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.addActionListener(new java.awt.event.\r
 466                                                ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         removeRedundancyMenuItem_actionPerformed(e);\r
 471       }\r
 472     });\r
 473     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 474     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 475                                                 ActionListener()\r
 476     {\r
 477       public void actionPerformed(ActionEvent e)\r
 478       {\r
 479         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 480       }\r
 481     });\r
 482     PCAMenuItem.setText("Principal Component Analysis");\r
 483     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 484     {\r
 485       public void actionPerformed(ActionEvent e)\r
 486       {\r
 487         PCAMenuItem_actionPerformed(e);\r
 488       }\r
 489     });\r
 490     averageDistanceTreeMenuItem.setText(\r
 491         "Average Distance Using % Identity");\r
 492     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 493                                                   ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         averageDistanceTreeMenuItem_actionPerformed(e);\r
 498       }\r
 499     });\r
 500     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 501     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         neighbourTreeMenuItem_actionPerformed(e);\r
 506       }\r
 507     });\r
 508     this.getContentPane().setLayout(borderLayout1);\r
 509     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 510     statusBar.setBackground(Color.white);\r
 511     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 512     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 513     statusBar.setText("Status bar");\r
 514     outputTextboxMenu.setMnemonic('T');\r
 515     outputTextboxMenu.setText("Output to Textbox");\r
 516     clustalColour.setText("Clustalx");\r
 517 \r
 518     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 519     {\r
 520       public void actionPerformed(ActionEvent e)\r
 521       {\r
 522         clustalColour_actionPerformed(e);\r
 523       }\r
 524     });\r
 525     zappoColour.setText("Zappo");\r
 526     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 527     {\r
 528       public void actionPerformed(ActionEvent e)\r
 529       {\r
 530         zappoColour_actionPerformed(e);\r
 531       }\r
 532     });\r
 533     taylorColour.setText("Taylor");\r
 534     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 535     {\r
 536       public void actionPerformed(ActionEvent e)\r
 537       {\r
 538         taylorColour_actionPerformed(e);\r
 539       }\r
 540     });\r
 541     hydrophobicityColour.setText("Hydrophobicity");\r
 542     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 543     {\r
 544       public void actionPerformed(ActionEvent e)\r
 545       {\r
 546         hydrophobicityColour_actionPerformed(e);\r
 547       }\r
 548     });\r
 549     helixColour.setText("Helix Propensity");\r
 550     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 551     {\r
 552       public void actionPerformed(ActionEvent e)\r
 553       {\r
 554         helixColour_actionPerformed(e);\r
 555       }\r
 556     });\r
 557     strandColour.setText("Strand Propensity");\r
 558     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 559     {\r
 560       public void actionPerformed(ActionEvent e)\r
 561       {\r
 562         strandColour_actionPerformed(e);\r
 563       }\r
 564     });\r
 565     turnColour.setText("Turn Propensity");\r
 566     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 567     {\r
 568       public void actionPerformed(ActionEvent e)\r
 569       {\r
 570         turnColour_actionPerformed(e);\r
 571       }\r
 572     });\r
 573     buriedColour.setText("Buried Index");\r
 574     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         buriedColour_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     userDefinedColour.setText("User Defined...");\r
 582     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 583     {\r
 584       public void actionPerformed(ActionEvent e)\r
 585       {\r
 586         userDefinedColour_actionPerformed(e);\r
 587       }\r
 588     });\r
 589     PIDColour.setText("Percentage Identity");\r
 590     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 591     {\r
 592       public void actionPerformed(ActionEvent e)\r
 593       {\r
 594         PIDColour_actionPerformed(e);\r
 595       }\r
 596     });\r
