src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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 \r
  25 import jalview.schemes.*;\r
  26 import java.awt.BorderLayout;\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   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  58   BorderLayout borderLayout1 = new BorderLayout();\r
  59   public JLabel statusBar = new JLabel();\r
  60   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  61   protected JMenu outputTextboxMenu = new JMenu();\r
  62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  66       JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  74   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  75   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  76   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  77   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  78   JMenuItem htmlMenuItem = new JMenuItem();\r
  79   JMenuItem overviewMenuItem = new JMenuItem();\r
  80   protected JMenuItem undoMenuItem = new JMenuItem();\r
  81   protected JMenuItem redoMenuItem = new JMenuItem();\r
  82   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  84   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   JMenu searchMenu = new JMenu();\r
  89   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  90   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  91   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  92   JMenuItem deleteGroups = new JMenuItem();\r
  93   JMenuItem delete = new JMenuItem();\r
  94   JMenuItem copy = new JMenuItem();\r
  95   JMenuItem cut = new JMenuItem();\r
  96   JMenu jMenu1 = new JMenu();\r
  97   JMenuItem pasteNew = new JMenuItem();\r
  98   JMenuItem pasteThis = new JMenuItem();\r
  99   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 100   JMenuItem createPNG = new JMenuItem();\r
 101   protected JMenuItem font = new JMenuItem();\r
 102   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 103   JMenuItem epsFile = new JMenuItem();\r
 104   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 105   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 106   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 107   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 108   protected JMenuItem modifyPID = new JMenuItem();\r
 109   protected JMenuItem modifyConservation = new JMenuItem();\r
 110   protected JMenu sortByTreeMenu = new JMenu();\r
 111   protected JMenu sort = new JMenu();\r
 112   JMenu calculate = new JMenu();\r
 113   JMenu jMenu2 = new JMenu();\r
 114   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 115   protected ButtonGroup colours = new ButtonGroup();\r
 116   JMenuItem vamsasStore = new JMenuItem();\r
 117   protected JMenuItem showTranslation = new JMenuItem();\r
 118   public JMenuItem featureSettings = new JMenuItem();\r
 119   JMenuItem fetchSequence = new JMenuItem();\r
 120   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 121   JMenuItem annotationColour = new JMenuItem();\r
 122   JMenuItem associatedData = new JMenuItem();\r
 123   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 124   JMenu addSequenceMenu = new JMenu();\r
 125   JMenuItem addFromFile = new JMenuItem();\r
 126   JMenuItem addFromText = new JMenuItem();\r
 127   JMenuItem addFromURL = new JMenuItem();\r
 128   JMenuItem exportAnnotations = new JMenuItem();\r
 129   JMenuItem exportFeatures = new JMenuItem();\r
 130   protected JPanel statusPanel = new JPanel();\r
 131   GridLayout gridLayout1 = new GridLayout();\r
 132   JMenu jMenu3 = new JMenu();\r
 133   JMenuItem showAllSeqs = new JMenuItem();\r
 134   JMenuItem showAllColumns = new JMenuItem();\r
 135   JMenu jMenu4 = new JMenu();\r
 136   JMenuItem hideSelSequences = new JMenuItem();\r
 137   JMenuItem hideSelColumns = new JMenuItem();\r
 138   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 139 \r
 140   public GAlignFrame()\r
 141   {\r
 142 \r
 143 \r
 144     try\r
 145     {\r
 146       jbInit();\r
 147       setJMenuBar(alignFrameMenuBar);\r
 148 \r
 149       // dynamically fill save as menu with available formats\r
 150       for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
 151       {\r
 152         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 153                              elementAt(\r
 154                                  i));\r
