src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 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 \r
  28 public class GAlignFrame\r
  29     extends JInternalFrame\r
  30 {\r
  31   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  32   protected JMenu fileMenu = new JMenu();\r
  33   protected JMenuItem closeMenuItem = new JMenuItem();\r
  34   protected JMenu editMenu = new JMenu();\r
  35   protected JMenu viewMenu = new JMenu();\r
  36   protected JMenu colourMenu = new JMenu();\r
  37   protected JMenu calculateMenu = new JMenu();\r
  38   protected JMenu webService = new JMenu();\r
  39   protected JMenuItem webServiceNoServices;\r
  40   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  41   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  42   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  43   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  44   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  45   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  46   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  47   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  48   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  49   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  50   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  51   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  54   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  57   BorderLayout borderLayout1 = new BorderLayout();\r
  58   public JLabel statusBar = new JLabel();\r
  59   protected JMenuItem saveAs = new JMenuItem();\r
  60   protected JMenu outputTextboxMenu = new JMenu();\r
  61   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  62   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  65       JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  73   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  74   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  75   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  76   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  77   JMenuItem htmlMenuItem = new JMenuItem();\r
  78   JMenuItem overviewMenuItem = new JMenuItem();\r
  79   protected JMenuItem undoMenuItem = new JMenuItem();\r
  80   protected JMenuItem redoMenuItem = new JMenuItem();\r
  81   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  82   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  83   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  84   JMenuItem printMenuItem = new JMenuItem();\r
  85   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  86   JMenuItem findMenuItem = new JMenuItem();\r
  87   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  88   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  89   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  90   JMenuItem deleteGroups = new JMenuItem();\r
  91   JMenuItem delete = new JMenuItem();\r
  92   JMenuItem copy = new JMenuItem();\r
  93   JMenuItem cut = new JMenuItem();\r
  94   JMenu pasteMenu = new JMenu();\r
  95   JMenuItem pasteNew = new JMenuItem();\r
  96   JMenuItem pasteThis = new JMenuItem();\r
  97   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
  98   JMenuItem createPNG = new JMenuItem();\r
  99   protected JMenuItem font = new JMenuItem();\r
 100   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 101   JMenuItem epsFile = new JMenuItem();\r
 102   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 103   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 104   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 105   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 106   protected JMenuItem modifyPID = new JMenuItem();\r
 107   protected JMenuItem modifyConservation = new JMenuItem();\r
 108   protected JMenu sortByTreeMenu = new JMenu();\r
 109   protected JMenu sort = new JMenu();\r
 110   JMenu calculate = new JMenu();\r
 111   JMenu jMenu2 = new JMenu();\r
 112   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 113   protected ButtonGroup colours = new ButtonGroup();\r
 114   JMenuItem vamsasStore = new JMenuItem();\r
 115   protected JMenuItem showTranslation = new JMenuItem();\r
 116   public JMenuItem featureSettings = new JMenuItem();\r
 117   JMenuItem fetchSequence = new JMenuItem();\r
 118   JMenuItem annotationColour = new JMenuItem();\r
 119   JMenuItem associatedData = new JMenuItem();\r
 120   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 121   JMenu addSequenceMenu = new JMenu();\r
 122   JMenuItem addFromFile = new JMenuItem();\r
 123   JMenuItem addFromText = new JMenuItem();\r
 124   JMenuItem addFromURL = new JMenuItem();\r
 125   JMenuItem exportAnnotations = new JMenuItem();\r
 126   JMenuItem exportFeatures = new JMenuItem();\r
 127   protected JPanel statusPanel = new JPanel();\r
 128   GridLayout gridLayout1 = new GridLayout();\r
 129   JMenu jMenu3 = new JMenu();\r
 130   JMenuItem showAllSeqs = new JMenuItem();\r
 131   JMenuItem showAllColumns = new JMenuItem();\r
 132   JMenu hideMenu = new JMenu();\r
 133   JMenuItem hideSelSequences = new JMenuItem();\r
 134   JMenuItem hideSelColumns = new JMenuItem();\r
 135   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 136   JMenuItem invertColSel = new JMenuItem();\r
 137   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 138   JMenuItem save = new JMenuItem();\r
 139   protected JMenuItem reload = new JMenuItem();\r
 140   JMenuItem newView = new JMenuItem();\r
 141   JMenuItem textColour = new JMenuItem();\r
 142   JMenu formatMenu = new JMenu();\r
 143   JMenu selectMenu = new JMenu();\r
 144   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
 145   protected JMenuItem gatherViews = new JMenuItem();\r
 146   protected JMenuItem expandViews = new JMenuItem();\r
 147   JMenuItem pageSetup = new JMenuItem();\r
 148   public GAlignFrame()\r
 149   {\r
 150     try\r
 151     {\r
 152       jbInit();\r
 153       setJMenuBar(alignFrameMenuBar);\r
 154 \r
 155       // dynamically fill save as menu with available formats\r
 156       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 157       {\r
 158         JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.\r
 159                                        WRITEABLE_FORMATS[i]);\r
 160 \r
 161         item.addActionListener(new java.awt.event.ActionListener()\r
 162         {\r
 163           public void actionPerformed(ActionEvent e)\r
 164           {\r
 165             outputText_actionPerformed(e);\r
 166           }\r
 167         });\r
 168 \r
 169         outputTextboxMenu.add(item);\r
 170       }\r
 171     }\r
 172     catch (Exception e)\r
 173     {\r
 174     }\r
 175 \r
 176     if (!System.getProperty("os.name").startsWith("Mac"))\r
 177     {\r
 178       closeMenuItem.setMnemonic('C');\r
 179       outputTextboxMenu.setMnemonic('T');\r
 180       undoMenuItem.setMnemonic('Z');\r
 181       redoMenuItem.setMnemonic('0');\r