 597     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 598     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 599     {\r
 600       public void actionPerformed(ActionEvent e)\r
 601       {\r
 602         BLOSUM62Colour_actionPerformed(e);\r
 603       }\r
 604     });\r
 605     avDistanceTreeBlosumMenuItem.setText(\r
 606         "Average Distance Using BLOSUM62");\r
 607     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 608         ActionListener()\r
 609     {\r
 610       public void actionPerformed(ActionEvent e)\r
 611       {\r
 612         avTreeBlosumMenuItem_actionPerformed(e);\r
 613       }\r
 614     });\r
 615     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 616     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 617     {\r
 618       public void actionPerformed(ActionEvent e)\r
 619       {\r
 620         njTreeBlosumMenuItem_actionPerformed(e);\r
 621       }\r
 622     });\r
 623     annotationPanelMenuItem.setActionCommand("");\r
 624     annotationPanelMenuItem.setText("Show Annotations");\r
 625     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 626     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         annotationPanelMenuItem_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     colourTextMenuItem.setText("Colour Text");\r
 634     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 635     {\r
 636       public void actionPerformed(ActionEvent e)\r
 637       {\r
 638         colourTextMenuItem_actionPerformed(e);\r
 639       }\r
 640     });\r
 641     htmlMenuItem.setText("HTML");\r
 642     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 643     {\r
 644       public void actionPerformed(ActionEvent e)\r
 645       {\r
 646         htmlMenuItem_actionPerformed(e);\r
 647       }\r
 648     });\r
 649     overviewMenuItem.setText("Overview Window");\r
 650     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 651     {\r
 652       public void actionPerformed(ActionEvent e)\r
 653       {\r
 654         overviewMenuItem_actionPerformed(e);\r
 655       }\r
 656     });\r
 657     undoMenuItem.setEnabled(false);\r
 658     undoMenuItem.setMnemonic('Z');\r
 659     undoMenuItem.setText("Undo");\r
 660     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 661         java.awt.event.KeyEvent.VK_Z,\r
 662         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 663     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 664     {\r
 665       public void actionPerformed(ActionEvent e)\r
 666       {\r
 667         undoMenuItem_actionPerformed(e);\r
 668       }\r
 669     });\r
 670     redoMenuItem.setEnabled(false);\r
 671     redoMenuItem.setMnemonic('0');\r
 672     redoMenuItem.setText("Redo");\r
 673     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 674         event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 675     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 676     {\r
 677       public void actionPerformed(ActionEvent e)\r
 678       {\r
 679         redoMenuItem_actionPerformed(e);\r
 680       }\r
 681     });\r
 682     conservationMenuItem.setText("By Conservation");\r
 683     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 684     {\r
 685       public void actionPerformed(ActionEvent e)\r
 686       {\r
 687         conservationMenuItem_actionPerformed(e);\r
 688       }\r
 689     });\r
 690     noColourmenuItem.setText("None");\r
 691     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 692     {\r
 693       public void actionPerformed(ActionEvent e)\r
 694       {\r
 695         noColourmenuItem_actionPerformed(e);\r
 696       }\r
 697     });\r
 698     wrapMenuItem.setText("Wrap");\r
 699     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 700     {\r
 701       public void actionPerformed(ActionEvent e)\r
 702       {\r
 703         wrapMenuItem_actionPerformed(e);\r
 704       }\r
 705     });\r
 706     printMenuItem.setText("Print");\r
 707     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 708     {\r
 709       public void actionPerformed(ActionEvent e)\r
 710       {\r
 711         printMenuItem_actionPerformed(e);\r
 712       }\r
 713     });\r
 714     renderGapsMenuItem.setText("Show Gaps");\r
 715     renderGapsMenuItem.setState(true);\r
 716     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 717     {\r
 718       public void actionPerformed(ActionEvent e)\r
 719       {\r
 720         renderGapsMenuItem_actionPerformed(e);\r
 721       }\r
 722     });\r
 723     findMenuItem.setText("Find...");\r
 724     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 725         java.awt.event.KeyEvent.VK_F,\r
