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   JMenuItem alignmentProperties = new JMenuItem();\r
 149   public GAlignFrame()\r
 150   {\r
 151     try\r
 152     {\r
 153       jbInit();\r
 154       setJMenuBar(alignFrameMenuBar);\r
 155 \r
 156       // dynamically fill save as menu with available formats\r
 157       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 158       {\r
 159         JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.\r
 160                                        WRITEABLE_FORMATS[i]);\r
 161 \r
 162         item.addActionListener(new java.awt.event.ActionListener()\r
 163         {\r
 164           public void actionPerformed(ActionEvent e)\r
 165           {\r
 166             outputText_actionPerformed(e);\r
 167           }\r
 168         });\r
 169 \r
 170         outputTextboxMenu.add(item);\r
 171       }\r
 172     }\r
 173     catch (Exception e)\r
 174     {\r
 175     }\r
 176 \r
 177     if (!System.getProperty("os.name").startsWith("Mac"))\r
 178     {\r
 179       closeMenuItem.setMnemonic('C');\r
 180       outputTextboxMenu.setMnemonic('T');\r
 181       undoMenuItem.setMnemonic('Z');\r
 182       redoMenuItem.setMnemonic('0');\r
 183       copy.setMnemonic('C');\r
 184       cut.setMnemonic('U');\r
 185       pasteMenu.setMnemonic('P');\r
 186       reload.setMnemonic('R');\r
 187     }\r
 188 \r
 189     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
 190     {\r
 191       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 192           getUserColourSchemes().keys();\r
 193 \r
 194       while (userColours.hasMoreElements())\r
 195       {\r
 196         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
 197             userColours.\r
 198             nextElement().toString());\r
 199         radioItem.setName("USER_DEFINED");\r
 200         radioItem.addMouseListener(new MouseAdapter()\r
 201         {\r
 202           public void mousePressed(MouseEvent evt)\r
 203           {\r
 204             if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 205             {\r
 206               radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 207 \r
 208               int option = JOptionPane.showInternalConfirmDialog(jalview.gui.\r
 209                   Desktop.desktop,\r
 210                   "Remove from default list?",\r
 211                   "Remove user defined colour",\r
 212                   JOptionPane.YES_NO_OPTION);\r
 213               if (option == JOptionPane.YES_OPTION)\r
 214               {\r
 215                 jalview.gui.UserDefinedColours.removeColourFromDefaults(\r
 216                     radioItem.getText());\r
 217                 colourMenu.remove(radioItem);\r
 218               }\r
 219               else\r
 220               {\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         });\r
 232         radioItem.addActionListener(new ActionListener()\r
 233         {\r
 234           public void actionPerformed(ActionEvent evt)\r
 235           {\r
 236             userDefinedColour_actionPerformed(evt);\r
 237           }\r
 238         });\r
 239         colourMenu.insert(radioItem, 15);\r
 240         colours.add(radioItem);\r
 241       }\r
 242     }\r
 243     colours.add(noColourmenuItem);\r
 244     colours.add(clustalColour);\r
 245     colours.add(zappoColour);\r
 246     colours.add(taylorColour);\r
 247     colours.add(hydrophobicityColour);\r
 248     colours.add(helixColour);\r
 249     colours.add(strandColour);\r
 250     colours.add(turnColour);\r
 251     colours.add(buriedColour);\r
 252     colours.add(userDefinedColour);\r
 253     colours.add(PIDColour);\r
 254     colours.add(BLOSUM62Colour);\r
 255     colours.add(nucleotideColour);\r
 256 \r
 257     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\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() |\r
 344         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 345     saveAs.addActionListener(new ActionListener()\r
 346     {\r
 347       public void actionPerformed(ActionEvent e)\r
 348       {\r
 349         saveAs_actionPerformed(e);\r
 350       }\r
 351     });\r
 352     closeMenuItem.setText("Close");\r
 353     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 354         event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 355     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 356     {\r
 357       public void actionPerformed(ActionEvent e)\r
 358       {\r
 359         closeMenuItem_actionPerformed(false);\r
 360       }\r
 361     });\r
 362     editMenu.setText("Edit");\r
 363     viewMenu.setText("View");\r
 364     colourMenu.setText("Colour");\r
 365     calculateMenu.setText("Calculate");\r
 366     webService.setText("Web Service");\r
 367     selectAllSequenceMenuItem.setText("Select All");\r
 368     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 369         java.awt.event.KeyEvent.VK_A,\r
 370         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 371     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 372                                                 ActionListener()\r
 373     {\r
 374       public void actionPerformed(ActionEvent e)\r
 375       {\r
 376         selectAllSequenceMenuItem_actionPerformed(e);\r
 377       }\r
 378     });\r
 379     deselectAllSequenceMenuItem.setText("Deselect All");\r
 380     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 381                                                getKeyStroke(\r
 382         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 383     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 384                                                   ActionListener()\r
 385     {\r
 386       public void actionPerformed(ActionEvent e)\r
 387       {\r
 388         deselectAllSequenceMenuItem_actionPerformed(e);\r
 389       }\r
 390     });\r
 391     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 392     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 393         java.awt.event.KeyEvent.VK_I,\r
 394         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 395     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         invertSequenceMenuItem_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     remove2LeftMenuItem.setText("Remove Left");\r
 403     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 404         awt.event.KeyEvent.VK_L,\r
 405         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 406     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 407     {\r
