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   BorderLayout borderLayout1 = new BorderLayout();\r
  62   public JLabel statusBar = new JLabel();\r
  63   protected JMenuItem saveAs = new JMenuItem();\r
  64   protected JMenu outputTextboxMenu = new JMenu();\r
  65   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  69       JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  75   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  76   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  77   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  78   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  79   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  80   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  81   JMenuItem htmlMenuItem = new JMenuItem();\r
  82   JMenuItem overviewMenuItem = new JMenuItem();\r
  83   protected JMenuItem undoMenuItem = new JMenuItem();\r
  84   protected JMenuItem redoMenuItem = new JMenuItem();\r
  85   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  86   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  87   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  88   JMenuItem printMenuItem = new JMenuItem();\r
  89   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  90   JMenuItem findMenuItem = new JMenuItem();\r
  91   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  92   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  93   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  94   JMenuItem deleteGroups = new JMenuItem();\r
  95   JMenuItem delete = new JMenuItem();\r
  96   JMenuItem copy = new JMenuItem();\r
  97   JMenuItem cut = new JMenuItem();\r
  98   JMenu pasteMenu = new JMenu();\r
  99   JMenuItem pasteNew = new JMenuItem();\r
 100   JMenuItem pasteThis = new JMenuItem();\r
 101   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 102   JMenuItem createPNG = new JMenuItem();\r
 103   protected JMenuItem font = new JMenuItem();\r
 104   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 105   JMenuItem epsFile = new JMenuItem();\r
 106   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 107   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 108   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 109   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 110   protected JMenuItem modifyPID = new JMenuItem();\r
 111   protected JMenuItem modifyConservation = new JMenuItem();\r
 112   protected JMenu sortByTreeMenu = new JMenu();\r
 113   protected JMenu sort = new JMenu();\r
 114   JMenu calculate = new JMenu();\r
 115   JMenu jMenu2 = new JMenu();\r
 116   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 117   protected ButtonGroup colours = new ButtonGroup();\r
 118   JMenuItem vamsasStore = new JMenuItem();\r
 119   protected JMenuItem showTranslation = new JMenuItem();\r
 120   public JMenuItem featureSettings = new JMenuItem();\r
 121   JMenuItem fetchSequence = new JMenuItem();\r
 122   JMenuItem annotationColour = new JMenuItem();\r
 123   JMenuItem associatedData = new JMenuItem();\r
 124   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 125   JMenu addSequenceMenu = new JMenu();\r
 126   JMenuItem addFromFile = new JMenuItem();\r
 127   JMenuItem addFromText = new JMenuItem();\r
 128   JMenuItem addFromURL = new JMenuItem();\r
 129   JMenuItem exportAnnotations = new JMenuItem();\r
 130   JMenuItem exportFeatures = new JMenuItem();\r
 131   protected JPanel statusPanel = new JPanel();\r
 132   GridLayout gridLayout1 = new GridLayout();\r
 133   JMenu jMenu3 = new JMenu();\r
 134   JMenuItem showAllSeqs = new JMenuItem();\r
 135   JMenuItem showAllColumns = new JMenuItem();\r
 136   JMenu hideMenu = new JMenu();\r
 137   JMenuItem hideSelSequences = new JMenuItem();\r
 138   JMenuItem hideSelColumns = new JMenuItem();\r
 139   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 140   JMenuItem invertColSel = new JMenuItem();\r
 141   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 142   JMenuItem save = new JMenuItem();\r
 143   JMenuItem jMenuItem1 = new JMenuItem();\r
 144   protected JMenuItem reload = new JMenuItem();\r
 145   JMenuItem newView = new JMenuItem();\r
 146   JMenuItem textColour = new JMenuItem();\r
 147   JMenu jMenu1 = new JMenu();\r
 148   JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();\r
 149   JMenu jMenu4 = new JMenu();\r
 150   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
 151   protected JMenuItem gatherViews = new JMenuItem();\r
 152   protected JMenuItem expandViews = new JMenuItem();\r
 153   public GAlignFrame()\r
 154   {\r
 155     try\r
 156     {\r
 157       jbInit();\r
 158       setJMenuBar(alignFrameMenuBar);\r
 159 \r
 160       // dynamically fill save as menu with available formats\r
 161       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 162       {\r
 163         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 164 \r
 165         item.addActionListener(new java.awt.event.ActionListener()\r
 166         {\r
 167           public void actionPerformed(ActionEvent e)\r
 168           {\r
 169             outputText_actionPerformed(e);\r
 170           }\r
 171         });\r
 172 \r
 173         outputTextboxMenu.add(item);\r
 174       }\r
 175     }\r
 176     catch (Exception e)\r
 177     {\r
 178     }\r
 179 \r
 180     if (!System.getProperty("os.name").startsWith("Mac"))\r
 181     {\r
 182       closeMenuItem.setMnemonic('C');\r
 183       outputTextboxMenu.setMnemonic('T');\r
 184       undoMenuItem.setMnemonic('Z');\r
 185       redoMenuItem.setMnemonic('0');\r
 186       copy.setMnemonic('C');\r
 187       cut.setMnemonic('U');\r
 188       pasteMenu.setMnemonic('P');\r
 189       reload.setMnemonic('R');\r
 190     }\r
 191 \r
 192 \r
 193     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 194     {\r
 195       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 196           getUserColourSchemes().keys();\r
 197 \r
 198       while (userColours.hasMoreElements())\r
 199       {\r
 200         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 201             nextElement().toString());\r
 202         radioItem.setName("USER_DEFINED");\r
 203         radioItem.addMouseListener(new MouseAdapter()\r
 204             {\r
 205               public void mousePressed(MouseEvent evt)\r
 206               {\r
 207                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 208                 {\r
 209                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 210 \r
 211                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 212                       "Remove from default list?",\r
 213                       "Remove user defined colour",\r
 214                       JOptionPane.YES_NO_OPTION);\r
 215                   if(option == JOptionPane.YES_OPTION)\r
 216                   {\r
 217                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 218                     colourMenu.remove(radioItem);\r
 219                   }\r
 220                   else\r
 221                     radioItem.addActionListener(new ActionListener()\r
 222                     {\r
