqLimit_actionPerformed(e);\r
 843       }\r
 844     });\r
 845     epsFile.setText("EPS");\r
 846     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 847     {\r
 848       public void actionPerformed(ActionEvent e)\r
 849       {\r
 850         createEPS(null);\r
 851       }\r
 852     });\r
 853     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 854     LoadtreeMenuItem.setText("Load Associated Tree");\r
 855     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 856     {\r
 857       public void actionPerformed(ActionEvent e)\r
 858       {\r
 859         LoadtreeMenuItem_actionPerformed(e);\r
 860       }\r
 861     });\r
 862     scaleAbove.setVisible(false);\r
 863     scaleAbove.setText("Scale Above");\r
 864     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 865     {\r
 866       public void actionPerformed(ActionEvent e)\r
 867       {\r
 868         scaleAbove_actionPerformed(e);\r
 869       }\r
 870     });\r
 871     scaleLeft.setVisible(false);\r
 872     scaleLeft.setSelected(true);\r
 873     scaleLeft.setText("Scale Left");\r
 874     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 875     {\r
 876       public void actionPerformed(ActionEvent e)\r
 877       {\r
 878         scaleLeft_actionPerformed(e);\r
 879       }\r
 880     });\r
 881     scaleRight.setVisible(false);\r
 882     scaleRight.setSelected(true);\r
 883     scaleRight.setText("Scale Right");\r
 884     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 885     {\r
 886       public void actionPerformed(ActionEvent e)\r
 887       {\r
 888         scaleRight_actionPerformed(e);\r
 889       }\r
 890     });\r
 891     modifyPID.setText("Modify Identity Threshold...");\r
 892     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 893     {\r
 894       public void actionPerformed(ActionEvent e)\r
 895       {\r
 896         modifyPID_actionPerformed(e);\r
 897       }\r
 898     });\r
 899     modifyConservation.setText("Modify Conservation Threshold...");\r
 900     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 901     {\r
 902       public void actionPerformed(ActionEvent e)\r
 903       {\r
 904         modifyConservation_actionPerformed(e);\r
 905       }\r
 906     });\r
 907     sortByTreeMenu.setText("By Tree Order");\r
 908     sort.setText("Sort");\r
 909     calculate.setText("Calculate Tree");\r
 910 \r
 911     jMenu2.setText("Export");\r
 912     padGapsMenuitem.setText("Pad Gaps");\r
 913     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 914     padGapsMenuitem.addActionListener(new ActionListener()\r
 915     {\r
 916       public void actionPerformed(ActionEvent e)\r
 917       {\r
 918         padGapsMenuitem_actionPerformed(e);\r
 919       }\r
 920     });\r
 921     vamsasStore.setVisible(false);\r
 922     vamsasStore.setText("VAMSAS store");\r
 923     vamsasStore.addActionListener(new ActionListener()\r
 924     {\r
 925       public void actionPerformed(ActionEvent e)\r
 926       {\r
 927         vamsasStore_actionPerformed(e);\r
 928       }\r
 929     });\r
 930     showTranslation.setText("Translate cDNA");\r
 931     showTranslation.addActionListener(new ActionListener()\r
 932     {\r
 933       public void actionPerformed(ActionEvent e)\r
 934       {\r
 935         showTranslation_actionPerformed(e);\r
 936       }\r
 937     });\r
 938 \r
 939    /* tabbedPane.addChangeListener(new ChangeListener()\r
 940         {\r
 941           public void stateChanged(ChangeEvent ece)\r
 942           {\r
 943 \r
 944             tabSelected();\r
 945           }\r
 946         });*/\r
 947     featureSettings.setText("Feature Settings...");\r
 948     featureSettings.addActionListener(new ActionListener()\r
 949     {\r
 950       public void actionPerformed(ActionEvent e)\r
 951       {\r