 155         item.addActionListener(new java.awt.event.ActionListener()\r
 156         {\r
 157           public void actionPerformed(ActionEvent e)\r
 158           {\r
 159             outputText_actionPerformed(e);\r
 160           }\r
 161         });\r
 162 \r
 163         outputTextboxMenu.add(item);\r
 164       }\r
 165     }\r
 166     catch (Exception e)\r
 167     {\r
 168     }\r
 169 \r
 170 \r
 171     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 172     {\r
 173       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 174           getUserColourSchemes().keys();\r
 175 \r
 176       while (userColours.hasMoreElements())\r
 177       {\r
 178         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 179             nextElement().toString());\r
 180         radioItem.setName("USER_DEFINED");\r
 181         radioItem.addMouseListener(new MouseAdapter()\r
 182             {\r
 183               public void mousePressed(MouseEvent evt)\r
 184               {\r
 185                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 186                 {\r
 187                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 188 \r
 189                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 190                       "Remove from default list?",\r
 191                       "Remove user defined colour",\r
 192                       JOptionPane.YES_NO_OPTION);\r
 193                   if(option == JOptionPane.YES_OPTION)\r
 194                   {\r
 195                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 196                     colourMenu.remove(radioItem);\r
 197                   }\r
 198                   else\r
 199                     radioItem.addActionListener(new ActionListener()\r
 200                     {\r
 201                       public void actionPerformed(ActionEvent evt)\r
 202                       {\r
 203                         userDefinedColour_actionPerformed(evt);\r
 204                       }\r
 205                     });\r
 206                 }\r
 207               }\r
 208             });\r
 209         radioItem.addActionListener(new ActionListener()\r
 210         {\r
 211           public void actionPerformed(ActionEvent evt)\r
 212           {\r
 213             userDefinedColour_actionPerformed(evt);\r
 214           }\r
 215         });\r
 216         colourMenu.insert(radioItem, 15);\r
 217         colours.add(radioItem);\r
 218       }\r
 219     }\r
 220     colours.add(noColourmenuItem);\r
 221     colours.add(clustalColour);\r
 222     colours.add(zappoColour);\r
 223     colours.add(taylorColour);\r
 224     colours.add(hydrophobicityColour);\r
 225     colours.add(helixColour);\r
 226     colours.add(strandColour);\r
 227     colours.add(turnColour);\r
 228     colours.add(buriedColour);\r
 229     colours.add(userDefinedColour);\r
 230     colours.add(PIDColour);\r
 231     colours.add(BLOSUM62Colour);\r
 232     colours.add(nucleotideColour);\r
 233 \r
 234     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 235 \r
 236 \r
 237   }\r
 238 \r
 239   public void setColourSelected(String defaultColour)\r
 240   {\r
 241 \r
 242     if (defaultColour != null)\r
 243     {\r
 244       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 245 \r
 246       switch (index)\r
 247       {\r
 248         case ColourSchemeProperty.NONE:\r
 249               noColourmenuItem.setSelected(true);\r
 250               break;\r
 251         case ColourSchemeProperty.CLUSTAL:\r
 252           clustalColour.setSelected(true);\r
 253 \r
 254           break;\r
 255 \r
 256         case ColourSchemeProperty.BLOSUM:\r
 257           BLOSUM62Colour.setSelected(true);\r
 258 \r
 259           break;\r
 260 \r
 261         case ColourSchemeProperty.PID:\r
 262           PIDColour.setSelected(true);\r
 263 \r
 264           break;\r
 265 \r
 266         case ColourSchemeProperty.ZAPPO:\r
 267           zappoColour.setSelected(true);\r
 268 \r
 269           break;\r
 270 \r
 271         case ColourSchemeProperty.TAYLOR:\r
 272           taylorColour.setSelected(true);\r
 273           break;\r
 274 \r
 275         case ColourSchemeProperty.HYDROPHOBIC:\r
 276           hydrophobicityColour.setSelected(true);\r
 277 \r
 278           break;\r
 279 \r
 280         case ColourSchemeProperty.HELIX:\r