 182       copy.setMnemonic('C');\r
 183       cut.setMnemonic('U');\r
 184       pasteMenu.setMnemonic('P');\r
 185       reload.setMnemonic('R');\r
 186     }\r
 187 \r
 188     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
 189     {\r
 190       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 191           getUserColourSchemes().keys();\r
 192 \r
 193       while (userColours.hasMoreElements())\r
 194       {\r
 195         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
 196             userColours.\r
 197             nextElement().toString());\r
 198         radioItem.setName("USER_DEFINED");\r
 199         radioItem.addMouseListener(new MouseAdapter()\r
 200         {\r
 201           public void mousePressed(MouseEvent evt)\r
 202           {\r
 203             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 204             {\r
 205               radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 206 \r
 207               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.\r
 208                   Desktop.desktop,\r
 209                   "Remove from default list?",\r
 210                   "Remove user defined colour",\r
 211                   JOptionPane.YES_NO_OPTION);\r
 212               if (option == JOptionPane.YES_OPTION)\r
 213               {\r
 214                 jalview.gui.UserDefinedColours.removeColourFromDefaults(\r
 215                     radioItem.getText());\r
 216                 colourMenu.remove(radioItem);\r
 217               }\r
 218               else\r
 219               {\r
 220                 radioItem.addActionListener(new ActionListener()\r
 221                 {\r
 222                   public void actionPerformed(ActionEvent evt)\r
 223                   {\r
 224                     userDefinedColour_actionPerformed(evt);\r
 225                   }\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   public void setColourSelected(String defaultColour)\r
 261   {\r
 262 \r
 263     if (defaultColour != null)\r
 264     {\r
 265       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 266 \r
 267       switch (index)\r
 268       {\r
 269         case ColourSchemeProperty.NONE:\r
 270           noColourmenuItem.setSelected(true);\r
 271           break;\r
 272         case ColourSchemeProperty.CLUSTAL:\r
 273           clustalColour.setSelected(true);\r
 274 \r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.BLOSUM:\r
 278           BLOSUM62Colour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.PID:\r
 283           PIDColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.ZAPPO:\r
 288           zappoColour.setSelected(true);\r
 289 \r
 290           break;\r
 291 \r
 292         case ColourSchemeProperty.TAYLOR:\r
 293           taylorColour.setSelected(true);\r
 294           break;\r
 295 \r
 296         case ColourSchemeProperty.HYDROPHOBIC:\r
 297           hydrophobicityColour.setSelected(true);\r
 298 \r
 299           break;\r
 300 \r
 301         case ColourSchemeProperty.HELIX:\r
 302           helixColour.setSelected(true);\r
 303 \r
 304           break;\r
 305 \r
 306         case ColourSchemeProperty.STRAND:\r
 307           strandColour.setSelected(true);\r
 308 \r
 309           break;\r
 310 \r
 311         case ColourSchemeProperty.TURN:\r
 312           turnColour.setSelected(true);\r
 313 \r
 314           break;\r
 315 \r
 316         case ColourSchemeProperty.BURIED:\r
 317           buriedColour.setSelected(true);\r
 318 \r
 319           break;\r
 320 \r
 321         case ColourSchemeProperty.NUCLEOTIDE:\r
 322           nucleotideColour.setSelected(true);\r
 323 \r
 324           break;\r
 325 \r
 326         case ColourSchemeProperty.USER_DEFINED:\r
 327           userDefinedColour.setSelected(true);\r
 328 \r
 329           break;\r
 330       }\r
 331     }\r
 332 \r
 333   }\r
 334 \r
 335   private void jbInit()\r
 336       throws Exception\r
 337   {\r
 338     fileMenu.setText("File");\r
 339     saveAs.setText("Save As...");\r
 340     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 341         KeyEvent.VK_S,\r
 342         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
 343         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,\r
 404         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 405     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 406     {\r
 407       public void actionPerformed(ActionEvent e)\r
 408       {\r
 409         remove2LeftMenuItem_actionPerformed(e);\r
 410       }\r
 411     });\r
 412     remove2RightMenuItem.setText("Remove Right");\r
 413     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 414         awt.event.KeyEvent.VK_R,\r
 415         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 416     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 417     {\r
 418       public void actionPerformed(ActionEvent e)\r
 419       {\r
 420         remove2RightMenuItem_actionPerformed(e);\r
 421       }\r
 422     });\r
 423     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 424     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 425                                               getKeyStroke(java.awt.event.\r
 426         KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 427     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 428                                                  ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         removeGappedColumnMenuItem_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 436     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 437         java.awt.event.KeyEvent.VK_E,\r
 438         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
 439         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 440     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 441     {\r
 442       public void actionPerformed(ActionEvent e)\r
 443       {\r
 444         removeAllGapsMenuItem_actionPerformed(e);\r
 445       }\r
 446     });\r
 447     viewBoxesMenuItem.setText("Boxes");\r
 448     viewBoxesMenuItem.setState(true);\r
 449     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         viewBoxesMenuItem_actionPerformed(e);\r
 454       }\r
 455     });\r
 456     viewTextMenuItem.setText("Text");\r
 457     viewTextMenuItem.setState(true);\r
 458     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         viewTextMenuItem_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 466     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         sortPairwiseMenuItem_actionPerformed(e);\r
 471       }\r
 472     });\r
 473     sortIDMenuItem.setText("by ID");\r
 474     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 475     {\r
 476       public void actionPerformed(ActionEvent e)\r
 477       {\r
 478         sortIDMenuItem_actionPerformed(e);\r
 479       }\r
 480     });\r
 481     sortGroupMenuItem.setText("by Group");\r