 952         featureSettings_actionPerformed(e);\r
 953       }\r
 954     });\r
 955     fetchSequence.setText("Fetch Sequence(s)...");\r
 956     fetchSequence.addActionListener(new ActionListener()\r
 957     {\r
 958       public void actionPerformed(ActionEvent e)\r
 959       {\r
 960         fetchSequence_actionPerformed(e);\r
 961       }\r
 962     });\r
 963     smoothFont.setText("Smooth Fonts");\r
 964     smoothFont.addActionListener(new ActionListener()\r
 965     {\r
 966       public void actionPerformed(ActionEvent e)\r
 967       {\r
 968         smoothFont_actionPerformed(e);\r
 969       }\r
 970     });\r
 971     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 972     annotationColour.setText("By Annotation...");\r
 973     annotationColour.addActionListener(new ActionListener()\r
 974     {\r
 975       public void actionPerformed(ActionEvent e)\r
 976       {\r
 977         annotationColour_actionPerformed(e);\r
 978       }\r
 979     });\r
 980     associatedData.setText("Load Features / Annotations");\r
 981     associatedData.addActionListener(new ActionListener()\r
 982     {\r
 983       public void actionPerformed(ActionEvent e)\r
 984       {\r
 985         associatedData_actionPerformed(e);\r
 986       }\r
 987     });\r
 988     autoCalculate.setText("Autocalculate Consensus");\r
 989     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 990     autoCalculate.addActionListener(new ActionListener()\r
 991     {\r
 992       public void actionPerformed(ActionEvent e)\r
 993       {\r
 994         autoCalculate_actionPerformed(e);\r
 995       }\r
 996     });\r
 997     addSequenceMenu.setText("Add Sequences");\r
 998     addFromFile.setText("From File");\r
 999     addFromFile.addActionListener(new ActionListener()\r
1000     {\r
1001       public void actionPerformed(ActionEvent e)\r
1002       {\r
1003         addFromFile_actionPerformed(e);\r
1004       }\r
1005     });\r
1006     addFromText.setText("From Textbox");\r
1007     addFromText.addActionListener(new ActionListener()\r
1008     {\r
1009       public void actionPerformed(ActionEvent e)\r
1010       {\r
1011         addFromText_actionPerformed(e);\r
1012       }\r
1013     });\r
1014     addFromURL.setText("From URL");\r
1015     addFromURL.addActionListener(new ActionListener()\r
1016     {\r
1017       public void actionPerformed(ActionEvent e)\r
1018       {\r
1019         addFromURL_actionPerformed(e);\r
1020       }\r
1021     });\r
1022     exportFeatures.setText("Export Features...");\r
1023     exportFeatures.addActionListener(new ActionListener()\r
1024     {\r
1025       public void actionPerformed(ActionEvent e)\r
1026       {\r
1027         exportFeatures_actionPerformed(e);\r
1028       }\r
1029     });\r
1030     exportAnnotations.setText("Export Annotations...");\r
1031     exportAnnotations.addActionListener(new ActionListener()\r
1032     {\r
1033       public void actionPerformed(ActionEvent e)\r
1034       {\r
1035         exportAnnotations_actionPerformed(e);\r
1036       }\r
1037     });\r
1038     statusPanel.setLayout(gridLayout1);\r
1039     jMenu3.setText("Show");\r
1040     showAllSeqs.setText("All Sequences");\r
1041     showAllSeqs.addActionListener(new ActionListener()\r
1042     {\r
1043       public void actionPerformed(ActionEvent e)\r
1044       {\r
1045         showAllSeqs_actionPerformed(e);\r
1046       }\r
1047     });\r
1048     showAllColumns.setText("All Columns");\r
1049     showAllColumns.addActionListener(new ActionListener()\r
1050     {\r
1051       public void actionPerformed(ActionEvent e)\r
1052       {\r
1053         showAllColumns_actionPerformed(e);\r
1054       }\r
1055     });\r
1056     hideMenu.setText("Hide");\r
1057     hideSelSequences.setText("Selected Sequences");\r
1058     hideSelSequences.addActionListener(new ActionListener()\r