 408       public void actionPerformed(ActionEvent e)\r
 409       {\r
 410         remove2LeftMenuItem_actionPerformed(e);\r
 411       }\r
 412     });\r
 413     remove2RightMenuItem.setText("Remove Right");\r
 414     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 415         awt.event.KeyEvent.VK_R,\r
 416         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 417     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 418     {\r
 419       public void actionPerformed(ActionEvent e)\r
 420       {\r
 421         remove2RightMenuItem_actionPerformed(e);\r
 422       }\r
 423     });\r
 424     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 425     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 426                                               getKeyStroke(java.awt.event.\r
 427         KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 428     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 429                                                  ActionListener()\r
 430     {\r
 431       public void actionPerformed(ActionEvent e)\r
 432       {\r
 433         removeGappedColumnMenuItem_actionPerformed(e);\r
 434       }\r
 435     });\r
 436     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 437     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 438         java.awt.event.KeyEvent.VK_E,\r
 439         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
 440         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 441     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 442     {\r
 443       public void actionPerformed(ActionEvent e)\r
 444       {\r
 445         removeAllGapsMenuItem_actionPerformed(e);\r
 446       }\r
 447     });\r
 448     viewBoxesMenuItem.setText("Boxes");\r
 449     viewBoxesMenuItem.setState(true);\r
 450     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         viewBoxesMenuItem_actionPerformed(e);\r
 455       }\r
 456     });\r
 457     viewTextMenuItem.setText("Text");\r
 458     viewTextMenuItem.setState(true);\r
 459     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 460     {\r
 461       public void actionPerformed(ActionEvent e)\r
 462       {\r
 463         viewTextMenuItem_actionPerformed(e);\r
 464       }\r
 465     });\r
 466     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 467     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 468     {\r
 469       public void actionPerformed(ActionEvent e)\r
 470       {\r
 471         sortPairwiseMenuItem_actionPerformed(e);\r
 472       }\r
 473     });\r
 474     sortIDMenuItem.setText("by ID");\r
 475     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 476     {\r
 477       public void actionPerformed(ActionEvent e)\r
 478       {\r
 479         sortIDMenuItem_actionPerformed(e);\r
 480       }\r
 481     });\r
 482     sortGroupMenuItem.setText("by Group");\r
 483     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 484     {\r
 485       public void actionPerformed(ActionEvent e)\r
 486       {\r
 487         sortGroupMenuItem_actionPerformed(e);\r
 488       }\r
 489     });\r
 490     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 491     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 492         java.awt.event.KeyEvent.VK_D,\r
 493         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 494     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 495                                                ActionListener()\r
 496     {\r
 497       public void actionPerformed(ActionEvent e)\r
 498       {\r
 499         removeRedundancyMenuItem_actionPerformed(e);\r
 500       }\r
 501     });\r
 502     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 503     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 504                                                 ActionListener()\r
 505     {\r
 506       public void actionPerformed(ActionEvent e)\r
 507       {\r
 508         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 509       }\r
 510     });\r
 511     PCAMenuItem.setText("Principal Component Analysis");\r
 512     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 513     {\r
 514       public void actionPerformed(ActionEvent e)\r
 515       {\r
 516         PCAMenuItem_actionPerformed(e);\r
 517       }\r
 518     });\r
 519     averageDistanceTreeMenuItem.setText(\r
 520         "Average Distance Using % Identity");\r
 521     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 522                                                   ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         averageDistanceTreeMenuItem_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 530     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         neighbourTreeMenuItem_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     this.getContentPane().setLayout(borderLayout1);\r
 538     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 539     statusBar.setBackground(Color.white);\r
 540     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 541     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 542     statusBar.setText("Status bar");\r
 543     outputTextboxMenu.setText("Output to Textbox");\r
 544     clustalColour.setText("Clustalx");\r
 545 \r
 546     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         clustalColour_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     zappoColour.setText("Zappo");\r
 554     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         zappoColour_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     taylorColour.setText("Taylor");\r
 562     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 563     {\r
 564       public void actionPerformed(ActionEvent e)\r
 565       {\r
 566         taylorColour_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     hydrophobicityColour.setText("Hydrophobicity");\r
 570     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent e)\r
 573       {\r
 574         hydrophobicityColour_actionPerformed(e);\r
 575       }\r
 576     });\r
 577     helixColour.setText("Helix Propensity");\r
 578     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent e)\r
 581       {\r
 582         helixColour_actionPerformed(e);\r
 583       }\r
 584     });\r
 585     strandColour.setText("Strand Propensity");\r
 586     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 587     {\r
 588       public void actionPerformed(ActionEvent e)\r