 482     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         sortGroupMenuItem_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 490     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 491         java.awt.event.KeyEvent.VK_D,\r
 492         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 493     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 494                                                ActionListener()\r
 495     {\r
 496       public void actionPerformed(ActionEvent e)\r
 497       {\r
 498         removeRedundancyMenuItem_actionPerformed(e);\r
 499       }\r
 500     });\r
 501     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 502     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 503                                                 ActionListener()\r
 504     {\r
 505       public void actionPerformed(ActionEvent e)\r
 506       {\r
 507         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 508       }\r
 509     });\r
 510     PCAMenuItem.setText("Principal Component Analysis");\r
 511     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 512     {\r
 513       public void actionPerformed(ActionEvent e)\r
 514       {\r
 515         PCAMenuItem_actionPerformed(e);\r
 516       }\r
 517     });\r
 518     averageDistanceTreeMenuItem.setText(\r
 519         "Average Distance Using % Identity");\r
 520     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 521                                                   ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         averageDistanceTreeMenuItem_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 529     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         neighbourTreeMenuItem_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     this.getContentPane().setLayout(borderLayout1);\r
 537     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 538     statusBar.setBackground(Color.white);\r
 539     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 540     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 541     statusBar.setText("Status bar");\r
 542     outputTextboxMenu.setText("Output to Textbox");\r
 543     clustalColour.setText("Clustalx");\r
 544 \r
 545     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         clustalColour_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     zappoColour.setText("Zappo");\r
 553     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         zappoColour_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     taylorColour.setText("Taylor");\r
 561     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         taylorColour_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     hydrophobicityColour.setText("Hydrophobicity");\r
 569     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         hydrophobicityColour_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     helixColour.setText("Helix Propensity");\r
 577     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 578     {\r
 579       public void actionPerformed(ActionEvent e)\r
 580       {\r
 581         helixColour_actionPerformed(e);\r
 582       }\r
 583     });\r
 584     strandColour.setText("Strand Propensity");\r
 585     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 586     {\r
 587       public void actionPerformed(ActionEvent e)\r
 588       {\r
 589         strandColour_actionPerformed(e);\r
 590       }\r
 591     });\r
 592     turnColour.setText("Turn Propensity");\r
 593     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 594     {\r
 595       public void actionPerformed(ActionEvent e)\r
 596       {\r
 597         turnColour_actionPerformed(e);\r
 598       }\r
 599     });\r
 600     buriedColour.setText("Buried Index");\r
 601     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 602     {\r
 603       public void actionPerformed(ActionEvent e)\r
 604       {\r
 605         buriedColour_actionPerformed(e);\r
 606       }\r
 607     });\r
 608     userDefinedColour.setText("User Defined...");\r
 609     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 610     {\r
 611       public void actionPerformed(ActionEvent e)\r
 612       {\r
 613         userDefinedColour_actionPerformed(e);\r
 614       }\r
 615     });\r
 616     PIDColour.setText("Percentage Identity");\r
 617     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 618     {\r
 619       public void actionPerformed(ActionEvent e)\r
 620       {\r
 621         PIDColour_actionPerformed(e);\r
 622       }\r
 623     });\r
 624     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 625     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 626     {\r
 627       public void actionPerformed(ActionEvent e)\r
 628       {\r
 629         BLOSUM62Colour_actionPerformed(e);\r
 630       }\r
 631     });\r
 632     avDistanceTreeBlosumMenuItem.setText(\r
 633         "Average Distance Using BLOSUM62");\r
 634     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 635         ActionListener()\r
 636     {\r
 637       public void actionPerformed(ActionEvent e)\r
 638       {\r
 639         avTreeBlosumMenuItem_actionPerformed(e);\r
 640       }\r
 641     });\r
 642     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 643     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 644     {\r
 645       public void actionPerformed(ActionEvent e)\r
 646       {\r
 647         njTreeBlosumMenuItem_actionPerformed(e);\r
 648       }\r
 649     });\r
 650     annotationPanelMenuItem.setActionCommand("");\r
 651     annotationPanelMenuItem.setText("Show Annotations");\r
 652     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(\r
 653         "SHOW_ANNOTATIONS", true));\r
 654     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 655     {\r
 656       public void actionPerformed(ActionEvent e)\r
 657       {\r
 658         annotationPanelMenuItem_actionPerformed(e);\r
 659       }\r
 660     });\r
 661     colourTextMenuItem.setText("Colour Text");\r
 662     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 663     {\r
 664       public void actionPerformed(ActionEvent e)\r
 665       {\r
 666         colourTextMenuItem_actionPerformed(e);\r
 667       }\r
 668     });\r
 669     htmlMenuItem.setText("HTML");\r
 670     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 671     {\r
 672       public void actionPerformed(ActionEvent e)\r
 673       {\r
 674         htmlMenuItem_actionPerformed(e);\r
 675       }\r
 676     });\r
 677     overviewMenuItem.setText("Overview Window");\r
 678     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 679     {\r
 680       public void actionPerformed(ActionEvent e)\r
 681       {\r
 682         overviewMenuItem_actionPerformed(e);\r
 683       }\r
 684     });\r
 685     undoMenuItem.setEnabled(false);\r
 686     undoMenuItem.setText("Undo");\r
 687     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 688         java.awt.event.KeyEvent.VK_Z,\r