 223                       public void actionPerformed(ActionEvent evt)\r
 224                       {\r
 225                         userDefinedColour_actionPerformed(evt);\r
 226                       }\r
 227                     });\r
 228                 }\r
 229               }\r
 230             });\r
 231         radioItem.addActionListener(new ActionListener()\r
 232         {\r
 233           public void actionPerformed(ActionEvent evt)\r
 234           {\r
 235             userDefinedColour_actionPerformed(evt);\r
 236           }\r
 237         });\r
 238         colourMenu.insert(radioItem, 15);\r
 239         colours.add(radioItem);\r
 240       }\r
 241     }\r
 242     colours.add(noColourmenuItem);\r
 243     colours.add(clustalColour);\r
 244     colours.add(zappoColour);\r
 245     colours.add(taylorColour);\r
 246     colours.add(hydrophobicityColour);\r
 247     colours.add(helixColour);\r
 248     colours.add(strandColour);\r
 249     colours.add(turnColour);\r
 250     colours.add(buriedColour);\r
 251     colours.add(userDefinedColour);\r
 252     colours.add(PIDColour);\r
 253     colours.add(BLOSUM62Colour);\r
 254     colours.add(nucleotideColour);\r
 255 \r
 256     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 257 \r
 258 \r
 259   }\r
 260 \r
 261   public void setColourSelected(String defaultColour)\r
 262   {\r
 263 \r
 264     if (defaultColour != null)\r
 265     {\r
 266       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 267 \r
 268       switch (index)\r
 269       {\r
 270         case ColourSchemeProperty.NONE:\r
 271               noColourmenuItem.setSelected(true);\r
 272               break;\r
 273         case ColourSchemeProperty.CLUSTAL:\r
 274           clustalColour.setSelected(true);\r
 275 \r
 276           break;\r
 277 \r
 278         case ColourSchemeProperty.BLOSUM:\r
 279           BLOSUM62Colour.setSelected(true);\r
 280 \r
 281           break;\r
 282 \r
 283         case ColourSchemeProperty.PID:\r
 284           PIDColour.setSelected(true);\r
 285 \r
 286           break;\r
 287 \r
 288         case ColourSchemeProperty.ZAPPO:\r
 289           zappoColour.setSelected(true);\r
 290 \r
 291           break;\r
 292 \r
 293         case ColourSchemeProperty.TAYLOR:\r
 294           taylorColour.setSelected(true);\r
 295           break;\r
 296 \r
 297         case ColourSchemeProperty.HYDROPHOBIC:\r
 298           hydrophobicityColour.setSelected(true);\r
 299 \r
 300           break;\r
 301 \r
 302         case ColourSchemeProperty.HELIX:\r
 303           helixColour.setSelected(true);\r
 304 \r
 305           break;\r
 306 \r
 307         case ColourSchemeProperty.STRAND:\r
 308           strandColour.setSelected(true);\r
 309 \r
 310           break;\r
 311 \r
 312         case ColourSchemeProperty.TURN:\r
 313           turnColour.setSelected(true);\r
 314 \r
 315           break;\r
 316 \r
 317         case ColourSchemeProperty.BURIED:\r
 318           buriedColour.setSelected(true);\r
 319 \r
 320           break;\r
 321 \r
 322         case ColourSchemeProperty.NUCLEOTIDE:\r
 323           nucleotideColour.setSelected(true);\r
 324 \r
 325           break;\r
 326 \r
 327         case ColourSchemeProperty.USER_DEFINED:\r
 328           userDefinedColour.setSelected(true);\r
 329 \r
 330           break;\r
 331       }\r
 332     }\r
 333 \r
 334   }\r
 335 \r
 336   private void jbInit()\r
 337       throws Exception\r
 338   {\r
 339     fileMenu.setText("File");\r
 340     saveAs.setText("Save As...");\r
 341     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 342         KeyEvent.VK_S,\r
 343         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 344     saveAs.addActionListener(new ActionListener()\r
 345     {\r
 346       public void actionPerformed(ActionEvent e)\r
 347       {\r
 348         saveAs_actionPerformed(e);\r
 349       }\r
 350     });\r
 351     closeMenuItem.setText("Close");\r
 352     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 353         event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 354     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 355     {\r
 356       public void actionPerformed(ActionEvent e)\r
 357       {\r
 358         closeMenuItem_actionPerformed(false);\r
 359       }\r
 360     });\r
 361     editMenu.setText("Edit");\r
 362     viewMenu.setText("View");\r
 363     colourMenu.setText("Colour");\r
 364     calculateMenu.setText("Calculate");\r
 365     webService.setText("Web Service");\r
 366     selectAllSequenceMenuItem.setText("Select All");\r
 367     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 368         java.awt.event.KeyEvent.VK_A,\r
 369         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 370     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 371                                                 ActionListener()\r
 372     {\r
 373       public void actionPerformed(ActionEvent e)\r
 374       {\r
 375         selectAllSequenceMenuItem_actionPerformed(e);\r
 376       }\r
 377     });\r
 378     deselectAllSequenceMenuItem.setText("Deselect All");\r
 379     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 380                                                getKeyStroke(\r
 381         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 382     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 383                                                   ActionListener()\r
 384     {\r
 385       public void actionPerformed(ActionEvent e)\r
 386       {\r
 387         deselectAllSequenceMenuItem_actionPerformed(e);\r
 388       }\r
 389     });\r
 390     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 391     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 392         java.awt.event.KeyEvent.VK_I,\r
 393         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 394     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         invertSequenceMenuItem_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     remove2LeftMenuItem.setText("Remove Left");\r
 402     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 403         awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 404     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 405     {\r
 406       public void actionPerformed(ActionEvent e)\r
 407       {\r
 408         remove2LeftMenuItem_actionPerformed(e);\r
 409       }\r
 410     });\r
 411     remove2RightMenuItem.setText("Remove Right");\r
 412     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 413         awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 414     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 415     {\r
 416       public void actionPerformed(ActionEvent e)\r
 417       {\r
 418         remove2RightMenuItem_actionPerformed(e);\r
 419       }\r
 420     });\r
 421     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 422     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 423                                               getKeyStroke(java.awt.event.\r
 424         KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 425     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 426                                                  ActionListener()\r