 726         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 727     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 728     {\r
 729       public void actionPerformed(ActionEvent e)\r
 730       {\r
 731         findMenuItem_actionPerformed(e);\r
 732       }\r
 733     });\r
 734     searchMenu.setText("Search");\r
 735 \r
 736     abovePIDThreshold.setText("Above Identity Threshold");\r
 737     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 738     {\r
 739       public void actionPerformed(ActionEvent e)\r
 740       {\r
 741         abovePIDThreshold_actionPerformed(e);\r
 742       }\r
 743     });\r
 744     showSeqFeatures.setText("Show Sequence Features");\r
 745     showSeqFeatures.addActionListener(new ActionListener()\r
 746     {\r
 747       public void actionPerformed(ActionEvent actionEvent)\r
 748       {\r
 749         showSeqFeatures_actionPerformed(actionEvent);\r
 750       }\r
 751     });\r
 752     nucleotideColour.setText("Nucleotide");\r
 753     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 754     {\r
 755       public void actionPerformed(ActionEvent e)\r
 756       {\r
 757         nucleotideColour_actionPerformed(e);\r
 758       }\r
 759     });\r
 760     deleteGroups.setText("Undefine groups");\r
 761     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 762     {\r
 763       public void actionPerformed(ActionEvent e)\r
 764       {\r
 765         deleteGroups_actionPerformed(e);\r
 766       }\r
 767     });\r
 768     copy.setText("Copy");\r
 769     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 770         java.awt.event.KeyEvent.VK_C,\r
 771         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 772     copy.setMnemonic(KeyEvent.VK_C);\r
 773 \r
 774     copy.addActionListener(new java.awt.event.ActionListener()\r
 775     {\r
 776       public void actionPerformed(ActionEvent e)\r
 777       {\r
 778         copy_actionPerformed(e);\r
 779       }\r
 780     });\r
 781     cut.setText("Cut");\r
 782     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 783         java.awt.event.KeyEvent.VK_X,\r
 784         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 785     cut.setMnemonic(KeyEvent.VK_X);\r
 786     cut.addActionListener(new java.awt.event.ActionListener()\r
 787     {\r
 788       public void actionPerformed(ActionEvent e)\r
 789       {\r
 790         cut_actionPerformed(e);\r
 791       }\r
 792     });\r
 793     delete.setText("Delete");\r
 794     delete.addActionListener(new java.awt.event.ActionListener()\r
 795     {\r
 796       public void actionPerformed(ActionEvent e)\r
 797       {\r
 798         delete_actionPerformed(e);\r
 799       }\r
 800     });\r
 801     jMenu1.setMnemonic('V');\r
 802     jMenu1.setText("Paste");\r
 803     pasteNew.setText("To New Alignment");\r
 804     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 805         java.awt.event.KeyEvent.VK_V,\r
 806         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 807     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 808     {\r
 809       public void actionPerformed(ActionEvent e)\r
 810       {\r
 811         pasteNew_actionPerformed(e);\r
 812       }\r
 813     });\r
 814     pasteThis.setText("Add To This Alignment");\r
 815     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 816     {\r
 817       public void actionPerformed(ActionEvent e)\r
 818       {\r
 819         pasteThis_actionPerformed(e);\r
 820       }\r
 821     });\r
 822     applyToAllGroups.setText("Apply Colour To All Groups");\r
 823     applyToAllGroups.setState(true);\r
 824     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 825     {\r
 826       public void actionPerformed(ActionEvent e)\r
 827       {\r
 828         applyToAllGroups_actionPerformed(e);\r
 829       }\r
 830     });\r
 831     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 832     {\r
 833       public void actionPerformed(ActionEvent e)\r
 834       {\r
 835         createPNG(null);\r
 836       }\r
 837     });\r
 838     createPNG.setActionCommand("Save As PNG Image");\r
 839     createPNG.setText("PNG");\r
 840     font.setText("Font...");\r
 841     font.addActionListener(new java.awt.event.ActionListener()\r
 842     {\r
 843       public void actionPerformed(ActionEvent e)\r
 844       {\r
 845         font_actionPerformed(e);\r
 846       }\r
 847     });\r
 848 \r
 849     seqLimits.setText("Show Sequence Limits");\r
 850     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 851     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 852     {\r
 853       public void actionPerformed(ActionEvent e)\r
 854       {\r