 689         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 690     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 691     {\r
 692       public void actionPerformed(ActionEvent e)\r
 693       {\r
 694         undoMenuItem_actionPerformed(e);\r
 695       }\r
 696     });\r
 697     redoMenuItem.setEnabled(false);\r
 698     redoMenuItem.setText("Redo");\r
 699     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 700         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 701     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 702     {\r
 703       public void actionPerformed(ActionEvent e)\r
 704       {\r
 705         redoMenuItem_actionPerformed(e);\r
 706       }\r
 707     });\r
 708     conservationMenuItem.setText("By Conservation");\r
 709     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 710     {\r
 711       public void actionPerformed(ActionEvent e)\r
 712       {\r
 713         conservationMenuItem_actionPerformed(e);\r
 714       }\r
 715     });\r
 716     noColourmenuItem.setText("None");\r
 717     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 718     {\r
 719       public void actionPerformed(ActionEvent e)\r
 720       {\r
 721         noColourmenuItem_actionPerformed(e);\r
 722       }\r
 723     });\r
 724     wrapMenuItem.setText("Wrap");\r
 725     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 726     {\r
 727       public void actionPerformed(ActionEvent e)\r
 728       {\r
 729         wrapMenuItem_actionPerformed(e);\r
 730       }\r
 731     });\r
 732     printMenuItem.setText("Print ...");\r
 733     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 734         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 735     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 736     {\r
 737       public void actionPerformed(ActionEvent e)\r
 738       {\r
 739         printMenuItem_actionPerformed(e);\r
 740       }\r
 741     });\r
 742     renderGapsMenuItem.setText("Show Gaps");\r
 743     renderGapsMenuItem.setState(true);\r
 744     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 745     {\r
 746       public void actionPerformed(ActionEvent e)\r
 747       {\r
 748         renderGapsMenuItem_actionPerformed(e);\r
 749       }\r
 750     });\r
 751     findMenuItem.setText("Find...");\r
 752     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 753         java.awt.event.KeyEvent.VK_F,\r
 754         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 755     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 756     {\r
 757       public void actionPerformed(ActionEvent e)\r
 758       {\r
 759         findMenuItem_actionPerformed(e);\r
 760       }\r
 761     });\r
 762     abovePIDThreshold.setText("Above Identity Threshold");\r
 763     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 764     {\r
 765       public void actionPerformed(ActionEvent e)\r
 766       {\r
 767         abovePIDThreshold_actionPerformed(e);\r
 768       }\r
 769     });\r
 770     showSeqFeatures.setText("Show Sequence Features");\r
 771     showSeqFeatures.addActionListener(new ActionListener()\r
 772     {\r
 773       public void actionPerformed(ActionEvent actionEvent)\r
 774       {\r
 775         showSeqFeatures_actionPerformed(actionEvent);\r
 776       }\r
 777     });\r
 778     nucleotideColour.setText("Nucleotide");\r
 779     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 780     {\r
 781       public void actionPerformed(ActionEvent e)\r
 782       {\r
 783         nucleotideColour_actionPerformed(e);\r
 784       }\r
 785     });\r
 786     deleteGroups.setText("Undefine groups");\r
 787     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 788         event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 789     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 790     {\r
 791       public void actionPerformed(ActionEvent e)\r
 792       {\r
 793         deleteGroups_actionPerformed(e);\r
 794       }\r
 795     });\r
 796     copy.setText("Copy");\r
 797     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 798         java.awt.event.KeyEvent.VK_C,\r
 799         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 800 \r
 801     copy.addActionListener(new java.awt.event.ActionListener()\r
 802     {\r
 803       public void actionPerformed(ActionEvent e)\r
 804       {\r
 805         copy_actionPerformed(e);\r
 806       }\r
 807     });\r
 808     cut.setText("Cut");\r
 809     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 810         java.awt.event.KeyEvent.VK_X,\r
 811         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 812     cut.addActionListener(new java.awt.event.ActionListener()\r
 813     {\r
 814       public void actionPerformed(ActionEvent e)\r
 815       {\r
 816         cut_actionPerformed(e);\r
 817       }\r
 818     });\r
 819     delete.setText("Delete");\r
 820     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 821         KeyEvent.VK_BACK_SPACE, 0, false));\r
 822     delete.addActionListener(new java.awt.event.ActionListener()\r
 823     {\r
 824       public void actionPerformed(ActionEvent e)\r
 825       {\r
 826         delete_actionPerformed(e);\r
 827       }\r
 828     });\r
 829     pasteMenu.setText("Paste");\r
 830     pasteNew.setText("To New Alignment");\r
 831     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 832         java.awt.event.KeyEvent.VK_V,\r
 833         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
 834         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 835     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 836     {\r
 837       public void actionPerformed(ActionEvent e)\r
 838       {\r
 839         pasteNew_actionPerformed(e);\r
 840       }\r
 841     });\r
 842     pasteThis.setText("Add To This Alignment");\r
 843     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 844         java.awt.event.KeyEvent.VK_V,\r
 845         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 846     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 847     {\r
 848       public void actionPerformed(ActionEvent e)\r
 849       {\r
 850         pasteThis_actionPerformed(e);\r
 851       }\r
 852     });\r
 853     applyToAllGroups.setText("Apply Colour To All Groups");\r
 854     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 855     {\r
 856       public void actionPerformed(ActionEvent e)\r
 857       {\r
 858         applyToAllGroups_actionPerformed(e);\r
 859       }\r
 860     });\r
 861     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 862     {\r
 863       public void actionPerformed(ActionEvent e)\r
 864       {\r
 865         createPNG(null);\r
 866       }\r
 867     });\r
 868     createPNG.setActionCommand("Save As PNG Image");\r
 869     createPNG.setText("PNG");\r
 870     font.setText("Font...");\r