 589       {\r
 590         strandColour_actionPerformed(e);\r
 591       }\r
 592     });\r
 593     turnColour.setText("Turn Propensity");\r
 594     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 595     {\r
 596       public void actionPerformed(ActionEvent e)\r
 597       {\r
 598         turnColour_actionPerformed(e);\r
 599       }\r
 600     });\r
 601     buriedColour.setText("Buried Index");\r
 602     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 603     {\r
 604       public void actionPerformed(ActionEvent e)\r
 605       {\r
 606         buriedColour_actionPerformed(e);\r
 607       }\r
 608     });\r
 609     userDefinedColour.setText("User Defined...");\r
 610     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 611     {\r
 612       public void actionPerformed(ActionEvent e)\r
 613       {\r
 614         userDefinedColour_actionPerformed(e);\r
 615       }\r
 616     });\r
 617     PIDColour.setText("Percentage Identity");\r
 618     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 619     {\r
 620       public void actionPerformed(ActionEvent e)\r
 621       {\r
 622         PIDColour_actionPerformed(e);\r
 623       }\r
 624     });\r
 625     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 626     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 627     {\r
 628       public void actionPerformed(ActionEvent e)\r
 629       {\r
 630         BLOSUM62Colour_actionPerformed(e);\r
 631       }\r
 632     });\r
 633     avDistanceTreeBlosumMenuItem.setText(\r
 634         "Average Distance Using BLOSUM62");\r
 635     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 636         ActionListener()\r
 637     {\r
 638       public void actionPerformed(ActionEvent e)\r
 639       {\r
 640         avTreeBlosumMenuItem_actionPerformed(e);\r
 641       }\r
 642     });\r
 643     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 644     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 645     {\r
 646       public void actionPerformed(ActionEvent e)\r
 647       {\r
 648         njTreeBlosumMenuItem_actionPerformed(e);\r
 649       }\r
 650     });\r
 651     annotationPanelMenuItem.setActionCommand("");\r
 652     annotationPanelMenuItem.setText("Show Annotations");\r
 653     annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(\r
 654         "SHOW_ANNOTATIONS", true));\r
 655     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 656     {\r
 657       public void actionPerformed(ActionEvent e)\r
 658       {\r
 659         annotationPanelMenuItem_actionPerformed(e);\r
 660       }\r
 661     });\r
 662     colourTextMenuItem.setText("Colour Text");\r
 663     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 664     {\r
 665       public void actionPerformed(ActionEvent e)\r
 666       {\r
 667         colourTextMenuItem_actionPerformed(e);\r
 668       }\r
 669     });\r
 670     htmlMenuItem.setText("HTML");\r
 671     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 672     {\r
 673       public void actionPerformed(ActionEvent e)\r
 674       {\r
 675         htmlMenuItem_actionPerformed(e);\r
 676       }\r
 677     });\r
 678     overviewMenuItem.setText("Overview Window");\r
 679     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 680     {\r
 681       public void actionPerformed(ActionEvent e)\r
 682       {\r
 683         overviewMenuItem_actionPerformed(e);\r
 684       }\r
 685     });\r
 686     undoMenuItem.setEnabled(false);\r
 687     undoMenuItem.setText("Undo");\r
 688     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 689         java.awt.event.KeyEvent.VK_Z,\r
 690         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 691     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 692     {\r
 693       public void actionPerformed(ActionEvent e)\r
 694       {\r
 695         undoMenuItem_actionPerformed(e);\r
 696       }\r
 697     });\r
 698     redoMenuItem.setEnabled(false);\r
 699     redoMenuItem.setText("Redo");\r
 700     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 701         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 702     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 703     {\r
 704       public void actionPerformed(ActionEvent e)\r
 705       {\r
 706         redoMenuItem_actionPerformed(e);\r
 707       }\r
 708     });\r
 709     conservationMenuItem.setText("By Conservation");\r
 710     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 711     {\r
 712       public void actionPerformed(ActionEvent e)\r
 713       {\r
 714         conservationMenuItem_actionPerformed(e);\r
 715       }\r
 716     });\r
 717     noColourmenuItem.setText("None");\r
 718     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 719     {\r
 720       public void actionPerformed(ActionEvent e)\r
 721       {\r
 722         noColourmenuItem_actionPerformed(e);\r
 723       }\r
 724     });\r
 725     wrapMenuItem.setText("Wrap");\r
 726     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 727     {\r
 728       public void actionPerformed(ActionEvent e)\r
 729       {\r
 730         wrapMenuItem_actionPerformed(e);\r
 731       }\r
 732     });\r
 733     printMenuItem.setText("Print ...");\r
 734     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 735         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 736     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 737     {\r
 738       public void actionPerformed(ActionEvent e)\r
 739       {\r
 740         printMenuItem_actionPerformed(e);\r
 741       }\r
 742     });\r
 743     renderGapsMenuItem.setText("Show Gaps");\r
 744     renderGapsMenuItem.setState(true);\r
 745     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 746     {\r
 747       public void actionPerformed(ActionEvent e)\r
 748       {\r
 749         renderGapsMenuItem_actionPerformed(e);\r
 750       }\r
 751     });\r
 752     findMenuItem.setText("Find...");\r
 753     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 754         java.awt.event.KeyEvent.VK_F,\r
 755         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 756     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 757     {\r
 758       public void actionPerformed(ActionEvent e)\r
 759       {\r
 760         findMenuItem_actionPerformed(e);\r
 761       }\r
 762     });\r
 763     abovePIDThreshold.setText("Above Identity Threshold");\r
 764     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 765     {\r