1059     {\r
1060       public void actionPerformed(ActionEvent e)\r
1061       {\r
1062         hideSelSequences_actionPerformed(e);\r
1063       }\r
1064     });\r
1065     hideSelColumns.setText("Selected Columns");\r
1066     hideSelColumns.addActionListener(new ActionListener()\r
1067     {\r
1068       public void actionPerformed(ActionEvent e)\r
1069       {\r
1070         hideSelColumns_actionPerformed(e);\r
1071       }\r
1072     });\r
1073     hiddenMarkers.setText("Hidden Markers");\r
1074     hiddenMarkers.setState(true);\r
1075     hiddenMarkers.addActionListener(new ActionListener()\r
1076     {\r
1077       public void actionPerformed(ActionEvent e)\r
1078       {\r
1079         hiddenMarkers_actionPerformed(e);\r
1080       }\r
1081     });\r
1082     invertColSel.setText("Invert Column Selection");\r
1083     invertColSel.addActionListener(new ActionListener()\r
1084     {\r
1085       public void actionPerformed(ActionEvent e)\r
1086       {\r
1087         invertColSel_actionPerformed(e);\r
1088       }\r
1089     });\r
1090     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1091     {\r
1092         public void stateChanged(ChangeEvent evt)\r
1093         {\r
1094             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1095             int sel = pane.getSelectedIndex();\r
1096             tabSelectionChanged(sel);\r
1097         }\r
1098     });\r
1099     tabbedPane.addMouseListener(new MouseAdapter()\r
1100     {\r
1101       public void mousePressed(MouseEvent e)\r
1102       {\r
1103         tabbedPane_mousePressed(e);\r
1104       }\r
1105     });\r
1106 \r
1107     alignFrameMenuBar.add(fileMenu);\r
1108     alignFrameMenuBar.add(editMenu);\r
1109     alignFrameMenuBar.add(searchMenu);\r
1110     alignFrameMenuBar.add(viewMenu);\r
1111     alignFrameMenuBar.add(colourMenu);\r
1112     alignFrameMenuBar.add(calculateMenu);\r
1113     alignFrameMenuBar.add(webService);\r
1114     fileMenu.add(addSequenceMenu);\r
1115     fileMenu.add(fetchSequence);\r
1116     fileMenu.addSeparator();\r
1117     fileMenu.add(vamsasStore);\r
1118     fileMenu.add(saveAlignmentMenu);\r
1119     fileMenu.add(jMenu2);\r
1120     fileMenu.add(outputTextboxMenu);\r
1121     fileMenu.add(printMenuItem);\r
1122     fileMenu.addSeparator();\r
1123     fileMenu.add(exportFeatures);\r
1124     fileMenu.add(exportAnnotations);\r
1125     fileMenu.add(LoadtreeMenuItem);\r
1126     fileMenu.add(associatedData);\r
1127     fileMenu.addSeparator();\r
1128     fileMenu.add(closeMenuItem);\r
1129     editMenu.add(undoMenuItem);\r
1130     editMenu.add(redoMenuItem);\r
1131     editMenu.add(cut);\r
1132     editMenu.add(copy);\r
1133     editMenu.add(jMenu1);\r
1134     editMenu.add(delete);\r
1135     editMenu.addSeparator();\r
1136     editMenu.add(selectAllSequenceMenuItem);\r
1137     editMenu.add(deselectAllSequenceMenuItem);\r
1138     editMenu.add(invertSequenceMenuItem);\r
1139     editMenu.add(invertColSel);\r
1140     editMenu.add(deleteGroups);\r
1141     editMenu.addSeparator();\r
1142     editMenu.add(remove2LeftMenuItem);\r
1143     editMenu.add(remove2RightMenuItem);\r
1144     editMenu.add(removeGappedColumnMenuItem);\r
1145     editMenu.add(removeAllGapsMenuItem);\r
1146     editMenu.add(removeRedundancyMenuItem);\r
1147     editMenu.addSeparator();\r
1148     editMenu.add(padGapsMenuitem);\r
1149     searchMenu.add(findMenuItem);\r
1150     viewMenu.add(font);\r
1151     viewMenu.add(smoothFont);\r
1152     viewMenu.addSeparator();\r
1153     viewMenu.add(jMenu3);\r
1154     viewMenu.add(hideMenu);\r
1155     viewMenu.add(hiddenMarkers);\r
1156     viewMenu.addSeparator();\r
1157     viewMenu.add(wrapMenuItem);\r
1158     viewMenu.add(seqLimits);\r
1159     viewMenu.add(scaleAbove);\r
1160     viewMenu.add(scaleLeft);\r