 281           helixColour.setSelected(true);\r
 282 \r
 283           break;\r
 284 \r
 285         case ColourSchemeProperty.STRAND:\r
 286           strandColour.setSelected(true);\r
 287 \r
 288           break;\r
 289 \r
 290         case ColourSchemeProperty.TURN:\r
 291           turnColour.setSelected(true);\r
 292 \r
 293           break;\r
 294 \r
 295         case ColourSchemeProperty.BURIED:\r
 296           buriedColour.setSelected(true);\r
 297 \r
 298           break;\r
 299 \r
 300         case ColourSchemeProperty.NUCLEOTIDE:\r
 301           nucleotideColour.setSelected(true);\r
 302 \r
 303           break;\r
 304 \r
 305         case ColourSchemeProperty.USER_DEFINED:\r
 306           userDefinedColour.setSelected(true);\r
 307 \r
 308           break;\r
 309       }\r
 310     }\r
 311 \r
 312   }\r
 313 \r
 314   private void jbInit()\r
 315       throws Exception\r
 316   {\r
 317     fileMenu.setMnemonic('F');\r
 318     fileMenu.setText("File");\r
 319     saveAlignmentMenu.setMnemonic('L');\r
 320     saveAlignmentMenu.setText("Save As");\r
 321     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 322         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 323     saveAlignmentMenu.addActionListener(new ActionListener()\r
 324     {\r
 325       public void actionPerformed(ActionEvent e)\r
 326       {\r
 327         saveAlignmentMenu_actionPerformed(e);\r
 328       }\r
 329     });\r
 330     closeMenuItem.setMnemonic('C');\r
 331     closeMenuItem.setText("Close");\r
 332     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 333     {\r
 334       public void actionPerformed(ActionEvent e)\r
 335       {\r
 336         closeMenuItem_actionPerformed(e);\r
 337       }\r
 338     });\r
 339     editMenu.setText("Edit");\r
 340     viewMenu.setText("View");\r
 341     colourMenu.setText("Colour");\r
 342     calculateMenu.setText("Calculate");\r
 343     webService.setText("Web Service");\r
 344     selectAllSequenceMenuItem.setText("Select all");\r
 345     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 346         java.awt.event.KeyEvent.VK_A,\r
 347         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 348     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 349                                                 ActionListener()\r
 350     {\r
 351       public void actionPerformed(ActionEvent e)\r
 352       {\r
 353         selectAllSequenceMenuItem_actionPerformed(e);\r
 354       }\r
 355     });\r
 356     deselectAllSequenceMenuItem.setText("Deselect All");\r
 357     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 358                                                getKeyStroke(\r
 359         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 360     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 361                                                   ActionListener()\r
 362     {\r
 363       public void actionPerformed(ActionEvent e)\r
 364       {\r
 365         deselectAllSequenceMenuItem_actionPerformed(e);\r
 366       }\r
 367     });\r
 368     invertSequenceMenuItem.setText("Invert Selection");\r
 369     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 370     {\r
 371       public void actionPerformed(ActionEvent e)\r
 372       {\r
 373         invertSequenceMenuItem_actionPerformed(e);\r
 374       }\r
 375     });\r
 376     remove2LeftMenuItem.setText("Remove Left");\r
 377     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 378     {\r
 379       public void actionPerformed(ActionEvent e)\r
 380       {\r
 381         remove2LeftMenuItem_actionPerformed(e);\r
 382       }\r
 383     });\r
 384     remove2RightMenuItem.setText("Remove Right");\r
 385     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 386     {\r
 387       public void actionPerformed(ActionEvent e)\r
 388       {\r
 389         remove2RightMenuItem_actionPerformed(e);\r
 390       }\r
 391     });\r
 392     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 393     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 394                                                  ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         removeGappedColumnMenuItem_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 402     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 403     {\r
 404       public void actionPerformed(ActionEvent e)\r