 766       public void actionPerformed(ActionEvent e)\r
 767       {\r
 768         abovePIDThreshold_actionPerformed(e);\r
 769       }\r
 770     });\r
 771     showSeqFeatures.setText("Show Sequence Features");\r
 772     showSeqFeatures.addActionListener(new ActionListener()\r
 773     {\r
 774       public void actionPerformed(ActionEvent actionEvent)\r
 775       {\r
 776         showSeqFeatures_actionPerformed(actionEvent);\r
 777       }\r
 778     });\r
 779     nucleotideColour.setText("Nucleotide");\r
 780     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 781     {\r
 782       public void actionPerformed(ActionEvent e)\r
 783       {\r
 784         nucleotideColour_actionPerformed(e);\r
 785       }\r
 786     });\r
 787     deleteGroups.setText("Undefine groups");\r
 788     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 789         event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 790     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 791     {\r
 792       public void actionPerformed(ActionEvent e)\r
 793       {\r
 794         deleteGroups_actionPerformed(e);\r
 795       }\r
 796     });\r
 797     copy.setText("Copy");\r
 798     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 799         java.awt.event.KeyEvent.VK_C,\r
 800         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 801 \r
 802     copy.addActionListener(new java.awt.event.ActionListener()\r
 803     {\r
 804       public void actionPerformed(ActionEvent e)\r
 805       {\r
 806         copy_actionPerformed(e);\r
 807       }\r
 808     });\r
 809     cut.setText("Cut");\r
 810     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 811         java.awt.event.KeyEvent.VK_X,\r
 812         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 813     cut.addActionListener(new java.awt.event.ActionListener()\r
 814     {\r
 815       public void actionPerformed(ActionEvent e)\r
 816       {\r
 817         cut_actionPerformed(e);\r
 818       }\r
 819     });\r
 820     delete.setText("Delete");\r
 821     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 822         KeyEvent.VK_BACK_SPACE, 0, false));\r
 823     delete.addActionListener(new java.awt.event.ActionListener()\r
 824     {\r
 825       public void actionPerformed(ActionEvent e)\r
 826       {\r
 827         delete_actionPerformed(e);\r
 828       }\r
 829     });\r
 830     pasteMenu.setText("Paste");\r
 831     pasteNew.setText("To New Alignment");\r
 832     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 833         java.awt.event.KeyEvent.VK_V,\r
 834         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
 835         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 836     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 837     {\r
 838       public void actionPerformed(ActionEvent e)\r
 839       {\r
 840         pasteNew_actionPerformed(e);\r
 841       }\r
 842     });\r
 843     pasteThis.setText("Add To This Alignment");\r
 844     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 845         java.awt.event.KeyEvent.VK_V,\r
 846         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 847     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 848     {\r
 849       public void actionPerformed(ActionEvent e)\r
 850       {\r
 851         pasteThis_actionPerformed(e);\r
 852       }\r
 853     });\r
 854     applyToAllGroups.setText("Apply Colour To All Groups");\r
 855     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 856     {\r
 857       public void actionPerformed(ActionEvent e)\r
 858       {\r
 859         applyToAllGroups_actionPerformed(e);\r
 860       }\r
 861     });\r
 862     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 863     {\r
 864       public void actionPerformed(ActionEvent e)\r
 865       {\r
 866         createPNG(null);\r
 867       }\r
 868     });\r
 869     createPNG.setActionCommand("Save As PNG Image");\r
 870     createPNG.setText("PNG");\r
 871     font.setText("Font...");\r
 872     font.addActionListener(new java.awt.event.ActionListener()\r
 873     {\r
 874       public void actionPerformed(ActionEvent e)\r
 875       {\r
 876         font_actionPerformed(e);\r
 877       }\r
 878     });\r
 879 \r
 880     seqLimits.setText("Show Sequence Limits");\r
 881     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));\r
 882     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 883     {\r
 884       public void actionPerformed(ActionEvent e)\r
 885       {\r
 886         seqLimit_actionPerformed(e);\r
 887       }\r
 888     });\r
 889     epsFile.setText("EPS");\r
 890     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 891     {\r
 892       public void actionPerformed(ActionEvent e)\r
 893       {\r
 894         createEPS(null);\r
 895       }\r
 896     });\r
 897     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 898     LoadtreeMenuItem.setText("Load Associated Tree");\r
 899     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 900     {\r
 901       public void actionPerformed(ActionEvent e)\r
 902       {\r
 903         LoadtreeMenuItem_actionPerformed(e);\r
 904       }\r
 905     });\r
 906     scaleAbove.setVisible(false);\r
 907     scaleAbove.setText("Scale Above");\r
 908     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 909     {\r
 910       public void actionPerformed(ActionEvent e)\r
 911       {\r
 912         scaleAbove_actionPerformed(e);\r
 913       }\r
 914     });\r
 915     scaleLeft.setVisible(false);\r
 916     scaleLeft.setSelected(true);\r
 917     scaleLeft.setText("Scale Left");\r
 918     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 919     {\r
 920       public void actionPerformed(ActionEvent e)\r
 921       {\r
 922         scaleLeft_actionPerformed(e);\r
 923       }\r
 924     });\r
 925     scaleRight.setVisible(false);\r
 926     scaleRight.setSelected(true);\r
 927     scaleRight.setText("Scale Right");\r
 928     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 929     {\r
 930       public void actionPerformed(ActionEvent e)\r
 931       {\r
 932         scaleRight_actionPerformed(e);\r
 933       }\r
 934     });\r
 935     modifyPID.setText("Modify Identity Threshold...");\r
 936     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 937     {\r
 938       public void actionPerformed(ActionEvent e)\r
 939       {\r
 940         modifyPID_actionPerformed(e);\r
 941       }\r
 942     });\r
 943     modifyConservation.setText("Modify Conservation Threshold...");\r