1161     viewMenu.add(scaleRight);\r
1162     viewMenu.add(viewBoxesMenuItem);\r
1163     viewMenu.add(viewTextMenuItem);\r
1164     viewMenu.add(colourTextMenuItem);\r
1165     viewMenu.add(renderGapsMenuItem);\r
1166     viewMenu.add(annotationPanelMenuItem);\r
1167     viewMenu.addSeparator();\r
1168     viewMenu.add(showSeqFeatures);\r
1169     viewMenu.add(featureSettings);\r
1170     viewMenu.addSeparator();\r
1171     viewMenu.add(overviewMenuItem);\r
1172     colourMenu.add(applyToAllGroups);\r
1173     colourMenu.addSeparator();\r
1174     colourMenu.add(noColourmenuItem);\r
1175     colourMenu.add(clustalColour);\r
1176     colourMenu.add(BLOSUM62Colour);\r
1177     colourMenu.add(PIDColour);\r
1178     colourMenu.add(zappoColour);\r
1179     colourMenu.add(taylorColour);\r
1180     colourMenu.add(hydrophobicityColour);\r
1181     colourMenu.add(helixColour);\r
1182     colourMenu.add(strandColour);\r
1183     colourMenu.add(turnColour);\r
1184     colourMenu.add(buriedColour);\r
1185     colourMenu.add(nucleotideColour);\r
1186     colourMenu.add(userDefinedColour);\r
1187     colourMenu.addSeparator();\r
1188     colourMenu.add(conservationMenuItem);\r
1189     colourMenu.add(modifyConservation);\r
1190     colourMenu.add(abovePIDThreshold);\r
1191     colourMenu.add(modifyPID);\r
1192     colourMenu.add(annotationColour);\r
1193     calculateMenu.add(sort);\r
1194     calculateMenu.add(calculate);\r
1195     calculateMenu.addSeparator();\r
1196     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1197     calculateMenu.add(PCAMenuItem);\r
1198     calculateMenu.addSeparator();\r
1199     calculateMenu.add(showTranslation);\r
1200     calculateMenu.add(autoCalculate);\r
1201     webServiceNoServices=new JMenuItem("<No Services>");\r
1202     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1203     jMenu1.add(pasteThis);\r
1204     sort.add(sortIDMenuItem);\r
1205     sort.add(sortGroupMenuItem);\r
1206     sort.add(sortPairwiseMenuItem);\r
1207     calculate.add(averageDistanceTreeMenuItem);\r
1208     calculate.add(neighbourTreeMenuItem);\r
1209     calculate.add(avDistanceTreeBlosumMenuItem);\r
1210     calculate.add(njTreeBlosumMenuItem);\r
1211     jMenu2.add(htmlMenuItem);\r
1212     jMenu2.add(epsFile);\r
1213     jMenu2.add(createPNG);\r
1214     addSequenceMenu.add(addFromFile);\r
1215     addSequenceMenu.add(addFromText);\r
1216     addSequenceMenu.add(addFromURL);\r
1217     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1218     statusPanel.add(statusBar, null);\r
1219     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1220     jMenu3.add(showAllColumns);\r
1221     jMenu3.add(showAllSeqs);\r
1222     hideMenu.add(hideSelColumns);\r
1223     hideMenu.add(hideSelSequences);\r
1224   }\r
1225 \r
1226   protected void outputText_actionPerformed(ActionEvent e)\r
1227   {\r
1228   }\r
1229 \r
1230   public void addFromFile_actionPerformed(ActionEvent e)\r
1231   {\r
1232 \r
1233   }\r
1234 \r
1235   public void addFromText_actionPerformed(ActionEvent e)\r
1236   {\r
1237 \r
1238   }\r
1239 \r
1240   public void addFromURL_actionPerformed(ActionEvent e)\r
1241   {\r
1242 \r
1243   }\r
1244 \r
1245   public void exportFeatures_actionPerformed(ActionEvent e)\r
1246   {\r
1247 \r
1248   }\r
1249 \r
1250   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1251   {\r
1252 \r
1253   }\r
1254 \r
1255   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1256   {\r
1257   }\r
1258 \r
1259   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1260   {\r
1261   }\r
1262 \r
1263   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1264   {\r
1265   }\r
1266 \r
1267   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1268   {\r
1269   }\r
1270 \r
1271   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1272   {\r
1273   }\r
1274 \r