 855         seqLimit_actionPerformed(e);\r
 856       }\r
 857     });\r
 858     epsFile.setText("EPS");\r
 859     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 860     {\r
 861       public void actionPerformed(ActionEvent e)\r
 862       {\r
 863         createEPS(null);\r
 864       }\r
 865     });\r
 866     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 867     LoadtreeMenuItem.setText("Load Associated Tree");\r
 868     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 869     {\r
 870       public void actionPerformed(ActionEvent e)\r
 871       {\r
 872         LoadtreeMenuItem_actionPerformed(e);\r
 873       }\r
 874     });\r
 875     scaleAbove.setVisible(false);\r
 876     scaleAbove.setText("Scale Above");\r
 877     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 878     {\r
 879       public void actionPerformed(ActionEvent e)\r
 880       {\r
 881         scaleAbove_actionPerformed(e);\r
 882       }\r
 883     });\r
 884     scaleLeft.setVisible(false);\r
 885     scaleLeft.setSelected(true);\r
 886     scaleLeft.setText("Scale Left");\r
 887     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 888     {\r
 889       public void actionPerformed(ActionEvent e)\r
 890       {\r
 891         scaleLeft_actionPerformed(e);\r
 892       }\r
 893     });\r
 894     scaleRight.setVisible(false);\r
 895     scaleRight.setSelected(true);\r
 896     scaleRight.setText("Scale Right");\r
 897     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 898     {\r
 899       public void actionPerformed(ActionEvent e)\r
 900       {\r
 901         scaleRight_actionPerformed(e);\r
 902       }\r
 903     });\r
 904     modifyPID.setText("Modify Identity Threshold...");\r
 905     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 906     {\r
 907       public void actionPerformed(ActionEvent e)\r
 908       {\r
 909         modifyPID_actionPerformed(e);\r
 910       }\r
 911     });\r
 912     modifyConservation.setText("Modify Conservation Threshold...");\r
 913     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 914     {\r
 915       public void actionPerformed(ActionEvent e)\r
 916       {\r
 917         modifyConservation_actionPerformed(e);\r
 918       }\r
 919     });\r
 920     sortByTreeMenu.setText("By Tree Order");\r
 921     sort.setText("Sort");\r
 922     calculate.setText("Calculate Tree");\r
 923 \r
 924     jMenu2.setText("Export");\r
 925     padGapsMenuitem.setText("Pad Gaps");\r
 926     padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 927         event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 928     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 929     padGapsMenuitem.addActionListener(new ActionListener()\r
 930     {\r
 931       public void actionPerformed(ActionEvent e)\r
 932       {\r
 933         padGapsMenuitem_actionPerformed(e);\r
 934       }\r
 935     });\r
 936     vamsasStore.setVisible(false);\r
 937     vamsasStore.setText("VAMSAS store");\r
 938     vamsasStore.addActionListener(new ActionListener()\r
 939     {\r
 940       public void actionPerformed(ActionEvent e)\r
 941       {\r
 942         vamsasStore_actionPerformed(e);\r
 943       }\r
 944     });\r
 945     showTranslation.setText("Translate cDNA");\r
 946     showTranslation.addActionListener(new ActionListener()\r
 947     {\r
 948       public void actionPerformed(ActionEvent e)\r
 949       {\r
 950         showTranslation_actionPerformed(e);\r
 951       }\r
 952     });\r
 953 \r
 954    /* tabbedPane.addChangeListener(new ChangeListener()\r
 955         {\r
 956           public void stateChanged(ChangeEvent ece)\r
 957           {\r
 958 \r
 959             tabSelected();\r
 960           }\r
 961         });*/\r
 962     featureSettings.setText("Feature Settings...");\r
 963     featureSettings.addActionListener(new ActionListener()\r
 964     {\r
 965       public void actionPerformed(ActionEvent e)\r
 966       {\r
 967         featureSettings_actionPerformed(e);\r
 968       }\r
 969     });\r
 970     fetchSequence.setText("Fetch Sequence(s)...");\r
 971     fetchSequence.addActionListener(new ActionListener()\r
 972     {\r
 973       public void actionPerformed(ActionEvent e)\r
 974       {\r
 975         fetchSequence_actionPerformed(e);\r
 976       }\r
 977     });\r
 978     smoothFont.setText("Smooth Fonts");\r
 979     smoothFont.addActionListener(new ActionListener()\r
 980     {\r
 981       public void actionPerformed(ActionEvent e)\r
 982       {\r
 983         smoothFont_actionPerformed(e);\r
 984       }\r
 985     });\r
 986     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 987     annotationColour.setText("By Annotation...");\r