 944     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 945     {\r
 946       public void actionPerformed(ActionEvent e)\r
 947       {\r
 948         modifyConservation_actionPerformed(e);\r
 949       }\r
 950     });\r
 951     sortByTreeMenu.setText("By Tree Order");\r
 952     sort.setText("Sort");\r
 953     sort.addMenuListener(new MenuListener()\r
 954     {\r
 955       public void menuSelected(MenuEvent e)\r
 956       {\r
 957         buildTreeMenu();\r
 958       }\r
 959 \r
 960       public void menuDeselected(MenuEvent e)\r
 961       {\r
 962       }\r
 963 \r
 964       public void menuCanceled(MenuEvent e)\r
 965       {\r
 966       }\r
 967     });\r
 968     calculate.setText("Calculate Tree");\r
 969 \r
 970     jMenu2.setText("Export Image");\r
 971     padGapsMenuitem.setText("Pad Gaps");\r
 972     padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 973     padGapsMenuitem.addActionListener(new ActionListener()\r
 974     {\r
 975       public void actionPerformed(ActionEvent e)\r
 976       {\r
 977         padGapsMenuitem_actionPerformed(e);\r
 978       }\r
 979     });\r
 980     vamsasStore.setVisible(false);\r
 981     vamsasStore.setText("VAMSAS store");\r
 982     vamsasStore.addActionListener(new ActionListener()\r
 983     {\r
 984       public void actionPerformed(ActionEvent e)\r
 985       {\r
 986         vamsasStore_actionPerformed(e);\r
 987       }\r
 988     });\r
 989     showTranslation.setText("Translate cDNA");\r
 990     showTranslation.addActionListener(new ActionListener()\r
 991     {\r
 992       public void actionPerformed(ActionEvent e)\r
 993       {\r
 994         showTranslation_actionPerformed(e);\r
 995       }\r
 996     });\r
 997 \r
 998     featureSettings.setText("Feature Settings...");\r
 999     featureSettings.addActionListener(new ActionListener()\r
1000     {\r
1001       public void actionPerformed(ActionEvent e)\r
1002       {\r
1003         featureSettings_actionPerformed(e);\r
1004       }\r
1005     });\r
1006     fetchSequence.setText("Fetch Sequence(s)...");\r
1007     fetchSequence.addActionListener(new ActionListener()\r
1008     {\r
1009       public void actionPerformed(ActionEvent e)\r
1010       {\r
1011         fetchSequence_actionPerformed(e);\r
1012       }\r
1013     });\r
1014 \r
1015     annotationColour.setText("By Annotation...");\r
1016     annotationColour.addActionListener(new ActionListener()\r
1017     {\r
1018       public void actionPerformed(ActionEvent e)\r
1019       {\r
1020         annotationColour_actionPerformed(e);\r
1021       }\r
1022     });\r
1023     associatedData.setText("Load Features / Annotations");\r
1024     associatedData.addActionListener(new ActionListener()\r
1025     {\r
1026       public void actionPerformed(ActionEvent e)\r
1027       {\r
1028         associatedData_actionPerformed(e);\r
1029       }\r
1030     });\r
1031     autoCalculate.setText("Autocalculate Consensus");\r
1032     autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1033     autoCalculate.addActionListener(new ActionListener()\r
1034     {\r
1035       public void actionPerformed(ActionEvent e)\r
1036       {\r
1037         autoCalculate_actionPerformed(e);\r
1038       }\r
1039     });\r
1040     addSequenceMenu.setText("Add Sequences");\r
1041     addFromFile.setText("From File");\r
1042     addFromFile.addActionListener(new ActionListener()\r
1043     {\r
1044       public void actionPerformed(ActionEvent e)\r
1045       {\r
1046         addFromFile_actionPerformed(e);\r
1047       }\r
1048     });\r
1049     addFromText.setText("From Textbox");\r
1050     addFromText.addActionListener(new ActionListener()\r
1051     {\r
1052       public void actionPerformed(ActionEvent e)\r
1053       {\r
1054         addFromText_actionPerformed(e);\r
1055       }\r
1056     });\r
1057     addFromURL.setText("From URL");\r
1058     addFromURL.addActionListener(new ActionListener()\r
1059     {\r
1060       public void actionPerformed(ActionEvent e)\r
1061       {\r
1062         addFromURL_actionPerformed(e);\r
1063       }\r
1064     });\r
1065     exportFeatures.setText("Export Features...");\r
1066     exportFeatures.addActionListener(new ActionListener()\r
1067     {\r
1068       public void actionPerformed(ActionEvent e)\r
1069       {\r
1070         exportFeatures_actionPerformed(e);\r
1071       }\r
1072     });\r
1073     exportAnnotations.setText("Export Annotations...");\r
1074     exportAnnotations.addActionListener(new ActionListener()\r
1075     {\r
1076       public void actionPerformed(ActionEvent e)\r
1077       {\r
1078         exportAnnotations_actionPerformed(e);\r
1079       }\r
1080     });\r
1081     statusPanel.setLayout(gridLayout1);\r
1082     jMenu3.setText("Show");\r
1083     showAllSeqs.setText("All Sequences");\r
1084     showAllSeqs.addActionListener(new ActionListener()\r
1085     {\r
1086       public void actionPerformed(ActionEvent e)\r
1087       {\r
1088         showAllSeqs_actionPerformed(e);\r
1089       }\r
1090     });\r
1091     showAllColumns.setText("All Columns");\r
1092     showAllColumns.addActionListener(new ActionListener()\r
1093     {\r
1094       public void actionPerformed(ActionEvent e)\r
1095       {\r
1096         showAllColumns_actionPerformed(e);\r
1097       }\r
1098     });\r
1099     hideMenu.setText("Hide");\r
1100     hideSelSequences.setText("Selected Sequences");\r
1101     hideSelSequences.addActionListener(new ActionListener()\r
1102     {\r
1103       public void actionPerformed(ActionEvent e)\r
1104       {\r
1105         hideSelSequences_actionPerformed(e);\r
1106       }\r
1107     });\r
1108     hideSelColumns.setText("Selected Columns");\r
1109     hideSelColumns.addActionListener(new ActionListener()\r
1110     {\r
1111       public void actionPerformed(ActionEvent e)\r
1112       {\r
1113         hideSelColumns_actionPerformed(e);\r
1114       }\r
1115     });\r
1116     hiddenMarkers.setText("Show Hidden Markers");\r
1117     hiddenMarkers.addActionListener(new ActionListener()\r
1118     {\r
1119       public void actionPerformed(ActionEvent e)\r
1120       {\r
1121         hiddenMarkers_actionPerformed(e);\r
1122       }\r
1123     });\r
1124     invertColSel.setText("Invert Column Selection");\r
1125     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1126         event.KeyEvent.VK_I,\r
1127         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
1128         | java.awt.event.KeyEvent.ALT_MASK,\r