1275   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1276   {\r
1277   }\r
1278 \r
1279   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1280   {\r
1281   }\r
1282 \r
1283   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1284   {\r
1285   }\r
1286 \r
1287   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1288   {\r
1289   }\r
1290 \r
1291   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1292   {\r
1293   }\r
1294 \r
1295   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1296   {\r
1297   }\r
1298 \r
1299   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1300   {\r
1301   }\r
1302 \r
1303   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1304   {\r
1305   }\r
1306 \r
1307   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1308   {\r
1309   }\r
1310 \r
1311   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1312   {\r
1313   }\r
1314 \r
1315   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1316   {\r
1317   }\r
1318 \r
1319   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1320   {\r
1321   }\r
1322 \r
1323   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1324   {\r
1325   }\r
1326 \r
1327   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1328   {\r
1329   }\r
1330 \r
1331   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1332   {\r
1333   }\r
1334 \r
1335   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1336   {\r
1337   }\r
1338 \r
1339   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1340   {\r
1341   }\r
1342 \r
1343   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1344   {\r
1345   }\r
1346 \r
1347   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1348   {\r
1349   }\r
1350 \r
1351   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1352   {\r
1353   }\r
1354 \r
1355   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1356   {\r
1357   }\r
1358 \r
1359   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1360   {\r
1361   }\r
1362 \r
1363   protected void clustalColour_actionPerformed(ActionEvent e)\r
1364   {\r
1365   }\r
1366 \r
1367   protected void zappoColour_actionPerformed(ActionEvent e)\r
1368   {\r
1369   }\r
1370 \r
1371   protected void taylorColour_actionPerformed(ActionEvent e)\r
1372   {\r
1373   }\r
1374 \r
1375   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1376   {\r
1377   }\r
1378 \r
1379   protected void helixColour_actionPerformed(ActionEvent e)\r
1380   {\r
1381   }\r
1382 \r
1383   protected void strandColour_actionPerformed(ActionEvent e)\r
1384   {\r
1385   }\r
1386 \r
1387   protected void turnColour_actionPerformed(ActionEvent e)\r
1388   {\r
1389   }\r
1390 \r
1391   protected void buriedColour_actionPerformed(ActionEvent e)\r
1392   {\r
1393   }\r
1394 \r
1395   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1396   {\r
1397   }\r
1398 \r
1399   protected void PIDColour_actionPerformed(ActionEvent e)\r
1400   {\r
1401   }\r
1402 \r
1403   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1404   {\r
1405   }\r
1406 \r
1407   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1408   {\r
1409   }\r
1410 \r
1411   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1412   {\r
1413   }\r
1414 \r
1415   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1416   {\r
1417   }\r
1418 \r
1419   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1420   {\r
1421   }\r
1422 \r
1423   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1424   {\r
1425   }\r
1426 \r
1427   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1428   {\r
1429   }\r
1430 \r
1431   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1432   {\r
1433   }\r
1434 \r
1435   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1436   {\r
1437   }\r
1438 \r
1439   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1440   {\r
1441   }\r