 427     {\r
 428       public void actionPerformed(ActionEvent e)\r
 429       {\r
 430         removeGappedColumnMenuItem_actionPerformed(e);\r
 431       }\r
 432     });\r
 433     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 434     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 435         java.awt.event.KeyEvent.VK_E,\r
 436         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 437     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 438     {\r
 439       public void actionPerformed(ActionEvent e)\r
 440       {\r
 441         removeAllGapsMenuItem_actionPerformed(e);\r
 442       }\r
 443     });\r
 444     viewBoxesMenuItem.setText("Boxes");\r
 445     viewBoxesMenuItem.setState(true);\r
 446     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 447     {\r
 448       public void actionPerformed(ActionEvent e)\r
 449       {\r
 450         viewBoxesMenuItem_actionPerformed(e);\r
 451       }\r
 452     });\r
 453     viewTextMenuItem.setText("Text");\r
 454     viewTextMenuItem.setState(true);\r
 455     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 456     {\r
 457       public void actionPerformed(ActionEvent e)\r
 458       {\r
 459         viewTextMenuItem_actionPerformed(e);\r
 460       }\r
 461     });\r
 462     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 463     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 464     {\r
 465       public void actionPerformed(ActionEvent e)\r
 466       {\r
 467         sortPairwiseMenuItem_actionPerformed(e);\r
 468       }\r
 469     });\r
 470     sortIDMenuItem.setText("by ID");\r
 471     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 472     {\r
 473       public void actionPerformed(ActionEvent e)\r
 474       {\r
 475         sortIDMenuItem_actionPerformed(e);\r
 476       }\r
 477     });\r
 478     sortGroupMenuItem.setText("by Group");\r
 479     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 480     {\r
 481       public void actionPerformed(ActionEvent e)\r
 482       {\r
 483         sortGroupMenuItem_actionPerformed(e);\r
 484       }\r
 485     });\r
 486     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 487     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 488         java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 489     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 490                                                ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         removeRedundancyMenuItem_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 498     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 499                                                 ActionListener()\r
 500     {\r
 501       public void actionPerformed(ActionEvent e)\r
 502       {\r
 503         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 504       }\r
 505     });\r
 506     PCAMenuItem.setText("Principal Component Analysis");\r
 507     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 508     {\r
 509       public void actionPerformed(ActionEvent e)\r
 510       {\r
 511         PCAMenuItem_actionPerformed(e);\r
 512       }\r
 513     });\r
 514     averageDistanceTreeMenuItem.setText(\r
 515         "Average Distance Using % Identity");\r
 516     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 517                                                   ActionListener()\r
 518     {\r
 519       public void actionPerformed(ActionEvent e)\r
 520       {\r
 521         averageDistanceTreeMenuItem_actionPerformed(e);\r
 522       }\r
 523     });\r
 524     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 525     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 526     {\r
 527       public void actionPerformed(ActionEvent e)\r
 528       {\r
 529         neighbourTreeMenuItem_actionPerformed(e);\r
 530       }\r
 531     });\r
 532     this.getContentPane().setLayout(borderLayout1);\r
 533     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 534     statusBar.setBackground(Color.white);\r
 535     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 536     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 537     statusBar.setText("Status bar");\r
 538     outputTextboxMenu.setText("Output to Textbox");\r
 539     clustalColour.setText("Clustalx");\r
 540 \r
 541     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 542     {\r
 543       public void actionPerformed(ActionEvent e)\r
 544       {\r
 545         clustalColour_actionPerformed(e);\r
 546       }\r
 547     });\r
 548     zappoColour.setText("Zappo");\r
 549     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 550     {\r
 551       public void actionPerformed(ActionEvent e)\r
 552       {\r
 553         zappoColour_actionPerformed(e);\r
 554       }\r
 555     });\r
 556     taylorColour.setText("Taylor");\r
 557     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 558     {\r
 559       public void actionPerformed(ActionEvent e)\r
 560       {\r
 561         taylorColour_actionPerformed(e);\r
 562       }\r
 563     });\r
 564     hydrophobicityColour.setText("Hydrophobicity");\r
 565     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 566     {\r
 567       public void actionPerformed(ActionEvent e)\r
 568       {\r
 569         hydrophobicityColour_actionPerformed(e);\r
 570       }\r
 571     });\r
 572     helixColour.setText("Helix Propensity");\r
 573     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 574     {\r
 575       public void actionPerformed(ActionEvent e)\r
 576       {\r
 577         helixColour_actionPerformed(e);\r
 578       }\r
 579     });\r
 580     strandColour.setText("Strand Propensity");\r
 581     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 582     {\r
 583       public void actionPerformed(ActionEvent e)\r
 584       {\r
 585         strandColour_actionPerformed(e);\r
 586       }\r
 587     });\r
 588     turnColour.setText("Turn Propensity");\r
 589     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 590     {\r
 591       public void actionPerformed(ActionEvent e)\r
 592       {\r
 593         turnColour_actionPerformed(e);\r
 594       }\r
 595     });\r
 596     buriedColour.setText("Buried Index");\r
 597     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 598     {\r
 599       public void actionPerformed(ActionEvent e)\r
 600       {\r
 601         buriedColour_actionPerformed(e);\r
 602       }\r
 603     });\r
 604     userDefinedColour.setText("User Defined...");\r
 605     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 606     {\r
 607       public void actionPerformed(ActionEvent e)\r
 608       {\r
 609         userDefinedColour_actionPerformed(e);\r
 610       }\r
 611     });\r
 612     PIDColour.setText("Percentage Identity");\r
 613     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 614     {\r
 615       public void actionPerformed(ActionEvent e)\r
 616       {\r
 617         PIDColour_actionPerformed(e);\r
 618       }\r
 619     });\r
 620     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 621     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 622     {\r