 405       {\r
 406         removeAllGapsMenuItem_actionPerformed(e);\r
 407       }\r
 408     });\r
 409     viewBoxesMenuItem.setText("Boxes");\r
 410     viewBoxesMenuItem.setState(true);\r
 411     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 412     {\r
 413       public void actionPerformed(ActionEvent e)\r
 414       {\r
 415         viewBoxesMenuItem_actionPerformed(e);\r
 416       }\r
 417     });\r
 418     viewTextMenuItem.setText("Text");\r
 419     viewTextMenuItem.setState(true);\r
 420     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 421     {\r
 422       public void actionPerformed(ActionEvent e)\r
 423       {\r
 424         viewTextMenuItem_actionPerformed(e);\r
 425       }\r
 426     });\r
 427     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 428     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 429     {\r
 430       public void actionPerformed(ActionEvent e)\r
 431       {\r
 432         sortPairwiseMenuItem_actionPerformed(e);\r
 433       }\r
 434     });\r
 435     sortIDMenuItem.setText("by ID");\r
 436     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 437     {\r
 438       public void actionPerformed(ActionEvent e)\r
 439       {\r
 440         sortIDMenuItem_actionPerformed(e);\r
 441       }\r
 442     });\r
 443     sortGroupMenuItem.setText("by Group");\r
 444     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         sortGroupMenuItem_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 452     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 453                                                ActionListener()\r
 454     {\r
 455       public void actionPerformed(ActionEvent e)\r
 456       {\r
 457         removeRedundancyMenuItem_actionPerformed(e);\r
 458       }\r
 459     });\r
 460     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 461     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 462                                                 ActionListener()\r
 463     {\r
 464       public void actionPerformed(ActionEvent e)\r
 465       {\r
 466         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 467       }\r
 468     });\r
 469     PCAMenuItem.setText("Principal Component Analysis");\r
 470     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 471     {\r
 472       public void actionPerformed(ActionEvent e)\r
 473       {\r
 474         PCAMenuItem_actionPerformed(e);\r
 475       }\r
 476     });\r
 477     averageDistanceTreeMenuItem.setText(\r
 478         "Average Distance Using % Identity");\r
 479     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 480                                                   ActionListener()\r
 481     {\r
 482       public void actionPerformed(ActionEvent e)\r
 483       {\r
 484         averageDistanceTreeMenuItem_actionPerformed(e);\r
 485       }\r
 486     });\r
 487     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 488     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 489     {\r
 490       public void actionPerformed(ActionEvent e)\r
 491       {\r
 492         neighbourTreeMenuItem_actionPerformed(e);\r
 493       }\r
 494     });\r
 495     this.getContentPane().setLayout(borderLayout1);\r
 496     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 497     statusBar.setBackground(Color.white);\r
 498     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 499     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 500     statusBar.setText("Status bar");\r
 501     outputTextboxMenu.setMnemonic('T');\r
 502     outputTextboxMenu.setText("Output to Textbox");\r
 503     clustalColour.setText("Clustalx");\r
 504 \r
 505     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         clustalColour_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     zappoColour.setText("Zappo");\r
 513     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 514     {\r
 515       public void actionPerformed(ActionEvent e)\r
 516       {\r
 517         zappoColour_actionPerformed(e);\r
 518       }\r
 519     });\r
 520     taylorColour.setText("Taylor");\r
 521     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         taylorColour_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     hydrophobicityColour.setText("Hydrophobicity");\r