 871     font.addActionListener(new java.awt.event.ActionListener()\r
 872     {\r
 873       public void actionPerformed(ActionEvent e)\r
 874       {\r
 875         font_actionPerformed(e);\r
 876       }\r
 877     });\r
 878 \r
 879     seqLimits.setText("Show Sequence Limits");\r
 880     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));\r
 881     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 882     {\r
 883       public void actionPerformed(ActionEvent e)\r
 884       {\r
 885         seqLimit_actionPerformed(e);\r
 886       }\r
 887     });\r
 888     epsFile.setText("EPS");\r
 889     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 890     {\r
 891       public void actionPerformed(ActionEvent e)\r
 892       {\r
 893         createEPS(null);\r
 894       }\r
 895     });\r
 896     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 897     LoadtreeMenuItem.setText("Load Associated Tree");\r
 898     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 899     {\r
 900       public void actionPerformed(ActionEvent e)\r
 901       {\r
 902         LoadtreeMenuItem_actionPerformed(e);\r
 903       }\r
 904     });\r
 905     scaleAbove.setVisible(false);\r
 906     scaleAbove.setText("Scale Above");\r
 907     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 908     {\r
 909       public void actionPerformed(ActionEvent e)\r
 910       {\r
 911         scaleAbove_actionPerformed(e);\r
 912       }\r
 913     });\r
 914     scaleLeft.setVisible(false);\r
 915     scaleLeft.setSelected(true);\r
 916     scaleLeft.setText("Scale Left");\r
 917     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 918     {\r
 919       public void actionPerformed(ActionEvent e)\r
 920       {\r
 921         scaleLeft_actionPerformed(e);\r
 922       }\r
 923     });\r
 924     scaleRight.setVisible(false);\r
 925     scaleRight.setSelected(true);\r
 926     scaleRight.setText("Scale Right");\r
 927     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 928     {\r
 929       public void actionPerformed(ActionEvent e)\r
 930       {\r
 931         scaleRight_actionPerformed(e);\r
 932       }\r
 933     });\r
 934     modifyPID.setText("Modify Identity Threshold...");\r
 935     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 936     {\r
 937       public void actionPerformed(ActionEvent e)\r
 938       {\r
 939         modifyPID_actionPerformed(e);\r
 940       }\r
 941     });\r
 942     modifyConservation.setText("Modify Conservation Threshold...");\r
 943     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 944     {\r
 945       public void actionPerformed(ActionEvent e)\r
 946       {\r
 947         modifyConservation_actionPerformed(e);\r
 948       }\r
 949     });\r
 950     sortByTreeMenu.setText("By Tree Order");\r
 951     sort.setText("Sort");\r
 952     sort.addMenuListener(new MenuListener()\r
 953     {\r
 954       public void menuSelected(MenuEvent e)\r
 955       {\r
 956         buildTreeMenu();\r
 957       }\r
 958 \r
 959       public void menuDeselected(MenuEvent e)\r
 960       {\r
 961       }\r
 962 \r
 963       public void menuCanceled(MenuEvent e)\r
 964       {\r
 965       }\r
 966     });\r
 967     calculate.setText("Calculate Tree");\r
 968 \r
 969     jMenu2.setText("Export Image");\r
 970     padGapsMenuitem.setText("Pad Gaps");\r
 971     padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 972     padGapsMenuitem.addActionListener(new ActionListener()\r
 973     {\r
 974       public void actionPerformed(ActionEvent e)\r
 975       {\r
 976         padGapsMenuitem_actionPerformed(e);\r
 977       }\r
 978     });\r
 979     vamsasStore.setVisible(false);\r
 980     vamsasStore.setText("VAMSAS store");\r
 981     vamsasStore.addActionListener(new ActionListener()\r
 982     {\r
 983       public void actionPerformed(ActionEvent e)\r
 984       {\r
 985         vamsasStore_actionPerformed(e);\r
 986       }\r
 987     });\r
 988     showTranslation.setText("Translate cDNA");\r
 989     showTranslation.addActionListener(new ActionListener()\r
 990     {\r
 991       public void actionPerformed(ActionEvent e)\r
 992       {\r
 993         showTranslation_actionPerformed(e);\r
 994       }\r
 995     });\r
 996 \r
 997     featureSettings.setText("Feature Settings...");\r
 998     featureSettings.addActionListener(new ActionListener()\r
 999     {\r
1000       public void actionPerformed(ActionEvent e)\r
1001       {\r
1002         featureSettings_actionPerformed(e);\r
1003       }\r
1004     });\r
1005     fetchSequence.setText("Fetch Sequence(s)...");\r
1006     fetchSequence.addActionListener(new ActionListener()\r
1007     {\r
1008       public void actionPerformed(ActionEvent e)\r
1009       {\r
1010         fetchSequence_actionPerformed(e);\r
1011       }\r
1012     });\r
1013 \r
1014     annotationColour.setText("By Annotation...");\r
1015     annotationColour.addActionListener(new ActionListener()\r
1016     {\r
1017       public void actionPerformed(ActionEvent e)\r
1018       {\r
1019         annotationColour_actionPerformed(e);\r
1020       }\r
1021     });\r
1022     associatedData.setText("Load Features / Annotations");\r
1023     associatedData.addActionListener(new ActionListener()\r
1024     {\r
1025       public void actionPerformed(ActionEvent e)\r
1026       {\r
1027         associatedData_actionPerformed(e);\r
1028       }\r
1029     });\r
1030     autoCalculate.setText("Autocalculate Consensus");\r
1031     autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1032     autoCalculate.addActionListener(new ActionListener()\r
1033     {\r
1034       public void actionPerformed(ActionEvent e)\r
1035       {\r
1036         autoCalculate_actionPerformed(e);\r
1037       }\r
1038     });\r
1039     addSequenceMenu.setText("Add Sequences");\r
1040     addFromFile.setText("From File");\r
1041     addFromFile.addActionListener(new ActionListener()\r
1042     {\r
1043       public void actionPerformed(ActionEvent e)\r
1044       {\r
1045         addFromFile_actionPerformed(e);\r
1046       }\r
1047     });\r
1048     addFromText.setText("From Textbox");\r
1049     addFromText.addActionListener(new ActionListener()\r
1050     {\r
1051       public void actionPerformed(ActionEvent e)\r
1052       {\r
1053         addFromText_actionPerformed(e);\r
1054       }\r
1055     });\r
1056     addFromURL.setText("From URL");\r
1057     addFromURL.addActionListener(new ActionListener()\r
1058     {\r
1059       public void actionPerformed(ActionEvent e)\r
1060       {\r
1061         addFromURL_actionPerformed(e);\r
1062       }\r
1063     });\r
1064     exportFeatures.setText("Export Features...");\r
1065     exportFeatures.addActionListener(new ActionListener()\r
1066     {\r
1067       public void actionPerformed(ActionEvent e)\r
1068       {\r
1069         exportFeatures_actionPerformed(e);\r
1070       }\r
1071     });\r
1072     exportAnnotations.setText("Export Annotations...");\r