1442 \r
1443   protected void copy_actionPerformed(ActionEvent e)\r
1444   {\r
1445   }\r
1446 \r
1447   protected void cut_actionPerformed(ActionEvent e)\r
1448   {\r
1449   }\r
1450 \r
1451   protected void delete_actionPerformed(ActionEvent e)\r
1452   {\r
1453   }\r
1454 \r
1455   protected void pasteNew_actionPerformed(ActionEvent e)\r
1456   {\r
1457   }\r
1458 \r
1459   protected void pasteThis_actionPerformed(ActionEvent e)\r
1460   {\r
1461   }\r
1462 \r
1463   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1464   {\r
1465   }\r
1466 \r
1467   public void createPNG(java.io.File f)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void font_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void seqLimit_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   public void seqDBRef_actionPerformed(ActionEvent e)\r
1480   {\r
1481 \r
1482   }\r
1483 \r
1484 \r
1485   public void createEPS(java.io.File f)\r
1486   {\r
1487   }\r
1488 \r
1489   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1490   {\r
1491   }\r
1492 \r
1493   protected void jpred_actionPerformed(ActionEvent e)\r
1494   {\r
1495   }\r
1496 \r
1497   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1498   {\r
1499   }\r
1500 \r
1501   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1502   {\r
1503   }\r
1504 \r
1505   protected void scaleRight_actionPerformed(ActionEvent e)\r
1506   {\r
1507   }\r
1508 \r
1509   protected void modifyPID_actionPerformed(ActionEvent e)\r
1510   {\r
1511   }\r
1512 \r
1513   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1514   {\r
1515   }\r
1516 \r
1517 \r
1518 \r
1519   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1520   {\r
1521   }\r
1522 \r
1523   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1524   {\r
1525   }\r
1526 \r
1527 \r
1528   public void vamsasStore_actionPerformed(ActionEvent e)\r
1529   {\r
1530 \r
1531   }\r
1532 \r
1533   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1534   {\r
1535 \r
1536   }\r
1537 \r
1538   public void showTranslation_actionPerformed(ActionEvent e)\r
1539   {\r
1540 \r
1541   }\r
1542 \r
1543   public void featureSettings_actionPerformed(ActionEvent e)\r
1544   {\r
1545 \r
1546   }\r
1547 \r
1548   public void fetchSequence_actionPerformed(ActionEvent e)\r
1549   {\r
1550 \r
1551   }\r
1552 \r
1553   public void smoothFont_actionPerformed(ActionEvent e)\r
1554   {\r
1555 \r
1556   }\r
1557 \r
1558   public void annotationColour_actionPerformed(ActionEvent e)\r
1559   {\r
1560 \r
1561   }\r
1562 \r
1563 \r
1564   public void associatedData_actionPerformed(ActionEvent e)\r
1565   {\r
1566 \r
1567   }\r
1568 \r
1569   public void autoCalculate_actionPerformed(ActionEvent e)\r
1570   {\r
1571 \r
1572   }\r
1573 \r
1574   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1575   {\r
1576 \r
1577   }\r
1578 \r
1579   public void showAllColumns_actionPerformed(ActionEvent e)\r
1580   {\r
1581 \r
1582   }\r
1583 \r
1584   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1585   {\r
1586 \r
1587   }\r
1588 \r
1589   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1590   {\r
1591 \r
1592   }\r
1593 \r
1594   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1595   {\r
1596 \r
1597   }\r
1598 \r
1599   public void findPdbId_actionPerformed(ActionEvent e)\r
1600   {\r
1601 \r
1602   }\r
1603 \r
1604   public void enterPdbId_actionPerformed(ActionEvent e)\r
1605   {\r
1606 \r
1607   }\r
1608 \r
1609   public void pdbFile_actionPerformed(ActionEvent e)\r
1610   {\r
1611 \r
1612   }\r
1613 \r
1614   public void invertColSel_actionPerformed(ActionEvent e)\r
1615   {\r
1616 \r
1617   }\r
1618 \r
1619   public void tabSelectionChanged(int sel)\r
1620   {\r
1621 \r
1622   }\r
1623 \r
1624   public void tabbedPane_mousePressed(MouseEvent e)\r
1625   {\r
1626 \r
1627   }\r
1628 }\r