 529     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         hydrophobicityColour_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     helixColour.setText("Helix Propensity");\r
 537     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         helixColour_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     strandColour.setText("Strand Propensity");\r
 545     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         strandColour_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     turnColour.setText("Turn Propensity");\r
 553     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         turnColour_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     buriedColour.setText("Buried Index");\r
 561     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         buriedColour_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     userDefinedColour.setText("User Defined...");\r
 569     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         userDefinedColour_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     PIDColour.setText("Percentage Identity");\r
 577     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 578     {\r
 579       public void actionPerformed(ActionEvent e)\r
 580       {\r
 581         PIDColour_actionPerformed(e);\r
 582       }\r
 583     });\r
 584     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 585     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 586     {\r
 587       public void actionPerformed(ActionEvent e)\r
 588       {\r
 589         BLOSUM62Colour_actionPerformed(e);\r
 590       }\r
 591     });\r
 592     avDistanceTreeBlosumMenuItem.setText(\r
 593         "Average Distance Using BLOSUM62");\r
 594     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 595         ActionListener()\r
 596     {\r
 597       public void actionPerformed(ActionEvent e)\r
 598       {\r
 599         avTreeBlosumMenuItem_actionPerformed(e);\r
 600       }\r
 601     });\r
 602     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 603     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 604     {\r
 605       public void actionPerformed(ActionEvent e)\r
 606       {\r
 607         njTreeBlosumMenuItem_actionPerformed(e);\r
 608       }\r
 609     });\r
 610     annotationPanelMenuItem.setActionCommand("");\r
 611     annotationPanelMenuItem.setText("Show Annotations");\r
 612     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 613     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 614     {\r
 615       public void actionPerformed(ActionEvent e)\r
 616       {\r
 617         annotationPanelMenuItem_actionPerformed(e);\r
 618       }\r
 619     });\r
 620     colourTextMenuItem.setText("Colour Text");\r
 621     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 622     {\r
 623       public void actionPerformed(ActionEvent e)\r
 624       {\r
 625         colourTextMenuItem_actionPerformed(e);\r
 626       }\r
 627     });\r
 628     htmlMenuItem.setText("HTML");\r
 629     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 630     {\r
 631       public void actionPerformed(ActionEvent e)\r
 632       {\r
 633         htmlMenuItem_actionPerformed(e);\r
 634       }\r
 635     });\r
 636     overviewMenuItem.setText("Overview Window");\r
 637     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 638     {\r
 639       public void actionPerformed(ActionEvent e)\r
 640       {\r
 641         overviewMenuItem_actionPerformed(e);\r
 642       }\r
 643     });\r
 644     undoMenuItem.setEnabled(false);\r
 645     undoMenuItem.setMnemonic('Z');\r
 646     undoMenuItem.setText("Undo");\r
 647     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 648         java.awt.event.KeyEvent.VK_Z,\r
 649         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 650     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 651     {\r
 652       public void actionPerformed(ActionEvent e)\r
 653       {\r
 654         undoMenuItem_actionPerformed(e);\r
 655       }\r
 656     });\r
 657     redoMenuItem.setEnabled(false);\r
 658     redoMenuItem.setMnemonic('0');\r
 659     redoMenuItem.setText("Redo");\r
 660     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 661     {\r
 662       public void actionPerformed(ActionEvent e)\r
 663       {\r
 664         redoMenuItem_actionPerformed(e);\r
 665       }\r
 666     });\r