 623       public void actionPerformed(ActionEvent e)\r
 624       {\r
 625         BLOSUM62Colour_actionPerformed(e);\r
 626       }\r
 627     });\r
 628     avDistanceTreeBlosumMenuItem.setText(\r
 629         "Average Distance Using BLOSUM62");\r
 630     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 631         ActionListener()\r
 632     {\r
 633       public void actionPerformed(ActionEvent e)\r
 634       {\r
 635         avTreeBlosumMenuItem_actionPerformed(e);\r
 636       }\r
 637     });\r
 638     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 639     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 640     {\r
 641       public void actionPerformed(ActionEvent e)\r
 642       {\r
 643         njTreeBlosumMenuItem_actionPerformed(e);\r
 644       }\r
 645     });\r
 646     annotationPanelMenuItem.setActionCommand("");\r
 647     annotationPanelMenuItem.setText("Show Annotations");\r
 648     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 649     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 650     {\r
 651       public void actionPerformed(ActionEvent e)\r
 652       {\r
 653         annotationPanelMenuItem_actionPerformed(e);\r
 654       }\r
 655     });\r
 656     colourTextMenuItem.setText("Colour Text");\r
 657     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 658     {\r
 659       public void actionPerformed(ActionEvent e)\r
 660       {\r
 661         colourTextMenuItem_actionPerformed(e);\r
 662       }\r
 663     });\r
 664     htmlMenuItem.setText("HTML");\r
 665     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 666     {\r
 667       public void actionPerformed(ActionEvent e)\r
 668       {\r
 669         htmlMenuItem_actionPerformed(e);\r
 670       }\r
 671     });\r
 672     overviewMenuItem.setText("Overview Window");\r
 673     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 674     {\r
 675       public void actionPerformed(ActionEvent e)\r
 676       {\r
 677         overviewMenuItem_actionPerformed(e);\r
 678       }\r
 679     });\r
 680     undoMenuItem.setEnabled(false);\r
 681     undoMenuItem.setText("Undo");\r
 682     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 683         java.awt.event.KeyEvent.VK_Z,\r
 684         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 685     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 686     {\r
 687       public void actionPerformed(ActionEvent e)\r
 688       {\r
 689         undoMenuItem_actionPerformed(e);\r
 690       }\r
 691     });\r
 692     redoMenuItem.setEnabled(false);\r
 693     redoMenuItem.setText("Redo");\r
 694     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 695         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 696     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 697     {\r
 698       public void actionPerformed(ActionEvent e)\r
 699       {\r
 700         redoMenuItem_actionPerformed(e);\r
 701       }\r
 702     });\r
 703     conservationMenuItem.setText("By Conservation");\r
 704     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 705     {\r
 706       public void actionPerformed(ActionEvent e)\r
 707       {\r
 708         conservationMenuItem_actionPerformed(e);\r
 709       }\r
 710     });\r
 711     noColourmenuItem.setText("None");\r
 712     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 713     {\r
 714       public void actionPerformed(ActionEvent e)\r
 715       {\r
 716         noColourmenuItem_actionPerformed(e);\r
 717       }\r
 718     });\r
 719     wrapMenuItem.setText("Wrap");\r
 720     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 721     {\r
 722       public void actionPerformed(ActionEvent e)\r
 723       {\r
 724         wrapMenuItem_actionPerformed(e);\r
 725       }\r
 726     });\r
 727     printMenuItem.setText("Print");\r
 728     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 729         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 730     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 731     {\r
 732       public void actionPerformed(ActionEvent e)\r
 733       {\r
 734         printMenuItem_actionPerformed(e);\r
 735       }\r
 736     });\r
 737     renderGapsMenuItem.setText("Show Gaps");\r
 738     renderGapsMenuItem.setState(true);\r
 739     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 740     {\r
 741       public void actionPerformed(ActionEvent e)\r
 742       {\r
 743         renderGapsMenuItem_actionPerformed(e);\r
 744       }\r
 745     });\r
 746     findMenuItem.setText("Find...");\r
 747     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 748         java.awt.event.KeyEvent.VK_F,\r
 749         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 750     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 751     {\r
 752       public void actionPerformed(ActionEvent e)\r
 753       {\r
 754         findMenuItem_actionPerformed(e);\r
 755       }\r
 756     });\r
 757     abovePIDThreshold.setText("Above Identity Threshold");\r
 758     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 759     {\r
 760       public void actionPerformed(ActionEvent e)\r
 761       {\r
 762         abovePIDThreshold_actionPerformed(e);\r
 763       }\r
 764     });\r
 765     showSeqFeatures.setText("Show Sequence Features");\r
 766     showSeqFeatures.addActionListener(new ActionListener()\r
 767     {\r
 768       public void actionPerformed(ActionEvent actionEvent)\r
 769       {\r
 770         showSeqFeatures_actionPerformed(actionEvent);\r
 771       }\r
 772     });\r
 773     nucleotideColour.setText("Nucleotide");\r
 774     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 775     {\r
 776       public void actionPerformed(ActionEvent e)\r
 777       {\r
 778         nucleotideColour_actionPerformed(e);\r
 779       }\r
 780     });\r
 781     deleteGroups.setText("Undefine groups");\r
 782     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 783         event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 784     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 785     {\r
 786       public void actionPerformed(ActionEvent e)\r
 787       {\r
 788         deleteGroups_actionPerformed(e);\r
 789       }\r
 790     });\r
 791     copy.setText("Copy");\r
 792     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 793         java.awt.event.KeyEvent.VK_C,\r
 794         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 795 \r
 796     copy.addActionListener(new java.awt.event.ActionListener()\r
 797     {\r
 798       public void actionPerformed(ActionEvent e)\r
 799       {\r
 800         copy_actionPerformed(e);\r
 801       }\r
 802     });\r
 803     cut.setText("Cut");\r
 804     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 805         java.awt.event.KeyEvent.VK_X,\r
 806         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 807     cut.addActionListener(new java.awt.event.ActionListener()\r
 808     {\r
 809       public void actionPerformed(ActionEvent e)\r
 810       {\r
 811         cut_actionPerformed(e);\r
 812       }\r
 813     });\r
 814     delete.setText("Delete");\r