1129         false));\r
1130     invertColSel.addActionListener(new ActionListener()\r
1131     {\r
1132       public void actionPerformed(ActionEvent e)\r
1133       {\r
1134         invertColSel_actionPerformed(e);\r
1135       }\r
1136     });\r
1137     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1138     {\r
1139       public void stateChanged(ChangeEvent evt)\r
1140       {\r
1141         JTabbedPane pane = (JTabbedPane) evt.getSource();\r
1142         int sel = pane.getSelectedIndex();\r
1143         tabSelectionChanged(sel);\r
1144       }\r
1145     });\r
1146     tabbedPane.addMouseListener(new MouseAdapter()\r
1147     {\r
1148       public void mousePressed(MouseEvent e)\r
1149       {\r
1150         tabbedPane_mousePressed(e);\r
1151       }\r
1152     });\r
1153     tabbedPane.addFocusListener(new FocusAdapter()\r
1154     {\r
1155       public void focusGained(FocusEvent e)\r
1156       {\r
1157         tabbedPane_focusGained(e);\r
1158       }\r
1159     });\r
1160     save.setText("Save");\r
1161     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1162         KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1163     save.addActionListener(new ActionListener()\r
1164     {\r
1165       public void actionPerformed(ActionEvent e)\r
1166       {\r
1167         save_actionPerformed(e);\r
1168       }\r
1169     });\r
1170     reload.setEnabled(false);\r
1171     reload.setText("Reload");\r
1172     reload.addActionListener(new ActionListener()\r
1173     {\r
1174       public void actionPerformed(ActionEvent e)\r
1175       {\r
1176         reload_actionPerformed(e);\r
1177       }\r
1178     });\r
1179     newView.setText("New View");\r
1180     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1181         KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1182     newView.addActionListener(new ActionListener()\r
1183     {\r
1184       public void actionPerformed(ActionEvent e)\r
1185       {\r
1186         newView_actionPerformed(e);\r
1187       }\r
1188     });\r
1189     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
1190                               +\r
1191         "<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
1192     textColour.setText("Text Colour");\r
1193     textColour.addActionListener(new ActionListener()\r
1194     {\r
1195       public void actionPerformed(ActionEvent e)\r
1196       {\r
1197         textColour_actionPerformed(e);\r
1198       }\r
1199     });\r
1200     formatMenu.setText("Format");\r
1201     selectMenu.setText("Select");\r
1202     idRightAlign.setText("Right Align Sequence Id");\r
1203     idRightAlign.addActionListener(new ActionListener()\r
1204     {\r
1205       public void actionPerformed(ActionEvent e)\r
1206       {\r
1207         idRightAlign_actionPerformed(e);\r
1208       }\r
1209     });\r
1210     gatherViews.setEnabled(false);\r
1211     gatherViews.setText("Gather Views");\r
1212     gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1213         event.KeyEvent.VK_G, 0, false));\r
1214     gatherViews.addActionListener(new ActionListener()\r
1215     {\r
1216       public void actionPerformed(ActionEvent e)\r
1217       {\r
1218         gatherViews_actionPerformed(e);\r
1219       }\r
1220     });\r
1221     expandViews.setEnabled(false);\r
1222     expandViews.setText("Expand Views");\r
1223     expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1224         event.KeyEvent.VK_X, 0, false));\r
1225     expandViews.addActionListener(new ActionListener()\r
1226     {\r
1227       public void actionPerformed(ActionEvent e)\r
1228       {\r
1229         expandViews_actionPerformed(e);\r
1230       }\r
1231     });\r
1232     pageSetup.setText("Page Setup ...");\r
1233     pageSetup.addActionListener(new ActionListener()\r
1234     {\r
1235       public void actionPerformed(ActionEvent e)\r
1236       {\r
1237         pageSetup_actionPerformed(e);\r
1238       }\r
1239     });\r
1240     alignmentProperties.setText("Alignment Properties...");\r
1241     alignmentProperties.addActionListener(new ActionListener()\r
1242     {\r
1243       public void actionPerformed(ActionEvent actionEvent)\r
1244       {\r
1245         alignmentProperties();\r
1246       }\r
1247     });\r
1248 \r
1249     alignFrameMenuBar.add(fileMenu);\r
1250     alignFrameMenuBar.add(editMenu);\r
1251     alignFrameMenuBar.add(selectMenu);\r
1252     alignFrameMenuBar.add(viewMenu);\r
1253     alignFrameMenuBar.add(formatMenu);\r
1254     alignFrameMenuBar.add(colourMenu);\r
1255     alignFrameMenuBar.add(calculateMenu);\r
1256     alignFrameMenuBar.add(webService);\r
1257     fileMenu.add(fetchSequence);\r
1258     fileMenu.add(addSequenceMenu);\r
1259     fileMenu.add(reload);\r
1260     fileMenu.addSeparator();\r
1261     fileMenu.add(vamsasStore);\r
1262     fileMenu.add(save);\r
1263     fileMenu.add(saveAs);\r
1264     fileMenu.add(outputTextboxMenu);\r
1265     fileMenu.add(pageSetup);\r
1266     fileMenu.add(printMenuItem);\r
1267     fileMenu.addSeparator();\r
1268     fileMenu.add(jMenu2);\r
1269     fileMenu.add(exportFeatures);\r
1270     fileMenu.add(exportAnnotations);\r
1271     fileMenu.add(LoadtreeMenuItem);\r
1272     fileMenu.add(associatedData);\r
1273     fileMenu.addSeparator();\r
1274     fileMenu.add(closeMenuItem);\r
1275     editMenu.add(undoMenuItem);\r
1276     editMenu.add(redoMenuItem);\r
1277     editMenu.add(cut);\r
1278     editMenu.add(copy);\r
1279     editMenu.add(pasteMenu);\r
1280     editMenu.add(delete);\r
1281     editMenu.addSeparator();\r
1282     editMenu.add(remove2LeftMenuItem);\r
1283     editMenu.add(remove2RightMenuItem);\r
1284     editMenu.add(removeGappedColumnMenuItem);\r
1285     editMenu.add(removeAllGapsMenuItem);\r
1286     editMenu.add(removeRedundancyMenuItem);\r
1287     editMenu.addSeparator();\r
1288     editMenu.add(padGapsMenuitem);\r
1289     viewMenu.add(newView);\r
1290     viewMenu.add(expandViews);\r
1291     viewMenu.add(gatherViews);\r
1292     viewMenu.addSeparator();\r
1293     viewMenu.add(jMenu3);\r
1294     viewMenu.add(hideMenu);\r
1295     viewMenu.addSeparator();\r
1296     viewMenu.add(annotationPanelMenuItem);\r
1297     viewMenu.addSeparator();\r
1298     viewMenu.add(showSeqFeatures);\r
1299     viewMenu.add(featureSettings);\r
1300     viewMenu.addSeparator();\r
1301     viewMenu.add(alignmentProperties);\r
1302     viewMenu.addSeparator();\r
1303     viewMenu.add(overviewMenuItem);\r
1304     colourMenu.add(applyToAllGroups);\r