 667     conservationMenuItem.setText("By Conservation");\r
 668     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 669     {\r
 670       public void actionPerformed(ActionEvent e)\r
 671       {\r
 672         conservationMenuItem_actionPerformed(e);\r
 673       }\r
 674     });\r
 675     noColourmenuItem.setText("None");\r
 676     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 677     {\r
 678       public void actionPerformed(ActionEvent e)\r
 679       {\r
 680         noColourmenuItem_actionPerformed(e);\r
 681       }\r
 682     });\r
 683     wrapMenuItem.setText("Wrap");\r
 684     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 685     {\r
 686       public void actionPerformed(ActionEvent e)\r
 687       {\r
 688         wrapMenuItem_actionPerformed(e);\r
 689       }\r
 690     });\r
 691     printMenuItem.setText("Print");\r
 692     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 693     {\r
 694       public void actionPerformed(ActionEvent e)\r
 695       {\r
 696         printMenuItem_actionPerformed(e);\r
 697       }\r
 698     });\r
 699     renderGapsMenuItem.setText("Show Gaps");\r
 700     renderGapsMenuItem.setState(true);\r
 701     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 702     {\r
 703       public void actionPerformed(ActionEvent e)\r
 704       {\r
 705         renderGapsMenuItem_actionPerformed(e);\r
 706       }\r
 707     });\r
 708     findMenuItem.setText("Find...");\r
 709     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 710         java.awt.event.KeyEvent.VK_F,\r
 711         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 712     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 713     {\r
 714       public void actionPerformed(ActionEvent e)\r
 715       {\r
 716         findMenuItem_actionPerformed(e);\r
 717       }\r
 718     });\r
 719     searchMenu.setText("Search");\r
 720 \r
 721     abovePIDThreshold.setText("Above Identity Threshold");\r
 722     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 723     {\r
 724       public void actionPerformed(ActionEvent e)\r
 725       {\r
 726         abovePIDThreshold_actionPerformed(e);\r
 727       }\r
 728     });\r
 729     showSeqFeatures.setText("Show Sequence Features");\r
 730     showSeqFeatures.addActionListener(new ActionListener()\r
 731     {\r
 732       public void actionPerformed(ActionEvent actionEvent)\r
 733       {\r
 734         showSeqFeatures_actionPerformed(actionEvent);\r
 735       }\r
 736     });\r
 737     nucleotideColour.setText("Nucleotide");\r
 738     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 739     {\r
 740       public void actionPerformed(ActionEvent e)\r
 741       {\r
 742         nucleotideColour_actionPerformed(e);\r
 743       }\r
 744     });\r
 745     deleteGroups.setText("Undefine groups");\r
 746     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 747     {\r
 748       public void actionPerformed(ActionEvent e)\r
 749       {\r
 750         deleteGroups_actionPerformed(e);\r
 751       }\r
 752     });\r
 753     copy.setText("Copy");\r
 754     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 755         java.awt.event.KeyEvent.VK_C,\r
 756         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 757     copy.setMnemonic(KeyEvent.VK_C);\r
 758 \r
 759     copy.addActionListener(new java.awt.event.ActionListener()\r
 760     {\r
 761       public void actionPerformed(ActionEvent e)\r
 762       {\r
 763         copy_actionPerformed(e);\r
 764       }\r
 765     });\r
 766     cut.setText("Cut");\r
 767     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 768         java.awt.event.KeyEvent.VK_X,\r
 769         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 770     cut.setMnemonic(KeyEvent.VK_X);\r
 771     cut.addActionListener(new java.awt.event.ActionListener()\r
 772     {\r
 773       public void actionPerformed(ActionEvent e)\r
 774       {\r
 775         cut_actionPerformed(e);\r
 776       }\r
 777     });\r
 778     delete.setText("Delete");\r
 779     delete.addActionListener(new java.awt.event.ActionListener()\r
 780     {\r
 781       public void actionPerformed(ActionEvent e)\r
 782       {\r
 783         delete_actionPerformed(e);\r
 784       }\r
 785     });\r
 786     jMenu1.setMnemonic('V');\r
 787     jMenu1.setText("Paste");\r