1073     exportAnnotations.addActionListener(new ActionListener()\r
1074     {\r
1075       public void actionPerformed(ActionEvent e)\r
1076       {\r
1077         exportAnnotations_actionPerformed(e);\r
1078       }\r
1079     });\r
1080     statusPanel.setLayout(gridLayout1);\r
1081     jMenu3.setText("Show");\r
1082     showAllSeqs.setText("All Sequences");\r
1083     showAllSeqs.addActionListener(new ActionListener()\r
1084     {\r
1085       public void actionPerformed(ActionEvent e)\r
1086       {\r
1087         showAllSeqs_actionPerformed(e);\r
1088       }\r
1089     });\r
1090     showAllColumns.setText("All Columns");\r
1091     showAllColumns.addActionListener(new ActionListener()\r
1092     {\r
1093       public void actionPerformed(ActionEvent e)\r
1094       {\r
1095         showAllColumns_actionPerformed(e);\r
1096       }\r
1097     });\r
1098     hideMenu.setText("Hide");\r
1099     hideSelSequences.setText("Selected Sequences");\r
1100     hideSelSequences.addActionListener(new ActionListener()\r
1101     {\r
1102       public void actionPerformed(ActionEvent e)\r
1103       {\r
1104         hideSelSequences_actionPerformed(e);\r
1105       }\r
1106     });\r
1107     hideSelColumns.setText("Selected Columns");\r
1108     hideSelColumns.addActionListener(new ActionListener()\r
1109     {\r
1110       public void actionPerformed(ActionEvent e)\r
1111       {\r
1112         hideSelColumns_actionPerformed(e);\r
1113       }\r
1114     });\r
1115     hiddenMarkers.setText("Show Hidden Markers");\r
1116     hiddenMarkers.addActionListener(new ActionListener()\r
1117     {\r
1118       public void actionPerformed(ActionEvent e)\r
1119       {\r
1120         hiddenMarkers_actionPerformed(e);\r
1121       }\r
1122     });\r
1123     invertColSel.setText("Invert Column Selection");\r
1124     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1125         event.KeyEvent.VK_I,\r
1126         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
1127         | java.awt.event.KeyEvent.ALT_MASK,\r
1128         false));\r
1129     invertColSel.addActionListener(new ActionListener()\r
1130     {\r
1131       public void actionPerformed(ActionEvent e)\r
1132       {\r
1133         invertColSel_actionPerformed(e);\r
1134       }\r
1135     });\r
1136     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1137     {\r
1138       public void stateChanged(ChangeEvent evt)\r
1139       {\r
1140         JTabbedPane pane = (JTabbedPane) evt.getSource();\r
1141         int sel = pane.getSelectedIndex();\r
1142         tabSelectionChanged(sel);\r
1143       }\r
1144     });\r
1145     tabbedPane.addMouseListener(new MouseAdapter()\r
1146     {\r
1147       public void mousePressed(MouseEvent e)\r
1148       {\r
1149         tabbedPane_mousePressed(e);\r
1150       }\r
1151     });\r
1152     tabbedPane.addFocusListener(new FocusAdapter()\r
1153     {\r
1154       public void focusGained(FocusEvent e)\r
1155       {\r
1156         tabbedPane_focusGained(e);\r
1157       }\r
1158     });\r
1159     save.setText("Save");\r
1160     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1161         KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1162     save.addActionListener(new ActionListener()\r
1163     {\r
1164       public void actionPerformed(ActionEvent e)\r
1165       {\r
1166         save_actionPerformed(e);\r
1167       }\r
1168     });\r
1169     reload.setEnabled(false);\r
1170     reload.setText("Reload");\r
1171     reload.addActionListener(new ActionListener()\r
1172     {\r
1173       public void actionPerformed(ActionEvent e)\r
1174       {\r
1175         reload_actionPerformed(e);\r
1176       }\r
1177     });\r
1178     newView.setText("New View");\r
1179     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1180         KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1181     newView.addActionListener(new ActionListener()\r
1182     {\r
1183       public void actionPerformed(ActionEvent e)\r
1184       {\r
1185         newView_actionPerformed(e);\r
1186       }\r
1187     });\r
1188     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
1189                               +\r
1190         "<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
1191     textColour.setText("Text Colour");\r
1192     textColour.addActionListener(new ActionListener()\r
1193     {\r
1194       public void actionPerformed(ActionEvent e)\r
1195       {\r
1196         textColour_actionPerformed(e);\r
1197       }\r
1198     });\r
1199     formatMenu.setText("Format");\r
1200     selectMenu.setText("Select");\r
1201     idRightAlign.setText("Right Align Sequence Id");\r
1202     idRightAlign.addActionListener(new ActionListener()\r
1203     {\r
1204       public void actionPerformed(ActionEvent e)\r
1205       {\r
1206         idRightAlign_actionPerformed(e);\r
1207       }\r
1208     });\r
1209     gatherViews.setEnabled(false);\r
1210     gatherViews.setText("Gather Views");\r
1211     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1212         event.KeyEvent.VK_G, 0, false));\r
1213     gatherViews.addActionListener(new ActionListener()\r
1214     {\r
1215       public void actionPerformed(ActionEvent e)\r
1216       {\r
1217         gatherViews_actionPerformed(e);\r
1218       }\r
1219     });\r
1220     expandViews.setEnabled(false);\r
1221     expandViews.setText("Expand Views");\r
1222     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1223         event.KeyEvent.VK_X, 0, false));\r
1224     expandViews.addActionListener(new ActionListener()\r
1225     {\r
1226       public void actionPerformed(ActionEvent e)\r
1227       {\r
1228         expandViews_actionPerformed(e);\r
1229       }\r
1230     });\r
1231     pageSetup.setText("Page Setup ...");\r
1232     pageSetup.addActionListener(new ActionListener()\r
1233     {\r
1234       public void actionPerformed(ActionEvent e)\r
1235       {\r
1236         pageSetup_actionPerformed(e);\r
1237       }\r
1238     });\r
1239 \r
1240     alignFrameMenuBar.add(fileMenu);\r
1241     alignFrameMenuBar.add(editMenu);\r
1242     alignFrameMenuBar.add(selectMenu);\r
1243     alignFrameMenuBar.add(viewMenu);\r
1244     alignFrameMenuBar.add(formatMenu);\r
1245     alignFrameMenuBar.add(colourMenu);\r
1246     alignFrameMenuBar.add(calculateMenu);\r
1247     alignFrameMenuBar.add(webService);\r
1248     fileMenu.add(fetchSequence);\r
1249     fileMenu.add(addSequenceMenu);\r
1250     fileMenu.add(reload);\r
1251     fileMenu.addSeparator();\r
1252     fileMenu.add(vamsasStore);\r
1253     fileMenu.add(save);\r
1254     fileMenu.add(saveAs);\r
1255     fileMenu.add(outputTextboxMenu);\r
1256     fileMenu.add(pageSetup);\r
1257     fileMenu.add(printMenuItem);\r
1258     fileMenu.addSeparator();\r
1259     fileMenu.add(jMenu2);\r
1260     fileMenu.add(exportFeatures);\r
1261     fileMenu.add(exportAnnotations);\r
1262     fileMenu.add(LoadtreeMenuItem);\r