 988     annotationColour.addActionListener(new ActionListener()\r
 989     {\r
 990       public void actionPerformed(ActionEvent e)\r
 991       {\r
 992         annotationColour_actionPerformed(e);\r
 993       }\r
 994     });\r
 995     associatedData.setText("Load Features / Annotations");\r
 996     associatedData.addActionListener(new ActionListener()\r
 997     {\r
 998       public void actionPerformed(ActionEvent e)\r
 999       {\r
1000         associatedData_actionPerformed(e);\r
1001       }\r
1002     });\r
1003     autoCalculate.setText("Autocalculate Consensus");\r
1004     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1005     autoCalculate.addActionListener(new ActionListener()\r
1006     {\r
1007       public void actionPerformed(ActionEvent e)\r
1008       {\r
1009         autoCalculate_actionPerformed(e);\r
1010       }\r
1011     });\r
1012     addSequenceMenu.setText("Add Sequences");\r
1013     addFromFile.setText("From File");\r
1014     addFromFile.addActionListener(new ActionListener()\r
1015     {\r
1016       public void actionPerformed(ActionEvent e)\r
1017       {\r
1018         addFromFile_actionPerformed(e);\r
1019       }\r
1020     });\r
1021     addFromText.setText("From Textbox");\r
1022     addFromText.addActionListener(new ActionListener()\r
1023     {\r
1024       public void actionPerformed(ActionEvent e)\r
1025       {\r
1026         addFromText_actionPerformed(e);\r
1027       }\r
1028     });\r
1029     addFromURL.setText("From URL");\r
1030     addFromURL.addActionListener(new ActionListener()\r
1031     {\r
1032       public void actionPerformed(ActionEvent e)\r
1033       {\r
1034         addFromURL_actionPerformed(e);\r
1035       }\r
1036     });\r
1037     exportFeatures.setText("Export Features...");\r
1038     exportFeatures.addActionListener(new ActionListener()\r
1039     {\r
1040       public void actionPerformed(ActionEvent e)\r
1041       {\r
1042         exportFeatures_actionPerformed(e);\r
1043       }\r
1044     });\r
1045     exportAnnotations.setText("Export Annotations...");\r
1046     exportAnnotations.addActionListener(new ActionListener()\r
1047     {\r
1048       public void actionPerformed(ActionEvent e)\r
1049       {\r
1050         exportAnnotations_actionPerformed(e);\r
1051       }\r
1052     });\r
1053     statusPanel.setLayout(gridLayout1);\r
1054     jMenu3.setText("Show");\r
1055     showAllSeqs.setText("All Sequences");\r
1056     showAllSeqs.addActionListener(new ActionListener()\r
1057     {\r
1058       public void actionPerformed(ActionEvent e)\r
1059       {\r
1060         showAllSeqs_actionPerformed(e);\r
1061       }\r
1062     });\r
1063     showAllColumns.setText("All Columns");\r
1064     showAllColumns.addActionListener(new ActionListener()\r
1065     {\r
1066       public void actionPerformed(ActionEvent e)\r
1067       {\r
1068         showAllColumns_actionPerformed(e);\r
1069       }\r
1070     });\r
1071     hideMenu.setText("Hide");\r
1072     hideSelSequences.setText("Selected Sequences");\r
1073     hideSelSequences.addActionListener(new ActionListener()\r
1074     {\r
1075       public void actionPerformed(ActionEvent e)\r
1076       {\r
1077         hideSelSequences_actionPerformed(e);\r
1078       }\r
1079     });\r
1080     hideSelColumns.setText("Selected Columns");\r
1081     hideSelColumns.addActionListener(new ActionListener()\r
1082     {\r
1083       public void actionPerformed(ActionEvent e)\r
1084       {\r
1085         hideSelColumns_actionPerformed(e);\r
1086       }\r
1087     });\r
1088     hiddenMarkers.setText("Hidden Markers");\r
1089     hiddenMarkers.setState(true);\r
1090     hiddenMarkers.addActionListener(new ActionListener()\r
1091     {\r
1092       public void actionPerformed(ActionEvent e)\r
1093       {\r
1094         hiddenMarkers_actionPerformed(e);\r
1095       }\r
1096     });\r
1097     invertColSel.setText("Invert Column Selection");\r
1098     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1099         event.KeyEvent.VK_C, java.awt.event.KeyEvent.SHIFT_MASK, false));\r
1100     invertColSel.addActionListener(new ActionListener()\r
1101     {\r
1102       public void actionPerformed(ActionEvent e)\r
1103       {\r
1104         invertColSel_actionPerformed(e);\r
1105       }\r
1106     });\r
1107     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1108     {\r
1109         public void stateChanged(ChangeEvent evt)\r
1110         {\r
1111             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1112             int sel = pane.getSelectedIndex();\r
1113             tabSelectionChanged(sel);\r