1305     colourMenu.add(textColour);\r
1306     colourMenu.addSeparator();\r
1307     colourMenu.add(noColourmenuItem);\r
1308     colourMenu.add(clustalColour);\r
1309     colourMenu.add(BLOSUM62Colour);\r
1310     colourMenu.add(PIDColour);\r
1311     colourMenu.add(zappoColour);\r
1312     colourMenu.add(taylorColour);\r
1313     colourMenu.add(hydrophobicityColour);\r
1314     colourMenu.add(helixColour);\r
1315     colourMenu.add(strandColour);\r
1316     colourMenu.add(turnColour);\r
1317     colourMenu.add(buriedColour);\r
1318     colourMenu.add(nucleotideColour);\r
1319     colourMenu.add(userDefinedColour);\r
1320     colourMenu.addSeparator();\r
1321     colourMenu.add(conservationMenuItem);\r
1322     colourMenu.add(modifyConservation);\r
1323     colourMenu.add(abovePIDThreshold);\r
1324     colourMenu.add(modifyPID);\r
1325     colourMenu.add(annotationColour);\r
1326     calculateMenu.add(sort);\r
1327     calculateMenu.add(calculate);\r
1328     calculateMenu.addSeparator();\r
1329     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1330     calculateMenu.add(PCAMenuItem);\r
1331     calculateMenu.addSeparator();\r
1332     calculateMenu.add(showTranslation);\r
1333     calculateMenu.add(autoCalculate);\r
1334     webServiceNoServices = new JMenuItem("<No Services>");\r
1335     webService.add(webServiceNoServices);\r
1336     pasteMenu.add(pasteNew);\r
1337     pasteMenu.add(pasteThis);\r
1338     sort.add(sortIDMenuItem);\r
1339     sort.add(sortGroupMenuItem);\r
1340     sort.add(sortPairwiseMenuItem);\r
1341     sort.add(sortByTreeMenu);\r
1342     calculate.add(averageDistanceTreeMenuItem);\r
1343     calculate.add(neighbourTreeMenuItem);\r
1344     calculate.add(avDistanceTreeBlosumMenuItem);\r
1345     calculate.add(njTreeBlosumMenuItem);\r
1346     jMenu2.add(htmlMenuItem);\r
1347     jMenu2.add(epsFile);\r
1348     jMenu2.add(createPNG);\r
1349     addSequenceMenu.add(addFromFile);\r
1350     addSequenceMenu.add(addFromText);\r
1351     addSequenceMenu.add(addFromURL);\r
1352     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1353     statusPanel.add(statusBar, null);\r
1354     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1355     jMenu3.add(showAllColumns);\r
1356     jMenu3.add(showAllSeqs);\r
1357     hideMenu.add(hideSelColumns);\r
1358     hideMenu.add(hideSelSequences);\r
1359     formatMenu.add(font);\r
1360     formatMenu.addSeparator();\r
1361     formatMenu.add(wrapMenuItem);\r
1362     formatMenu.add(scaleAbove);\r
1363     formatMenu.add(scaleLeft);\r
1364     formatMenu.add(scaleRight);\r
1365     formatMenu.add(seqLimits);\r
1366     formatMenu.add(idRightAlign);\r
1367     formatMenu.add(hiddenMarkers);\r
1368     formatMenu.add(viewBoxesMenuItem);\r
1369     formatMenu.add(viewTextMenuItem);\r
1370     formatMenu.add(colourTextMenuItem);\r
1371     formatMenu.add(renderGapsMenuItem);\r
1372     selectMenu.add(findMenuItem);\r
1373     selectMenu.addSeparator();\r
1374     selectMenu.add(selectAllSequenceMenuItem);\r
1375     selectMenu.add(deselectAllSequenceMenuItem);\r
1376     selectMenu.add(invertSequenceMenuItem);\r
1377     selectMenu.add(invertColSel);\r
1378     selectMenu.add(deleteGroups);\r
1379   }\r
1380 \r
1381   protected void outputText_actionPerformed(ActionEvent e)\r
1382   {\r
1383   }\r
1384 \r
1385   public void addFromFile_actionPerformed(ActionEvent e)\r
1386   {\r
1387 \r
1388   }\r
1389 \r
1390   public void addFromText_actionPerformed(ActionEvent e)\r
1391   {\r
1392 \r
1393   }\r
1394 \r
1395   public void addFromURL_actionPerformed(ActionEvent e)\r
1396   {\r
1397 \r
1398   }\r
1399 \r
1400   public void exportFeatures_actionPerformed(ActionEvent e)\r
1401   {\r
1402 \r
1403   }\r
1404 \r
1405   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1406   {\r
1407 \r
1408   }\r
1409 \r
1410   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1411   {\r
1412   }\r
1413 \r
1414   protected void closeMenuItem_actionPerformed(boolean b)\r
1415   {\r
1416   }\r
1417 \r
1418   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1419   {\r
1420   }\r
1421 \r
1422   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1423   {\r
1424   }\r
1425 \r
1426   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1427   {\r
1428   }\r
1429 \r
1430   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1431   {\r
1432   }\r
1433 \r
1434   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1435   {\r
1436   }\r
1437 \r
1438   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1439   {\r
1440   }\r
1441 \r
1442   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1443   {\r
1444   }\r
1445 \r
1446   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1447   {\r
1448   }\r
1449 \r
1450   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1451   {\r
1452   }\r
1453 \r
1454   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1455   {\r
1456   }\r
1457 \r
1458   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1459   {\r
1460   }\r
1461 \r
1462   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1463   {\r
1464   }\r
1465 \r
1466   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1467   {\r
1468   }\r
1469 \r
1470   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1471   {\r
1472   }\r
1473 \r
1474   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1475   {\r
1476   }\r
1477 \r
1478   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1479   {\r
1480   }\r
1481 \r
1482   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1483   {\r
1484   }\r
1485 \r
1486   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1487   {\r
1488   }\r
1489 \r
1490   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1491   {\r
1492   }\r
1493 \r
1494   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1495   {\r
1496   }\r
1497 \r
1498   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1499   {\r
1500   }\r
1501 \r
1502   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1503   {\r
1504   }\r
1505 \r
1506   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1507   {\r
1508   }\r
1509 \r
1510   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1511   {\r
1512   }\r
1513 \r
1514   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1515   {\r
1516   }\r
1517 \r
1518   protected void clustalColour_actionPerformed(ActionEvent e)\r
1519   {\r
1520   }\r
1521 \r
1522   protected void zappoColour_actionPerformed(ActionEvent e)\r
1523   {\r
1524   }\r
1525 \r
1526   protected void taylorColour_actionPerformed(ActionEvent e)\r