1263     fileMenu.add(associatedData);\r
1264     fileMenu.addSeparator();\r
1265     fileMenu.add(closeMenuItem);\r
1266     editMenu.add(undoMenuItem);\r
1267     editMenu.add(redoMenuItem);\r
1268     editMenu.add(cut);\r
1269     editMenu.add(copy);\r
1270     editMenu.add(pasteMenu);\r
1271     editMenu.add(delete);\r
1272     editMenu.addSeparator();\r
1273     editMenu.add(remove2LeftMenuItem);\r
1274     editMenu.add(remove2RightMenuItem);\r
1275     editMenu.add(removeGappedColumnMenuItem);\r
1276     editMenu.add(removeAllGapsMenuItem);\r
1277     editMenu.add(removeRedundancyMenuItem);\r
1278     editMenu.addSeparator();\r
1279     editMenu.add(padGapsMenuitem);\r
1280     viewMenu.add(newView);\r
1281     viewMenu.add(expandViews);\r
1282     viewMenu.add(gatherViews);\r
1283     viewMenu.addSeparator();\r
1284     viewMenu.add(jMenu3);\r
1285     viewMenu.add(hideMenu);\r
1286     viewMenu.addSeparator();\r
1287     viewMenu.add(annotationPanelMenuItem);\r
1288     viewMenu.addSeparator();\r
1289     viewMenu.add(showSeqFeatures);\r
1290     viewMenu.add(featureSettings);\r
1291     viewMenu.addSeparator();\r
1292     viewMenu.add(overviewMenuItem);\r
1293     colourMenu.add(applyToAllGroups);\r
1294     colourMenu.add(textColour);\r
1295     colourMenu.addSeparator();\r
1296     colourMenu.add(noColourmenuItem);\r
1297     colourMenu.add(clustalColour);\r
1298     colourMenu.add(BLOSUM62Colour);\r
1299     colourMenu.add(PIDColour);\r
1300     colourMenu.add(zappoColour);\r
1301     colourMenu.add(taylorColour);\r
1302     colourMenu.add(hydrophobicityColour);\r
1303     colourMenu.add(helixColour);\r
1304     colourMenu.add(strandColour);\r
1305     colourMenu.add(turnColour);\r
1306     colourMenu.add(buriedColour);\r
1307     colourMenu.add(nucleotideColour);\r
1308     colourMenu.add(userDefinedColour);\r
1309     colourMenu.addSeparator();\r
1310     colourMenu.add(conservationMenuItem);\r
1311     colourMenu.add(modifyConservation);\r
1312     colourMenu.add(abovePIDThreshold);\r
1313     colourMenu.add(modifyPID);\r
1314     colourMenu.add(annotationColour);\r
1315     calculateMenu.add(sort);\r
1316     calculateMenu.add(calculate);\r
1317     calculateMenu.addSeparator();\r
1318     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1319     calculateMenu.add(PCAMenuItem);\r
1320     calculateMenu.addSeparator();\r
1321     calculateMenu.add(showTranslation);\r
1322     calculateMenu.add(autoCalculate);\r
1323     webServiceNoServices = new JMenuItem("<No Services>");\r
1324     webService.add(webServiceNoServices);\r
1325     pasteMenu.add(pasteNew);\r
1326     pasteMenu.add(pasteThis);\r
1327     sort.add(sortIDMenuItem);\r
1328     sort.add(sortGroupMenuItem);\r
1329     sort.add(sortPairwiseMenuItem);\r
1330     sort.add(sortByTreeMenu);\r
1331     calculate.add(averageDistanceTreeMenuItem);\r
1332     calculate.add(neighbourTreeMenuItem);\r
1333     calculate.add(avDistanceTreeBlosumMenuItem);\r
1334     calculate.add(njTreeBlosumMenuItem);\r
1335     jMenu2.add(htmlMenuItem);\r
1336     jMenu2.add(epsFile);\r
1337     jMenu2.add(createPNG);\r
1338     addSequenceMenu.add(addFromFile);\r
1339     addSequenceMenu.add(addFromText);\r
1340     addSequenceMenu.add(addFromURL);\r
1341     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1342     statusPanel.add(statusBar, null);\r
1343     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1344     jMenu3.add(showAllColumns);\r
1345     jMenu3.add(showAllSeqs);\r
1346     hideMenu.add(hideSelColumns);\r
1347     hideMenu.add(hideSelSequences);\r
1348     formatMenu.add(font);\r
1349     formatMenu.addSeparator();\r
1350     formatMenu.add(wrapMenuItem);\r
1351     formatMenu.add(scaleAbove);\r
1352     formatMenu.add(scaleLeft);\r
1353     formatMenu.add(scaleRight);\r
1354     formatMenu.add(seqLimits);\r
1355     formatMenu.add(idRightAlign);\r
1356     formatMenu.add(hiddenMarkers);\r
1357     formatMenu.add(viewBoxesMenuItem);\r
1358     formatMenu.add(viewTextMenuItem);\r
1359     formatMenu.add(colourTextMenuItem);\r
1360     formatMenu.add(renderGapsMenuItem);\r
1361     selectMenu.add(findMenuItem);\r
1362     selectMenu.addSeparator();\r
1363     selectMenu.add(selectAllSequenceMenuItem);\r
1364     selectMenu.add(deselectAllSequenceMenuItem);\r
1365     selectMenu.add(invertSequenceMenuItem);\r
1366     selectMenu.add(invertColSel);\r
1367     selectMenu.add(deleteGroups);\r
1368   }\r
1369 \r
1370   protected void outputText_actionPerformed(ActionEvent e)\r
1371   {\r
1372   }\r
1373 \r
1374   public void addFromFile_actionPerformed(ActionEvent e)\r
1375   {\r
1376 \r
1377   }\r
1378 \r
1379   public void addFromText_actionPerformed(ActionEvent e)\r
1380   {\r
1381 \r
1382   }\r
1383 \r
1384   public void addFromURL_actionPerformed(ActionEvent e)\r
1385   {\r
1386 \r
1387   }\r
1388 \r
1389   public void exportFeatures_actionPerformed(ActionEvent e)\r
1390   {\r
1391 \r
1392   }\r
1393 \r
1394   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1395   {\r
1396 \r
1397   }\r
1398 \r
1399   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1400   {\r
1401   }\r
1402 \r
1403   protected void closeMenuItem_actionPerformed(boolean b)\r
1404   {\r
1405   }\r
1406 \r
1407   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1408   {\r
1409   }\r
1410 \r
1411   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1412   {\r
1413   }\r
1414 \r
1415   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1416   {\r
1417   }\r
1418 \r
1419   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1420   {\r
1421   }\r
1422 \r
1423   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1424   {\r
1425   }\r
1426 \r
1427   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1428   {\r
1429   }\r
1430 \r
1431   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1432   {\r
1433   }\r
1434 \r
1435   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1436   {\r
1437   }\r
1438 \r
1439   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1440   {\r
1441   }\r
1442 \r
1443   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1444   {\r
1445   }\r
1446 \r
1447   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1448   {\r
1449   }\r
1450 \r
1451   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1452   {\r
1453   }\r
1454 \r
1455   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1456   {\r
1457   }\r
1458 \r
1459   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1460   {\r
1461   }\r
1462 \r
1463   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1464   {\r
1465   }\r
1466 \r
1467   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1480   {\r
1481   }\r
1482 \r
1483   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1484   {\r
1485   }\r
1486 \r
1487   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1488   {\r
1489   }\r
1490 \r
1491   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1492   {\r
1493   }\r