 788     pasteNew.setText("To New Alignment");\r
 789     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 790         java.awt.event.KeyEvent.VK_V,\r
 791         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 792     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 793     {\r
 794       public void actionPerformed(ActionEvent e)\r
 795       {\r
 796         pasteNew_actionPerformed(e);\r
 797       }\r
 798     });\r
 799     pasteThis.setText("Add To This Alignment");\r
 800     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 801     {\r
 802       public void actionPerformed(ActionEvent e)\r
 803       {\r
 804         pasteThis_actionPerformed(e);\r
 805       }\r
 806     });\r
 807     applyToAllGroups.setText("Apply Colour To All Groups");\r
 808     applyToAllGroups.setState(true);\r
 809     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 810     {\r
 811       public void actionPerformed(ActionEvent e)\r
 812       {\r
 813         applyToAllGroups_actionPerformed(e);\r
 814       }\r
 815     });\r
 816     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 817     {\r
 818       public void actionPerformed(ActionEvent e)\r
 819       {\r
 820         createPNG(null);\r
 821       }\r
 822     });\r
 823     createPNG.setActionCommand("Save As PNG Image");\r
 824     createPNG.setText("PNG");\r
 825     font.setText("Font...");\r
 826     font.addActionListener(new java.awt.event.ActionListener()\r
 827     {\r
 828       public void actionPerformed(ActionEvent e)\r
 829       {\r
 830         font_actionPerformed(e);\r
 831       }\r
 832     });\r
 833 \r
 834     seqLimits.setText("Show Sequence Limits");\r
 835     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 836     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 837     {\r
 838       public void actionPerformed(ActionEvent e)\r
 839       {\r
 840         seqLimit_actionPerformed(e);\r
 841       }\r
 842     });\r
 843     epsFile.setText("EPS");\r
 844     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 845     {\r
 846       public void actionPerformed(ActionEvent e)\r
 847       {\r
 848         createEPS(null);\r
 849       }\r
 850     });\r
 851     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 852     LoadtreeMenuItem.setText("Load Associated Tree");\r
 853     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 854     {\r
 855       public void actionPerformed(ActionEvent e)\r
 856       {\r
 857         LoadtreeMenuItem_actionPerformed(e);\r
 858       }\r
 859     });\r
 860     scaleAbove.setVisible(false);\r
 861     scaleAbove.setText("Scale Above");\r
 862     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 863     {\r
 864       public void actionPerformed(ActionEvent e)\r
 865       {\r
 866         scaleAbove_actionPerformed(e);\r
 867       }\r
 868     });\r
 869     scaleLeft.setVisible(false);\r
 870     scaleLeft.setSelected(true);\r
 871     scaleLeft.setText("Scale Left");\r
 872     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 873     {\r
 874       public void actionPerformed(ActionEvent e)\r
 875       {\r
 876         scaleLeft_actionPerformed(e);\r
 877       }\r
 878     });\r
 879     scaleRight.setVisible(false);\r
 880     scaleRight.setSelected(true);\r
 881     scaleRight.setText("Scale Right");\r
 882     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 883     {\r
 884       public void actionPerformed(ActionEvent e)\r
 885       {\r
 886         scaleRight_actionPerformed(e);\r
 887       }\r
 888     });\r
 889     modifyPID.setText("Modify Identity Threshold...");\r
 890     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 891     {\r
 892       public void actionPerformed(ActionEvent e)\r
 893       {\r
 894         modifyPID_actionPerformed(e);\r
 895       }\r
 896     });\r
 897     modifyConservation.setText("Modify Conservation Threshold...");\r
 898     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 899     {\r
 900       public void actionPerformed(ActionEvent e)\r
 901       {\r
 902         modifyConservation_actionPerformed(e);\r
 903       }\r
 904     });\r
 905     sortByTreeMenu.setText("By Tree Order");\r
 906     sort.setText("Sort");\r
 907     calculate.setText("Calculate Tree");\r
 908 \r
 909     jMenu2.setText("Export");\r
 910     padGapsMenuitem.setText("Pad Gaps");\r