1114         }\r
1115     });\r
1116     tabbedPane.addMouseListener(new MouseAdapter()\r
1117     {\r
1118       public void mousePressed(MouseEvent e)\r
1119       {\r
1120         tabbedPane_mousePressed(e);\r
1121       }\r
1122     });\r
1123 \r
1124     alignFrameMenuBar.add(fileMenu);\r
1125     alignFrameMenuBar.add(editMenu);\r
1126     alignFrameMenuBar.add(searchMenu);\r
1127     alignFrameMenuBar.add(viewMenu);\r
1128     alignFrameMenuBar.add(colourMenu);\r
1129     alignFrameMenuBar.add(calculateMenu);\r
1130     alignFrameMenuBar.add(webService);\r
1131     fileMenu.add(addSequenceMenu);\r
1132     fileMenu.add(fetchSequence);\r
1133     fileMenu.addSeparator();\r
1134     fileMenu.add(vamsasStore);\r
1135     fileMenu.add(saveAlignmentMenu);\r
1136     fileMenu.add(jMenu2);\r
1137     fileMenu.add(outputTextboxMenu);\r
1138     fileMenu.add(printMenuItem);\r
1139     fileMenu.addSeparator();\r
1140     fileMenu.add(exportFeatures);\r
1141     fileMenu.add(exportAnnotations);\r
1142     fileMenu.add(LoadtreeMenuItem);\r
1143     fileMenu.add(associatedData);\r
1144     fileMenu.addSeparator();\r
1145     fileMenu.add(closeMenuItem);\r
1146     editMenu.add(undoMenuItem);\r
1147     editMenu.add(redoMenuItem);\r
1148     editMenu.add(cut);\r
1149     editMenu.add(copy);\r
1150     editMenu.add(jMenu1);\r
1151     editMenu.add(delete);\r
1152     editMenu.addSeparator();\r
1153     editMenu.add(selectAllSequenceMenuItem);\r
1154     editMenu.add(deselectAllSequenceMenuItem);\r
1155     editMenu.add(invertSequenceMenuItem);\r
1156     editMenu.add(invertColSel);\r
1157     editMenu.add(deleteGroups);\r
1158     editMenu.addSeparator();\r
1159     editMenu.add(remove2LeftMenuItem);\r
1160     editMenu.add(remove2RightMenuItem);\r
1161     editMenu.add(removeGappedColumnMenuItem);\r
1162     editMenu.add(removeAllGapsMenuItem);\r
1163     editMenu.add(removeRedundancyMenuItem);\r
1164     editMenu.addSeparator();\r
1165     editMenu.add(padGapsMenuitem);\r
1166     searchMenu.add(findMenuItem);\r
1167     viewMenu.add(font);\r
1168     viewMenu.add(smoothFont);\r
1169     viewMenu.addSeparator();\r
1170     viewMenu.add(jMenu3);\r
1171     viewMenu.add(hideMenu);\r
1172     viewMenu.add(hiddenMarkers);\r
1173     viewMenu.addSeparator();\r
1174     viewMenu.add(wrapMenuItem);\r
1175     viewMenu.add(seqLimits);\r
1176     viewMenu.add(scaleAbove);\r
1177     viewMenu.add(scaleLeft);\r
1178     viewMenu.add(scaleRight);\r
1179     viewMenu.add(viewBoxesMenuItem);\r
1180     viewMenu.add(viewTextMenuItem);\r
1181     viewMenu.add(colourTextMenuItem);\r
1182     viewMenu.add(renderGapsMenuItem);\r
1183     viewMenu.add(annotationPanelMenuItem);\r
1184     viewMenu.addSeparator();\r
1185     viewMenu.add(showSeqFeatures);\r
1186     viewMenu.add(featureSettings);\r
1187     viewMenu.addSeparator();\r
1188     viewMenu.add(overviewMenuItem);\r
1189     colourMenu.add(applyToAllGroups);\r
1190     colourMenu.addSeparator();\r
1191     colourMenu.add(noColourmenuItem);\r
1192     colourMenu.add(clustalColour);\r
1193     colourMenu.add(BLOSUM62Colour);\r
1194     colourMenu.add(PIDColour);\r
1195     colourMenu.add(zappoColour);\r
1196     colourMenu.add(taylorColour);\r
1197     colourMenu.add(hydrophobicityColour);\r
1198     colourMenu.add(helixColour);\r
1199     colourMenu.add(strandColour);\r
1200     colourMenu.add(turnColour);\r
1201     colourMenu.add(buriedColour);\r
1202     colourMenu.add(nucleotideColour);\r
1203     colourMenu.add(userDefinedColour);\r
1204     colourMenu.addSeparator();\r
1205     colourMenu.add(conservationMenuItem);\r
1206     colourMenu.add(modifyConservation);\r
1207     colourMenu.add(abovePIDThreshold);\r
1208     colourMenu.add(modifyPID);\r
1209     colourMenu.add(annotationColour);\r
1210     calculateMenu.add(sort);\r
1211     calculateMenu.add(calculate);\r
1212     calculateMenu.addSeparator();\r
1213     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1214     calculateMenu.add(PCAMenuItem);\r
1215     calculateMenu.addSeparator();\r
1216     calculateMenu.add(showTranslation);\r
1217     calculateMenu.add(autoCalculate);\r
1218     webServiceNoServices=new JMenuItem("<No Services>");\r
1219     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1220     jMenu1.add(pasteThis);\r
1221     sort.add(sortIDMenuItem);\r
1222     sort.add(sortGroupMenuItem);\r
1223     sort.add(sortPairwiseMenuItem);\r
1224     calculate.add(averageDistanceTreeMenuItem);\r
1225     calculate.add(neighbourTreeMenuItem);\r
1226     calculate.add(avDistanceTreeBlosumMenuItem);\r
1227     calculate.add(njTreeBlosumMenuItem);\r