 815     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 816         KeyEvent.VK_BACK_SPACE, 0, false));\r
 817     delete.addActionListener(new java.awt.event.ActionListener()\r
 818     {\r
 819       public void actionPerformed(ActionEvent e)\r
 820       {\r
 821         delete_actionPerformed(e);\r
 822       }\r
 823     });\r
 824     pasteMenu.setText("Paste");\r
 825     pasteNew.setText("To New Alignment");\r
 826     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 827         java.awt.event.KeyEvent.VK_V,\r
 828         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 829     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 830     {\r
 831       public void actionPerformed(ActionEvent e)\r
 832       {\r
 833         pasteNew_actionPerformed(e);\r
 834       }\r
 835     });\r
 836     pasteThis.setText("Add To This Alignment");\r
 837     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 838         java.awt.event.KeyEvent.VK_V,\r
 839         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 840     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 841     {\r
 842       public void actionPerformed(ActionEvent e)\r
 843       {\r
 844         pasteThis_actionPerformed(e);\r
 845       }\r
 846     });\r
 847     applyToAllGroups.setText("Apply Colour To All Groups");\r
 848     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 849     {\r
 850       public void actionPerformed(ActionEvent e)\r
 851       {\r
 852         applyToAllGroups_actionPerformed(e);\r
 853       }\r
 854     });\r
 855     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 856     {\r
 857       public void actionPerformed(ActionEvent e)\r
 858       {\r
 859         createPNG(null);\r
 860       }\r
 861     });\r
 862     createPNG.setActionCommand("Save As PNG Image");\r
 863     createPNG.setText("PNG");\r
 864     font.setText("Font...");\r
 865     font.addActionListener(new java.awt.event.ActionListener()\r
 866     {\r
 867       public void actionPerformed(ActionEvent e)\r
 868       {\r
 869         font_actionPerformed(e);\r
 870       }\r
 871     });\r
 872 \r
 873     seqLimits.setText("Show Sequence Limits");\r
 874     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 875     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 876     {\r
 877       public void actionPerformed(ActionEvent e)\r
 878       {\r
 879         seqLimit_actionPerformed(e);\r
 880       }\r
 881     });\r
 882     epsFile.setText("EPS");\r
 883     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 884     {\r
 885       public void actionPerformed(ActionEvent e)\r
 886       {\r
 887         createEPS(null);\r
 888       }\r
 889     });\r
 890     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 891     LoadtreeMenuItem.setText("Load Associated Tree");\r
 892     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 893     {\r
 894       public void actionPerformed(ActionEvent e)\r
 895       {\r
 896         LoadtreeMenuItem_actionPerformed(e);\r
 897       }\r
 898     });\r
 899     scaleAbove.setVisible(false);\r
 900     scaleAbove.setText("Scale Above");\r
 901     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 902     {\r
 903       public void actionPerformed(ActionEvent e)\r
 904       {\r
 905         scaleAbove_actionPerformed(e);\r
 906       }\r
 907     });\r
 908     scaleLeft.setVisible(false);\r
 909     scaleLeft.setSelected(true);\r
 910     scaleLeft.setText("Scale Left");\r
 911     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 912     {\r
 913       public void actionPerformed(ActionEvent e)\r
 914       {\r
 915         scaleLeft_actionPerformed(e);\r
 916       }\r
 917     });\r
 918     scaleRight.setVisible(false);\r
 919     scaleRight.setSelected(true);\r
 920     scaleRight.setText("Scale Right");\r
 921     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 922     {\r
 923       public void actionPerformed(ActionEvent e)\r
 924       {\r
 925         scaleRight_actionPerformed(e);\r
 926       }\r
 927     });\r
 928     modifyPID.setText("Modify Identity Threshold...");\r
 929     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 930     {\r
 931       public void actionPerformed(ActionEvent e)\r
 932       {\r
 933         modifyPID_actionPerformed(e);\r
 934       }\r
 935     });\r
 936     modifyConservation.setText("Modify Conservation Threshold...");\r
 937     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 938     {\r
 939       public void actionPerformed(ActionEvent e)\r
 940       {\r
 941         modifyConservation_actionPerformed(e);\r
 942       }\r
 943     });\r
 944     sortByTreeMenu.setText("By Tree Order");\r
 945     sort.setText("Sort");\r
 946     calculate.setText("Calculate Tree");\r
 947 \r
 948     jMenu2.setText("Export Image");\r
 949     padGapsMenuitem.setText("Pad Gaps");\r
 950     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 951     padGapsMenuitem.addActionListener(new ActionListener()\r
 952     {\r
 953       public void actionPerformed(ActionEvent e)\r
 954       {\r
 955         padGapsMenuitem_actionPerformed(e);\r
 956       }\r
 957     });\r
 958     vamsasStore.setVisible(false);\r
 959     vamsasStore.setText("VAMSAS store");\r
 960     vamsasStore.addActionListener(new ActionListener()\r
 961     {\r
 962       public void actionPerformed(ActionEvent e)\r
 963       {\r
 964         vamsasStore_actionPerformed(e);\r
 965       }\r
 966     });\r
 967     showTranslation.setText("Translate cDNA");\r
 968     showTranslation.addActionListener(new ActionListener()\r
 969     {\r
 970       public void actionPerformed(ActionEvent e)\r
 971       {\r
 972         showTranslation_actionPerformed(e);\r
 973       }\r
 974     });\r
 975 \r
 976 \r
 977     featureSettings.setText("Feature Settings...");\r
 978     featureSettings.addActionListener(new ActionListener()\r
 979     {\r
 980       public void actionPerformed(ActionEvent e)\r
 981       {\r
 982         featureSettings_actionPerformed(e);\r
 983       }\r
 984     });\r
 985     fetchSequence.setText("Fetch Sequence(s)...");\r
 986     fetchSequence.addActionListener(new ActionListener()\r
 987     {\r
 988       public void actionPerformed(ActionEvent e)\r
 989       {\r
 990         fetchSequence_actionPerformed(e);\r
 991       }\r
 992     });\r
 993 \r
 994     annotationColour.setText("By Annotation...");\r
 995     annotationColour.addActionListener(new ActionListener()\r
 996     {\r
 997       public void actionPerformed(ActionEvent e)\r
 998       {\r
 999         annotationColour_actionPerformed(e);\r
1000       }\r
1001     });\r
1002     associatedData.setText("Load Features / Annotations");\r
1003     associatedData.addActionListener(new ActionListener()\r
1004     {\r
1005       public void actionPerformed(ActionEvent e)\r
1006       {\r
1007         associatedData_actionPerformed(e);\r
1008       }\r
1009     });\r
1010     autoCalculate.setText("Autocalculate Consensus");\r
1011     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1012     autoCalculate.addActionListener(new ActionListener()\r
1013     {\r
1014       public void actionPerformed(ActionEvent e)\r
1015       {\r
1016         autoCalculate_actionPerformed(e);\r