1494 \r
1495   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1496   {\r
1497   }\r
1498 \r
1499   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1500   {\r
1501   }\r
1502 \r
1503   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1504   {\r
1505   }\r
1506 \r
1507   protected void clustalColour_actionPerformed(ActionEvent e)\r
1508   {\r
1509   }\r
1510 \r
1511   protected void zappoColour_actionPerformed(ActionEvent e)\r
1512   {\r
1513   }\r
1514 \r
1515   protected void taylorColour_actionPerformed(ActionEvent e)\r
1516   {\r
1517   }\r
1518 \r
1519   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1520   {\r
1521   }\r
1522 \r
1523   protected void helixColour_actionPerformed(ActionEvent e)\r
1524   {\r
1525   }\r
1526 \r
1527   protected void strandColour_actionPerformed(ActionEvent e)\r
1528   {\r
1529   }\r
1530 \r
1531   protected void turnColour_actionPerformed(ActionEvent e)\r
1532   {\r
1533   }\r
1534 \r
1535   protected void buriedColour_actionPerformed(ActionEvent e)\r
1536   {\r
1537   }\r
1538 \r
1539   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1540   {\r
1541   }\r
1542 \r
1543   protected void PIDColour_actionPerformed(ActionEvent e)\r
1544   {\r
1545   }\r
1546 \r
1547   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1548   {\r
1549   }\r
1550 \r
1551   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1552   {\r
1553   }\r
1554 \r
1555   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1556   {\r
1557   }\r
1558 \r
1559   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1560   {\r
1561   }\r
1562 \r
1563   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1564   {\r
1565   }\r
1566 \r
1567   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1568   {\r
1569   }\r
1570 \r
1571   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1572   {\r
1573   }\r
1574 \r
1575   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1576   {\r
1577   }\r
1578 \r
1579   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1580   {\r
1581   }\r
1582 \r
1583   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1584   {\r
1585   }\r
1586 \r
1587   protected void copy_actionPerformed(ActionEvent e)\r
1588   {\r
1589   }\r
1590 \r
1591   protected void cut_actionPerformed(ActionEvent e)\r
1592   {\r
1593   }\r
1594 \r
1595   protected void delete_actionPerformed(ActionEvent e)\r
1596   {\r
1597   }\r
1598 \r
1599   protected void pasteNew_actionPerformed(ActionEvent e)\r
1600   {\r
1601   }\r
1602 \r
1603   protected void pasteThis_actionPerformed(ActionEvent e)\r
1604   {\r
1605   }\r
1606 \r
1607   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1608   {\r
1609   }\r
1610 \r
1611   public void createPNG(java.io.File f)\r
1612   {\r
1613   }\r
1614 \r
1615   protected void font_actionPerformed(ActionEvent e)\r
1616   {\r
1617   }\r
1618 \r
1619   protected void seqLimit_actionPerformed(ActionEvent e)\r
1620   {\r
1621   }\r
1622 \r
1623   public void seqDBRef_actionPerformed(ActionEvent e)\r
1624   {\r
1625 \r
1626   }\r
1627 \r
1628   public void createEPS(java.io.File f)\r
1629   {\r
1630   }\r
1631 \r
1632   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1633   {\r
1634   }\r
1635 \r
1636   protected void jpred_actionPerformed(ActionEvent e)\r
1637   {\r
1638   }\r
1639 \r
1640   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1641   {\r
1642   }\r
1643 \r
1644   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1645   {\r
1646   }\r
1647 \r
1648   protected void scaleRight_actionPerformed(ActionEvent e)\r
1649   {\r
1650   }\r
1651 \r
1652   protected void modifyPID_actionPerformed(ActionEvent e)\r
1653   {\r
1654   }\r
1655 \r
1656   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1657   {\r
1658   }\r
1659 \r
1660   protected void saveAs_actionPerformed(ActionEvent e)\r
1661   {\r
1662   }\r
1663 \r
1664   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1665   {\r
1666   }\r
1667 \r
1668   public void vamsasStore_actionPerformed(ActionEvent e)\r
1669   {\r
1670 \r
1671   }\r
1672 \r
1673   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1674   {\r
1675 \r
1676   }\r
1677 \r
1678   public void showTranslation_actionPerformed(ActionEvent e)\r
1679   {\r
1680 \r
1681   }\r
1682 \r
1683   public void featureSettings_actionPerformed(ActionEvent e)\r
1684   {\r
1685 \r
1686   }\r
1687 \r
1688   public void fetchSequence_actionPerformed(ActionEvent e)\r
1689   {\r
1690 \r
1691   }\r
1692 \r
1693   public void smoothFont_actionPerformed(ActionEvent e)\r
1694   {\r
1695 \r
1696   }\r
1697 \r
1698   public void annotationColour_actionPerformed(ActionEvent e)\r
1699   {\r
1700 \r
1701   }\r
1702 \r
1703   public void associatedData_actionPerformed(ActionEvent e)\r
1704   {\r
1705 \r
1706   }\r
1707 \r
1708   public void autoCalculate_actionPerformed(ActionEvent e)\r
1709   {\r
1710 \r
1711   }\r
1712 \r
1713   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1714   {\r
1715 \r
1716   }\r
1717 \r
1718   public void showAllColumns_actionPerformed(ActionEvent e)\r
1719   {\r
1720 \r
1721   }\r
1722 \r
1723   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1724   {\r
1725 \r
1726   }\r
1727 \r
1728   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1729   {\r
1730 \r
1731   }\r
1732 \r
1733   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1734   {\r
1735 \r
1736   }\r
1737 \r
1738   public void findPdbId_actionPerformed(ActionEvent e)\r
1739   {\r
1740 \r
1741   }\r
1742 \r
1743   public void enterPdbId_actionPerformed(ActionEvent e)\r
1744   {\r
1745 \r
1746   }\r
1747 \r
1748   public void pdbFile_actionPerformed(ActionEvent e)\r
1749   {\r
1750 \r
1751   }\r
1752 \r
1753   public void invertColSel_actionPerformed(ActionEvent e)\r
1754   {\r
1755 \r
1756   }\r
1757 \r
1758   public void tabSelectionChanged(int sel)\r
1759   {\r
1760 \r
1761   }\r
1762 \r
1763   public void tabbedPane_mousePressed(MouseEvent e)\r
1764   {\r
1765 \r
1766   }\r
1767 \r
1768   public void tabbedPane_focusGained(FocusEvent e)\r
1769   {\r
1770     requestFocus();\r
1771   }\r
1772 \r
1773   public void save_actionPerformed(ActionEvent e)\r
1774   {\r
1775 \r
1776   }\r
1777 \r
1778   public void reload_actionPerformed(ActionEvent e)\r
1779   {\r
1780 \r
1781   }\r
1782 \r
1783   public void newView_actionPerformed(ActionEvent e)\r
1784   {\r
1785 \r
1786   }\r
1787 \r
1788   public void textColour_actionPerformed(ActionEvent e)\r
1789   {\r
1790 \r
1791   }\r
1792 \r
1793   public void idRightAlign_actionPerformed(ActionEvent e)\r
1794   {\r
1795 \r
1796   }\r
1797 \r
1798   public void expandViews_actionPerformed(ActionEvent e)\r
1799   {\r
1800 \r
1801   }\r
1802 \r
1803   public void gatherViews_actionPerformed(ActionEvent e)\r
1804   {\r
1805 \r
1806   }\r
1807 \r
1808   public void buildTreeMenu()\r
1809   {\r
1810 \r
1811   }\r
1812 \r
1813   public void pageSetup_actionPerformed(ActionEvent e)\r
1814   {\r
1815 \r
1816   }\r
1817 }\r