1228     jMenu2.add(htmlMenuItem);\r
1229     jMenu2.add(epsFile);\r
1230     jMenu2.add(createPNG);\r
1231     addSequenceMenu.add(addFromFile);\r
1232     addSequenceMenu.add(addFromText);\r
1233     addSequenceMenu.add(addFromURL);\r
1234     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1235     statusPanel.add(statusBar, null);\r
1236     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1237     jMenu3.add(showAllColumns);\r
1238     jMenu3.add(showAllSeqs);\r
1239     hideMenu.add(hideSelColumns);\r
1240     hideMenu.add(hideSelSequences);\r
1241   }\r
1242 \r
1243   protected void outputText_actionPerformed(ActionEvent e)\r
1244   {\r
1245   }\r
1246 \r
1247   public void addFromFile_actionPerformed(ActionEvent e)\r
1248   {\r
1249 \r
1250   }\r
1251 \r
1252   public void addFromText_actionPerformed(ActionEvent e)\r
1253   {\r
1254 \r
1255   }\r
1256 \r
1257   public void addFromURL_actionPerformed(ActionEvent e)\r
1258   {\r
1259 \r
1260   }\r
1261 \r
1262   public void exportFeatures_actionPerformed(ActionEvent e)\r
1263   {\r
1264 \r
1265   }\r
1266 \r
1267   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1268   {\r
1269 \r
1270   }\r
1271 \r
1272   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1273   {\r
1274   }\r
1275 \r
1276   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1277   {\r
1278   }\r
1279 \r
1280   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1281   {\r
1282   }\r
1283 \r
1284   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1285   {\r
1286   }\r
1287 \r
1288   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1289   {\r
1290   }\r
1291 \r
1292   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1293   {\r
1294   }\r
1295 \r
1296   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1297   {\r
1298   }\r
1299 \r
1300   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1301   {\r
1302   }\r
1303 \r
1304   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1305   {\r
1306   }\r
1307 \r
1308   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1309   {\r
1310   }\r
1311 \r
1312   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1313   {\r
1314   }\r
1315 \r
1316   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1317   {\r
1318   }\r
1319 \r
1320   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1321   {\r
1322   }\r
1323 \r
1324   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1325   {\r
1326   }\r
1327 \r
1328   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1329   {\r
1330   }\r
1331 \r
1332   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1333   {\r
1334   }\r
1335 \r
1336   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1337   {\r
1338   }\r
1339 \r
1340   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1341   {\r
1342   }\r
1343 \r
1344   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1345   {\r
1346   }\r
1347 \r
1348   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1349   {\r
1350   }\r
1351 \r
1352   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1353   {\r
1354   }\r
1355 \r
1356   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1357   {\r
1358   }\r
1359 \r
1360   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1361   {\r
1362   }\r
1363 \r
1364   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1365   {\r
1366   }\r
1367 \r
1368   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1369   {\r
1370   }\r
1371 \r
1372   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1373   {\r
1374   }\r
1375 \r
1376   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1377   {\r
1378   }\r
1379 \r
1380   protected void clustalColour_actionPerformed(ActionEvent e)\r
1381   {\r
1382   }\r
1383 \r
1384   protected void zappoColour_actionPerformed(ActionEvent e)\r
1385   {\r
1386   }\r
1387 \r
1388   protected void taylorColour_actionPerformed(ActionEvent e)\r
1389   {\r
1390   }\r
1391 \r
1392   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1393   {\r
1394   }\r
1395 \r
1396   protected void helixColour_actionPerformed(ActionEvent e)\r
1397   {\r
1398   }\r
1399 \r
1400   protected void strandColour_actionPerformed(ActionEvent e)\r
1401   {\r
1402   }\r
1403 \r
1404   protected void turnColour_actionPerformed(ActionEvent e)\r
1405   {\r
1406   }\r
1407 \r
1408   protected void buriedColour_actionPerformed(ActionEvent e)\r
1409   {\r
1410   }\r
1411 \r
1412   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1413   {\r
1414   }\r
1415 \r
1416   protected void PIDColour_actionPerformed(ActionEvent e)\r
1417   {\r
1418   }\r
1419 \r
1420   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1421   {\r
1422   }\r
1423 \r