1017       }\r
1018     });\r
1019     addSequenceMenu.setText("Add Sequences");\r
1020     addFromFile.setText("From File");\r
1021     addFromFile.addActionListener(new ActionListener()\r
1022     {\r
1023       public void actionPerformed(ActionEvent e)\r
1024       {\r
1025         addFromFile_actionPerformed(e);\r
1026       }\r
1027     });\r
1028     addFromText.setText("From Textbox");\r
1029     addFromText.addActionListener(new ActionListener()\r
1030     {\r
1031       public void actionPerformed(ActionEvent e)\r
1032       {\r
1033         addFromText_actionPerformed(e);\r
1034       }\r
1035     });\r
1036     addFromURL.setText("From URL");\r
1037     addFromURL.addActionListener(new ActionListener()\r
1038     {\r
1039       public void actionPerformed(ActionEvent e)\r
1040       {\r
1041         addFromURL_actionPerformed(e);\r
1042       }\r
1043     });\r
1044     exportFeatures.setText("Export Features...");\r
1045     exportFeatures.addActionListener(new ActionListener()\r
1046     {\r
1047       public void actionPerformed(ActionEvent e)\r
1048       {\r
1049         exportFeatures_actionPerformed(e);\r
1050       }\r
1051     });\r
1052     exportAnnotations.setText("Export Annotations...");\r
1053     exportAnnotations.addActionListener(new ActionListener()\r
1054     {\r
1055       public void actionPerformed(ActionEvent e)\r
1056       {\r
1057         exportAnnotations_actionPerformed(e);\r
1058       }\r
1059     });\r
1060     statusPanel.setLayout(gridLayout1);\r
1061     jMenu3.setText("Show");\r
1062     showAllSeqs.setText("All Sequences");\r
1063     showAllSeqs.addActionListener(new ActionListener()\r
1064     {\r
1065       public void actionPerformed(ActionEvent e)\r
1066       {\r
1067         showAllSeqs_actionPerformed(e);\r
1068       }\r
1069     });\r
1070     showAllColumns.setText("All Columns");\r
1071     showAllColumns.addActionListener(new ActionListener()\r
1072     {\r
1073       public void actionPerformed(ActionEvent e)\r
1074       {\r
1075         showAllColumns_actionPerformed(e);\r
1076       }\r
1077     });\r
1078     hideMenu.setText("Hide");\r
1079     hideSelSequences.setText("Selected Sequences");\r
1080     hideSelSequences.addActionListener(new ActionListener()\r
1081     {\r
1082       public void actionPerformed(ActionEvent e)\r
1083       {\r
1084         hideSelSequences_actionPerformed(e);\r
1085       }\r
1086     });\r
1087     hideSelColumns.setText("Selected Columns");\r
1088     hideSelColumns.addActionListener(new ActionListener()\r
1089     {\r
1090       public void actionPerformed(ActionEvent e)\r
1091       {\r
1092         hideSelColumns_actionPerformed(e);\r
1093       }\r
1094     });\r
1095     hiddenMarkers.setText("Show Hidden Markers");\r
1096     hiddenMarkers.addActionListener(new ActionListener()\r
1097     {\r
1098       public void actionPerformed(ActionEvent e)\r
1099       {\r
1100         hiddenMarkers_actionPerformed(e);\r
1101       }\r
1102     });\r
1103     invertColSel.setText("Invert Column Selection");\r
1104     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1105         event.KeyEvent.VK_I,\r
1106         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
1107         |java.awt.event.KeyEvent.ALT_MASK,\r
1108         false));\r
1109     invertColSel.addActionListener(new ActionListener()\r
1110     {\r
1111       public void actionPerformed(ActionEvent e)\r
1112       {\r
1113         invertColSel_actionPerformed(e);\r
1114       }\r
1115     });\r
1116     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1117     {\r
1118         public void stateChanged(ChangeEvent evt)\r
1119         {\r
1120             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1121             int sel = pane.getSelectedIndex();\r
1122             tabSelectionChanged(sel);\r
1123         }\r
1124     });\r
1125     tabbedPane.addMouseListener(new MouseAdapter()\r
1126     {\r
1127       public void mousePressed(MouseEvent e)\r
1128       {\r
1129         tabbedPane_mousePressed(e);\r
1130       }\r
1131     });\r
1132     tabbedPane.addFocusListener(new FocusAdapter()\r
1133     {\r
1134       public void focusGained(FocusEvent e)\r
1135       {\r
1136         tabbedPane_focusGained(e);\r
1137       }\r
1138     });\r
1139     save.setText("Save");\r
1140     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1141         KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1142     save.addActionListener(new ActionListener()\r
1143     {\r
1144       public void actionPerformed(ActionEvent e)\r
1145       {\r
1146         save_actionPerformed(e);\r
1147       }\r
1148     });\r
1149     reload.setEnabled(false);\r
1150     reload.setText("Reload");\r
1151     reload.addActionListener(new ActionListener()\r
1152     {\r
1153       public void actionPerformed(ActionEvent e)\r
1154       {\r
1155         reload_actionPerformed(e);\r
1156       }\r
1157     });\r
1158     newView.setText("New View");\r
1159     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1160         KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1161     newView.addActionListener(new ActionListener()\r
1162     {\r
1163       public void actionPerformed(ActionEvent e)\r
1164       {\r
1165         newView_actionPerformed(e);\r
1166       }\r
1167     });\r
1168     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
1169                               +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
1170     textColour.setText("Text Colour");\r
1171     textColour.addActionListener(new ActionListener()\r
1172     {\r
1173       public void actionPerformed(ActionEvent e)\r
1174       {\r
1175         textColour_actionPerformed(e);\r
1176       }\r
1177     });\r
1178     jMenu1.setText("Format");\r
1179     jCheckBoxMenuItem1.setText("Right Align Ids");\r
1180     jMenu4.setText("Select");\r
1181     idRightAlign.setText("Right Align Sequence Id");\r
1182     idRightAlign.addActionListener(new ActionListener()\r
1183     {\r
1184       public void actionPerformed(ActionEvent e)\r
1185       {\r
1186         idRightAlign_actionPerformed(e);\r
1187       }\r
1188     });\r
1189     gatherViews.setEnabled(false);\r
1190     gatherViews.setText("Gather Views");\r
1191     gatherViews.addActionListener(new ActionListener()\r
1192     {\r
1193       public void actionPerformed(ActionEvent e)\r
1194       {\r
1195         gatherViews_actionPerformed(e);\r
1196       }\r
1197     });\r
1198     expandViews.setEnabled(false);\r
1199     expandViews.setText("Expand Views");\r
1200     expandViews.addActionListener(new ActionListener()\r
1201     {\r
1202       public void actionPerformed(ActionEvent e)\r
1203       {\r
1204         expandViews_actionPerformed(e);\r
1205       }\r
1206     });\r
1207 \r
1208     alignFrameMenuBar.add(fileMenu);\r
1209     alignFrameMenuBar.add(editMenu);\r
1210     alignFrameMenuBar.add(jMenu4);\r
1211     alignFrameMenuBar.add(viewMenu);\r
1212     alignFrameMenuBar.add(jMenu1);\r
1213     alignFrameMenuBar.add(colourMenu);\r
1214     alignFrameMenuBar.add(calculateMenu);\r
1215     alignFrameMenuBar.add(webService);\r
1216     fileMenu.add(fetchSequence);\r