1527   {\r
1528   }\r
1529 \r
1530   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1531   {\r
1532   }\r
1533 \r
1534   protected void helixColour_actionPerformed(ActionEvent e)\r
1535   {\r
1536   }\r
1537 \r
1538   protected void strandColour_actionPerformed(ActionEvent e)\r
1539   {\r
1540   }\r
1541 \r
1542   protected void turnColour_actionPerformed(ActionEvent e)\r
1543   {\r
1544   }\r
1545 \r
1546   protected void buriedColour_actionPerformed(ActionEvent e)\r
1547   {\r
1548   }\r
1549 \r
1550   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1551   {\r
1552   }\r
1553 \r
1554   protected void PIDColour_actionPerformed(ActionEvent e)\r
1555   {\r
1556   }\r
1557 \r
1558   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1559   {\r
1560   }\r
1561 \r
1562   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1563   {\r
1564   }\r
1565 \r
1566   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1567   {\r
1568   }\r
1569 \r
1570   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1571   {\r
1572   }\r
1573 \r
1574   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1575   {\r
1576   }\r
1577 \r
1578   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1579   {\r
1580   }\r
1581 \r
1582   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1583   {\r
1584   }\r
1585 \r
1586   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1587   {\r
1588   }\r
1589 \r
1590   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1591   {\r
1592   }\r
1593 \r
1594   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1595   {\r
1596   }\r
1597 \r
1598   protected void copy_actionPerformed(ActionEvent e)\r
1599   {\r
1600   }\r
1601 \r
1602   protected void cut_actionPerformed(ActionEvent e)\r
1603   {\r
1604   }\r
1605 \r
1606   protected void delete_actionPerformed(ActionEvent e)\r
1607   {\r
1608   }\r
1609 \r
1610   protected void pasteNew_actionPerformed(ActionEvent e)\r
1611   {\r
1612   }\r
1613 \r
1614   protected void pasteThis_actionPerformed(ActionEvent e)\r
1615   {\r
1616   }\r
1617 \r
1618   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1619   {\r
1620   }\r
1621 \r
1622   public void createPNG(java.io.File f)\r
1623   {\r
1624   }\r
1625 \r
1626   protected void font_actionPerformed(ActionEvent e)\r
1627   {\r
1628   }\r
1629 \r
1630   protected void seqLimit_actionPerformed(ActionEvent e)\r
1631   {\r
1632   }\r
1633 \r
1634   public void seqDBRef_actionPerformed(ActionEvent e)\r
1635   {\r
1636 \r
1637   }\r
1638 \r
1639   public void createEPS(java.io.File f)\r
1640   {\r
1641   }\r
1642 \r
1643   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1644   {\r
1645   }\r
1646 \r
1647   protected void jpred_actionPerformed(ActionEvent e)\r
1648   {\r
1649   }\r
1650 \r
1651   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1652   {\r
1653   }\r
1654 \r
1655   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1656   {\r
1657   }\r
1658 \r
1659   protected void scaleRight_actionPerformed(ActionEvent e)\r
1660   {\r
1661   }\r
1662 \r
1663   protected void modifyPID_actionPerformed(ActionEvent e)\r
1664   {\r
1665   }\r
1666 \r
1667   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1668   {\r
1669   }\r
1670 \r
1671   protected void saveAs_actionPerformed(ActionEvent e)\r
1672   {\r
1673   }\r
1674 \r
1675   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1676   {\r
1677   }\r
1678 \r
1679   public void vamsasStore_actionPerformed(ActionEvent e)\r
1680   {\r
1681 \r
1682   }\r
1683 \r
1684   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1685   {\r
1686 \r
1687   }\r
1688 \r
1689   public void showTranslation_actionPerformed(ActionEvent e)\r
1690   {\r
1691 \r
1692   }\r
1693 \r
1694   public void featureSettings_actionPerformed(ActionEvent e)\r
1695   {\r
1696 \r
1697   }\r
1698 \r
1699   public void fetchSequence_actionPerformed(ActionEvent e)\r
1700   {\r
1701 \r
1702   }\r
1703 \r
1704   public void smoothFont_actionPerformed(ActionEvent e)\r
1705   {\r
1706 \r
1707   }\r
1708 \r
1709   public void annotationColour_actionPerformed(ActionEvent e)\r
1710   {\r
1711 \r
1712   }\r
1713 \r
1714   public void associatedData_actionPerformed(ActionEvent e)\r
1715   {\r
1716 \r
1717   }\r
1718 \r
1719   public void autoCalculate_actionPerformed(ActionEvent e)\r
1720   {\r
1721 \r
1722   }\r
1723 \r
1724   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1725   {\r
1726 \r
1727   }\r
1728 \r
1729   public void showAllColumns_actionPerformed(ActionEvent e)\r
1730   {\r
1731 \r
1732   }\r
1733 \r
1734   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1735   {\r
1736 \r
1737   }\r
1738 \r
1739   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1740   {\r
1741 \r
1742   }\r
1743 \r
1744   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1745   {\r
1746 \r
1747   }\r
1748 \r
1749   public void findPdbId_actionPerformed(ActionEvent e)\r
1750   {\r
1751 \r
1752   }\r
1753 \r
1754   public void enterPdbId_actionPerformed(ActionEvent e)\r
1755   {\r
1756 \r
1757   }\r
1758 \r
1759   public void pdbFile_actionPerformed(ActionEvent e)\r
1760   {\r
1761 \r
1762   }\r
1763 \r
1764   public void invertColSel_actionPerformed(ActionEvent e)\r
1765   {\r
1766 \r
1767   }\r
1768 \r
1769   public void tabSelectionChanged(int sel)\r
1770   {\r
1771 \r
1772   }\r
1773 \r
1774   public void tabbedPane_mousePressed(MouseEvent e)\r
1775   {\r
1776 \r
1777   }\r
1778 \r
1779   public void tabbedPane_focusGained(FocusEvent e)\r
1780   {\r
1781     requestFocus();\r
1782   }\r
1783 \r
1784   public void save_actionPerformed(ActionEvent e)\r
1785   {\r
1786 \r
1787   }\r
1788 \r
1789   public void reload_actionPerformed(ActionEvent e)\r
1790   {\r
1791 \r
1792   }\r
1793 \r
1794   public void newView_actionPerformed(ActionEvent e)\r
1795   {\r
1796 \r
1797   }\r
1798 \r
1799   public void textColour_actionPerformed(ActionEvent e)\r
1800   {\r
1801 \r
1802   }\r
1803 \r
1804   public void idRightAlign_actionPerformed(ActionEvent e)\r
1805   {\r
1806 \r
1807   }\r
1808 \r
1809   public void expandViews_actionPerformed(ActionEvent e)\r
1810   {\r
1811 \r
1812   }\r
1813 \r
1814   public void gatherViews_actionPerformed(ActionEvent e)\r
1815   {\r
1816 \r
1817   }\r
1818 \r
1819   public void buildTreeMenu()\r
1820   {\r
1821 \r
1822   }\r
1823 \r
1824   public void pageSetup_actionPerformed(ActionEvent e)\r
1825   {\r
1826 \r
1827   }\r
1828 \r
1829   public void alignmentProperties()\r
1830   {\r
1831 \r
1832   }\r
1833 }\r