1424   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1425   {\r
1426   }\r
1427 \r
1428   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1429   {\r
1430   }\r
1431 \r
1432   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1433   {\r
1434   }\r
1435 \r
1436   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1437   {\r
1438   }\r
1439 \r
1440   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1441   {\r
1442   }\r
1443 \r
1444   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1445   {\r
1446   }\r
1447 \r
1448   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1449   {\r
1450   }\r
1451 \r
1452   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1453   {\r
1454   }\r
1455 \r
1456   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1457   {\r
1458   }\r
1459 \r
1460   protected void copy_actionPerformed(ActionEvent e)\r
1461   {\r
1462   }\r
1463 \r
1464   protected void cut_actionPerformed(ActionEvent e)\r
1465   {\r
1466   }\r
1467 \r
1468   protected void delete_actionPerformed(ActionEvent e)\r
1469   {\r
1470   }\r
1471 \r
1472   protected void pasteNew_actionPerformed(ActionEvent e)\r
1473   {\r
1474   }\r
1475 \r
1476   protected void pasteThis_actionPerformed(ActionEvent e)\r
1477   {\r
1478   }\r
1479 \r
1480   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1481   {\r
1482   }\r
1483 \r
1484   public void createPNG(java.io.File f)\r
1485   {\r
1486   }\r
1487 \r
1488   protected void font_actionPerformed(ActionEvent e)\r
1489   {\r
1490   }\r
1491 \r
1492   protected void seqLimit_actionPerformed(ActionEvent e)\r
1493   {\r
1494   }\r
1495 \r
1496   public void seqDBRef_actionPerformed(ActionEvent e)\r
1497   {\r
1498 \r
1499   }\r
1500 \r
1501 \r
1502   public void createEPS(java.io.File f)\r
1503   {\r
1504   }\r
1505 \r
1506   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1507   {\r
1508   }\r
1509 \r
1510   protected void jpred_actionPerformed(ActionEvent e)\r
1511   {\r
1512   }\r
1513 \r
1514   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1515   {\r
1516   }\r
1517 \r
1518   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1519   {\r
1520   }\r
1521 \r
1522   protected void scaleRight_actionPerformed(ActionEvent e)\r
1523   {\r
1524   }\r
1525 \r
1526   protected void modifyPID_actionPerformed(ActionEvent e)\r
1527   {\r
1528   }\r
1529 \r
1530   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1531   {\r
1532   }\r
1533 \r
1534 \r
1535 \r
1536   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1537   {\r
1538   }\r
1539 \r
1540   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1541   {\r
1542   }\r
1543 \r
1544 \r
1545   public void vamsasStore_actionPerformed(ActionEvent e)\r
1546   {\r
1547 \r
1548   }\r
1549 \r
1550   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1551   {\r
1552 \r
1553   }\r
1554 \r
1555   public void showTranslation_actionPerformed(ActionEvent e)\r
1556   {\r
1557 \r
1558   }\r
1559 \r
1560   public void featureSettings_actionPerformed(ActionEvent e)\r
1561   {\r
1562 \r
1563   }\r
1564 \r
1565   public void fetchSequence_actionPerformed(ActionEvent e)\r
1566   {\r
1567 \r
1568   }\r
1569 \r
1570   public void smoothFont_actionPerformed(ActionEvent e)\r
1571   {\r
1572 \r
1573   }\r
1574 \r
1575   public void annotationColour_actionPerformed(ActionEvent e)\r
1576   {\r
1577 \r
1578   }\r
1579 \r
1580 \r
1581   public void associatedData_actionPerformed(ActionEvent e)\r
1582   {\r
1583 \r
1584   }\r
1585 \r
1586   public void autoCalculate_actionPerformed(ActionEvent e)\r
1587   {\r
1588 \r
1589   }\r
1590 \r
1591   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1592   {\r
1593 \r
1594   }\r
1595 \r
1596   public void showAllColumns_actionPerformed(ActionEvent e)\r
1597   {\r
1598 \r
1599   }\r
1600 \r
1601   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1602   {\r
1603 \r
1604   }\r
1605 \r
1606   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1607   {\r
1608 \r
1609   }\r
1610 \r
1611   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1612   {\r
1613 \r
1614   }\r
1615 \r
1616   public void findPdbId_actionPerformed(ActionEvent e)\r
1617   {\r
1618 \r
1619   }\r
1620 \r
1621   public void enterPdbId_actionPerformed(ActionEvent e)\r
1622   {\r
1623 \r
1624   }\r
1625 \r
1626   public void pdbFile_actionPerformed(ActionEvent e)\r
1627   {\r
1628 \r
1629   }\r
1630 \r
1631   public void invertColSel_actionPerformed(ActionEvent e)\r
1632   {\r
1633 \r
1634   }\r
1635 \r
1636   public void tabSelectionChanged(int sel)\r
1637   {\r
1638 \r
1639   }\r
1640 \r
1641   public void tabbedPane_mousePressed(MouseEvent e)\r
1642   {\r
1643 \r
1644   }\r
1645 }\r