1217     fileMenu.add(addSequenceMenu);\r
1218     fileMenu.add(reload);\r
1219     fileMenu.addSeparator();\r
1220     fileMenu.add(vamsasStore);\r
1221     fileMenu.add(save);\r
1222     fileMenu.add(saveAs);\r
1223     fileMenu.add(outputTextboxMenu);\r
1224     fileMenu.add(printMenuItem);\r
1225     fileMenu.addSeparator();\r
1226     fileMenu.add(jMenu2);\r
1227     fileMenu.add(exportFeatures);\r
1228     fileMenu.add(exportAnnotations);\r
1229     fileMenu.add(LoadtreeMenuItem);\r
1230     fileMenu.add(associatedData);\r
1231     fileMenu.addSeparator();\r
1232     fileMenu.add(closeMenuItem);\r
1233     editMenu.add(undoMenuItem);\r
1234     editMenu.add(redoMenuItem);\r
1235     editMenu.add(cut);\r
1236     editMenu.add(copy);\r
1237     editMenu.add(pasteMenu);\r
1238     editMenu.add(delete);\r
1239     editMenu.addSeparator();\r
1240     editMenu.add(remove2LeftMenuItem);\r
1241     editMenu.add(remove2RightMenuItem);\r
1242     editMenu.add(removeGappedColumnMenuItem);\r
1243     editMenu.add(removeAllGapsMenuItem);\r
1244     editMenu.add(removeRedundancyMenuItem);\r
1245     editMenu.addSeparator();\r
1246     editMenu.add(padGapsMenuitem);\r
1247     viewMenu.add(newView);\r
1248     viewMenu.add(expandViews);\r
1249     viewMenu.add(gatherViews);\r
1250     viewMenu.addSeparator();\r
1251     viewMenu.add(jMenu3);\r
1252     viewMenu.add(hideMenu);\r
1253     viewMenu.addSeparator();\r
1254     viewMenu.add(annotationPanelMenuItem);\r
1255     viewMenu.addSeparator();\r
1256     viewMenu.add(showSeqFeatures);\r
1257     viewMenu.add(featureSettings);\r
1258     viewMenu.addSeparator();\r
1259     viewMenu.add(overviewMenuItem);\r
1260     colourMenu.add(applyToAllGroups);\r
1261     colourMenu.add(textColour);\r
1262     colourMenu.addSeparator();\r
1263     colourMenu.add(noColourmenuItem);\r
1264     colourMenu.add(clustalColour);\r
1265     colourMenu.add(BLOSUM62Colour);\r
1266     colourMenu.add(PIDColour);\r
1267     colourMenu.add(zappoColour);\r
1268     colourMenu.add(taylorColour);\r
1269     colourMenu.add(hydrophobicityColour);\r
1270     colourMenu.add(helixColour);\r
1271     colourMenu.add(strandColour);\r
1272     colourMenu.add(turnColour);\r
1273     colourMenu.add(buriedColour);\r
1274     colourMenu.add(nucleotideColour);\r
1275     colourMenu.add(userDefinedColour);\r
1276     colourMenu.addSeparator();\r
1277     colourMenu.add(conservationMenuItem);\r
1278     colourMenu.add(modifyConservation);\r
1279     colourMenu.add(abovePIDThreshold);\r
1280     colourMenu.add(modifyPID);\r
1281     colourMenu.add(annotationColour);\r
1282     calculateMenu.add(sort);\r
1283     calculateMenu.add(calculate);\r
1284     calculateMenu.addSeparator();\r
1285     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1286     calculateMenu.add(PCAMenuItem);\r
1287     calculateMenu.addSeparator();\r
1288     calculateMenu.add(showTranslation);\r
1289     calculateMenu.add(autoCalculate);\r
1290     webServiceNoServices=new JMenuItem("<No Services>");\r
1291     webService.add(webServiceNoServices);pasteMenu.add(pasteNew);\r
1292     pasteMenu.add(pasteThis);\r
1293     sort.add(sortIDMenuItem);\r
1294     sort.add(sortGroupMenuItem);\r
1295     sort.add(sortPairwiseMenuItem);\r
1296     calculate.add(averageDistanceTreeMenuItem);\r
1297     calculate.add(neighbourTreeMenuItem);\r
1298     calculate.add(avDistanceTreeBlosumMenuItem);\r
1299     calculate.add(njTreeBlosumMenuItem);\r
1300     jMenu2.add(htmlMenuItem);\r
1301     jMenu2.add(epsFile);\r
1302     jMenu2.add(createPNG);\r
1303     addSequenceMenu.add(addFromFile);\r
1304     addSequenceMenu.add(addFromText);\r
1305     addSequenceMenu.add(addFromURL);\r
1306     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1307     statusPanel.add(statusBar, null);\r
1308     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1309     jMenu3.add(showAllColumns);\r
1310     jMenu3.add(showAllSeqs);\r
1311     hideMenu.add(hideSelColumns);\r
1312     hideMenu.add(hideSelSequences);\r
1313     jMenu1.add(font);\r
1314     jMenu1.addSeparator();\r
1315     jMenu1.add(wrapMenuItem);\r
1316     jMenu1.add(scaleAbove);\r
1317     jMenu1.add(scaleLeft);\r
1318     jMenu1.add(scaleRight);\r
1319     jMenu1.add(seqLimits);\r
1320     jMenu1.add(idRightAlign);\r
1321     jMenu1.add(hiddenMarkers);\r
1322     jMenu1.add(viewBoxesMenuItem);\r
1323     jMenu1.add(viewTextMenuItem);\r
1324     jMenu1.add(colourTextMenuItem);\r
1325     jMenu1.add(renderGapsMenuItem);\r
1326     jMenu4.add(findMenuItem);\r
1327     jMenu4.addSeparator();\r
1328     jMenu4.add(selectAllSequenceMenuItem);\r
1329     jMenu4.add(deselectAllSequenceMenuItem);\r
1330     jMenu4.add(invertSequenceMenuItem);\r
1331     jMenu4.add(invertColSel);\r
1332     jMenu4.add(deleteGroups);\r
1333   }\r
1334 \r
1335   protected void outputText_actionPerformed(ActionEvent e)\r
1336   {\r
1337   }\r
1338 \r
1339   public void addFromFile_actionPerformed(ActionEvent e)\r
1340   {\r
1341 \r
1342   }\r
1343 \r
1344   public void addFromText_actionPerformed(ActionEvent e)\r
1345   {\r
1346 \r
1347   }\r
1348 \r
1349   public void addFromURL_actionPerformed(ActionEvent e)\r
1350   {\r
1351 \r
1352   }\r
1353 \r
1354   public void exportFeatures_actionPerformed(ActionEvent e)\r
1355   {\r
1356 \r
1357   }\r
1358 \r
1359   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1360   {\r
1361 \r
1362   }\r
1363 \r
1364   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1365   {\r
1366   }\r
1367 \r
1368   protected void closeMenuItem_actionPerformed(boolean b)\r
1369   {\r
1370   }\r
1371 \r
1372   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1373   {\r
1374   }\r
1375 \r
1376   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1377   {\r
1378   }\r
1379 \r
1380   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1381   {\r
1382   }\r
1383 \r
1384   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1385   {\r
1386   }\r
1387 \r
1388   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1389   {\r
1390   }\r
1391 \r
1392   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1393   {\r
1394   }\r
1395 \r
1396   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1397   {\r
1398   }\r
1399 \r
1400   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1401   {\r
1402   }\r
1403 \r
1404   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1405   {\r
1406   }\r
1407 \r
1408   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1409   {\r
1410   }\r
1411 \r
1412   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1413   {\r
1414   }\r
1415 \r
1416   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1417   {\r
1418   }\r
1419 \r
1420   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1421   {\r
1422   }\r
1423 \r
1424   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1425   {\r
1426   }\r
1427 \r
1428   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1429   {\r
1430   }\r
1431 \r
1432   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1433   {\r
1434   }\r
1435 \r
1436   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1437   {\r
1438   }\r
1439 \r
1440   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1441   {\r
1442   }\r
1443 \r
1444   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1445   {\r
1446   }\r
1447 \r
1448   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1449   {\r
1450   }\r
1451 \r
1452   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1453   {\r
1454   }\r
1455 \r
1456   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1457   {\r
1458   }\r
1459 \r
1460   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1461   {\r
1462   }\r
1463 \r
1464   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1465   {\r
1466   }\r
1467 \r
1468   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1469   {\r
1470   }\r
1471 \r
1472   protected void clustalColour_actionPerformed(ActionEvent e)\r
1473   {\r
1474   }\r
1475 \r
1476   protected void zappoColour_actionPerformed(ActionEvent e)\r
1477   {\r
1478   }\r
1479 \r
1480   protected void taylorColour_actionPerformed(ActionEvent e)\r
1481   {\r
1482   }\r
1483 \r
1484   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1485   {\r
1486   }\r
1487 \r
1488   protected void helixColour_actionPerformed(ActionEvent e)\r
1489   {\r
1490   }\r
1491 \r
1492   protected void strandColour_actionPerformed(ActionEvent e)\r
1493   {\r
1494   }\r
1495 \r
1496   protected void turnColour_actionPerformed(ActionEvent e)\r
1497   {\r
1498   }\r
1499 \r
1500   protected void buriedColour_actionPerformed(ActionEvent e)\r
1501   {\r
1502   }\r
1503 \r
1504   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1505   {\r
1506   }\r
1507 \r
1508   protected void PIDColour_actionPerformed(ActionEvent e)\r
1509   {\r
1510   }\r
1511 \r
1512   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1513   {\r
1514   }\r
1515 \r
1516   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1517   {\r
1518   }\r
1519 \r
1520   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1521   {\r
1522   }\r
1523 \r
1524   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1525   {\r
1526   }\r
1527 \r
1528   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1529   {\r
1530   }\r
1531 \r
1532   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1533   {\r
1534   }\r
1535 \r
1536   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1537   {\r
1538   }\r
1539 \r
1540   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1541   {\r
1542   }\r
1543 \r
1544   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1545   {\r
1546   }\r
1547 \r
1548   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1549   {\r
1550   }\r
1551 \r
1552   protected void copy_actionPerformed(ActionEvent e)\r
1553   {\r
1554   }\r
1555 \r
1556   protected void cut_actionPerformed(ActionEvent e)\r
1557   {\r
1558   }\r
1559 \r
1560   protected void delete_actionPerformed(ActionEvent e)\r
1561   {\r
1562   }\r
1563 \r
1564   protected void pasteNew_actionPerformed(ActionEvent e)\r
1565   {\r
1566   }\r
1567 \r
1568   protected void pasteThis_actionPerformed(ActionEvent e)\r
1569   {\r
1570   }\r
1571 \r
1572   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1573   {\r
1574   }\r
1575 \r
1576   public void createPNG(java.io.File f)\r
1577   {\r
1578   }\r
1579 \r
1580   protected void font_actionPerformed(ActionEvent e)\r
1581   {\r
1582   }\r
1583 \r
1584   protected void seqLimit_actionPerformed(ActionEvent e)\r
1585   {\r
1586   }\r
1587 \r
1588   public void seqDBRef_actionPerformed(ActionEvent e)\r
1589   {\r
1590 \r
1591   }\r
1592 \r
1593 \r
1594   public void createEPS(java.io.File f)\r
1595   {\r
1596   }\r
1597 \r
1598   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1599   {\r
1600   }\r
1601 \r
1602   protected void jpred_actionPerformed(ActionEvent e)\r
1603   {\r
1604   }\r
1605 \r
1606   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1607   {\r
1608   }\r
1609 \r
1610   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1611   {\r
1612   }\r
1613 \r
1614   protected void scaleRight_actionPerformed(ActionEvent e)\r
1615   {\r
1616   }\r
1617 \r
1618   protected void modifyPID_actionPerformed(ActionEvent e)\r
1619   {\r
1620   }\r
1621 \r
1622   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1623   {\r
1624   }\r
1625 \r
1626 \r
1627 \r
1628   protected void saveAs_actionPerformed(ActionEvent e)\r
1629   {\r
1630   }\r
1631 \r
1632   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1633   {\r
1634   }\r
1635 \r
1636 \r
1637   public void vamsasStore_actionPerformed(ActionEvent e)\r
1638   {\r
1639 \r
1640   }\r
1641 \r
1642   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1643   {\r
1644 \r
1645   }\r
1646 \r
1647   public void showTranslation_actionPerformed(ActionEvent e)\r
1648   {\r
1649 \r
1650   }\r
1651 \r
1652   public void featureSettings_actionPerformed(ActionEvent e)\r
1653   {\r
1654 \r
1655   }\r
1656 \r
1657   public void fetchSequence_actionPerformed(ActionEvent e)\r
1658   {\r
1659 \r
1660   }\r
1661 \r
1662   public void smoothFont_actionPerformed(ActionEvent e)\r
1663   {\r
1664 \r
1665   }\r
1666 \r
1667   public void annotationColour_actionPerformed(ActionEvent e)\r
1668   {\r
1669 \r
1670   }\r
1671 \r
1672 \r
1673   public void associatedData_actionPerformed(ActionEvent e)\r
1674   {\r
1675 \r
1676   }\r
1677 \r
1678   public void autoCalculate_actionPerformed(ActionEvent e)\r
1679   {\r
1680 \r
1681   }\r
1682 \r
1683   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1684   {\r
1685 \r
1686   }\r
1687 \r
1688   public void showAllColumns_actionPerformed(ActionEvent e)\r
1689   {\r
1690 \r
1691   }\r
1692 \r
1693   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1694   {\r
1695 \r
1696   }\r
1697 \r
1698   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1699   {\r
1700 \r
1701   }\r
1702 \r
1703   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1704   {\r
1705 \r
1706   }\r
1707 \r
1708   public void findPdbId_actionPerformed(ActionEvent e)\r
1709   {\r
1710 \r
1711   }\r
1712 \r
1713   public void enterPdbId_actionPerformed(ActionEvent e)\r
1714   {\r
1715 \r
1716   }\r
1717 \r
1718   public void pdbFile_actionPerformed(ActionEvent e)\r
1719   {\r
1720 \r
1721   }\r
1722 \r
1723   public void invertColSel_actionPerformed(ActionEvent e)\r
1724   {\r
1725 \r
1726   }\r
1727 \r
1728   public void tabSelectionChanged(int sel)\r
1729   {\r
1730 \r
1731   }\r
1732 \r
1733   public void tabbedPane_mousePressed(MouseEvent e)\r
1734   {\r
1735 \r
1736   }\r
1737 \r
1738   public void tabbedPane_focusGained(FocusEvent e)\r
1739   {\r
1740     requestFocus();\r
1741   }\r
1742 \r
1743   public void save_actionPerformed(ActionEvent e)\r
1744   {\r
1745 \r
1746   }\r
1747 \r
1748   public void reload_actionPerformed(ActionEvent e)\r
1749   {\r
1750 \r
1751   }\r
1752 \r
1753   public void newView_actionPerformed(ActionEvent e)\r
1754   {\r
1755 \r
1756   }\r
1757 \r
1758   public void textColour_actionPerformed(ActionEvent e)\r
1759   {\r
1760 \r
1761   }\r
1762 \r
1763   public void idRightAlign_actionPerformed(ActionEvent e)\r
1764   {\r
1765 \r
1766   }\r
1767 \r
1768   public void expandViews_actionPerformed(ActionEvent e)\r
1769   {\r
1770 \r
1771   }\r
1772 \r
1773   public void gatherViews_actionPerformed(ActionEvent e)\r
1774   {\r
1775 \r
1776   }\r
1777 }\r