 911     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 912     padGapsMenuitem.addActionListener(new ActionListener()\r
 913     {\r
 914       public void actionPerformed(ActionEvent e)\r
 915       {\r
 916         padGapsMenuitem_actionPerformed(e);\r
 917       }\r
 918     });\r
 919     vamsasStore.setVisible(false);\r
 920     vamsasStore.setText("VAMSAS store");\r
 921     vamsasStore.addActionListener(new ActionListener()\r
 922     {\r
 923       public void actionPerformed(ActionEvent e)\r
 924       {\r
 925         vamsasStore_actionPerformed(e);\r
 926       }\r
 927     });\r
 928     showTranslation.setText("Translate cDNA");\r
 929     showTranslation.addActionListener(new ActionListener()\r
 930     {\r
 931       public void actionPerformed(ActionEvent e)\r
 932       {\r
 933         showTranslation_actionPerformed(e);\r
 934       }\r
 935     });\r
 936 \r
 937    /* tabbedPane.addChangeListener(new ChangeListener()\r
 938         {\r
 939           public void stateChanged(ChangeEvent ece)\r
 940           {\r
 941 \r
 942             tabSelected();\r
 943           }\r
 944         });*/\r
 945     featureSettings.setText("Feature Settings...");\r
 946     featureSettings.addActionListener(new ActionListener()\r
 947     {\r
 948       public void actionPerformed(ActionEvent e)\r
 949       {\r
 950         featureSettings_actionPerformed(e);\r
 951       }\r
 952     });\r
 953     fetchSequence.setText("Fetch Sequence(s)...");\r
 954     fetchSequence.addActionListener(new ActionListener()\r
 955     {\r
 956       public void actionPerformed(ActionEvent e)\r
 957       {\r
 958         fetchSequence_actionPerformed(e);\r
 959       }\r
 960     });\r
 961     smoothFont.setText("Smooth Fonts");\r
 962     smoothFont.addActionListener(new ActionListener()\r
 963     {\r
 964       public void actionPerformed(ActionEvent e)\r
 965       {\r
 966         smoothFont_actionPerformed(e);\r
 967       }\r
 968     });\r
 969     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 970     annotationColour.setText("By Annotation...");\r
 971     annotationColour.addActionListener(new ActionListener()\r
 972     {\r
 973       public void actionPerformed(ActionEvent e)\r
 974       {\r
 975         annotationColour_actionPerformed(e);\r
 976       }\r
 977     });\r
 978     associatedData.setText("Load Features / Annotations");\r
 979     associatedData.addActionListener(new ActionListener()\r
 980     {\r
 981       public void actionPerformed(ActionEvent e)\r
 982       {\r
 983         associatedData_actionPerformed(e);\r
 984       }\r
 985     });\r
 986     autoCalculate.setText("Autocalculate Consensus");\r
 987     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 988     autoCalculate.addActionListener(new ActionListener()\r
 989     {\r
 990       public void actionPerformed(ActionEvent e)\r
 991       {\r
 992         autoCalculate_actionPerformed(e);\r
 993       }\r
 994     });\r
 995     addSequenceMenu.setText("Add Sequences");\r
 996     addFromFile.setText("From File");\r
 997     addFromFile.addActionListener(new ActionListener()\r
 998     {\r
 999       public void actionPerformed(ActionEvent e)\r
1000       {\r
1001         addFromFile_actionPerformed(e);\r
1002       }\r
1003     });\r
1004     addFromText.setText("From Textbox");\r
1005     addFromText.addActionListener(new ActionListener()\r
1006     {\r
1007       public void actionPerformed(ActionEvent e)\r
1008       {\r
1009         addFromText_actionPerformed(e);\r
1010       }\r
1011     });\r
1012     addFromURL.setText("From URL");\r
1013     addFromURL.addActionListener(new ActionListener()\r
1014     {\r
1015       public void actionPerformed(ActionEvent e)\r
1016       {\r
1017         addFromURL_actionPerformed(e);\r
1018       }\r
1019     });\r
1020     exportFeatures.setText("Export Features...");\r
1021     exportFeatures.addActionListener(new ActionListener()\r
1022     {\r
1023       public void actionPerformed(ActionEvent e)\r
1024       {\r
1025         exportFeatures_actionPerformed(e);\r
1026       }\r
1027     });\r
1028     exportAnnotations.setText("Export Annotations...");\r
1029     exportAnnotations.addActionListener(new ActionListener()\r
1030     {\r
1031       public void actionPerformed(ActionEvent e)\r
1032       {\r
1033         exportAnnotations_actionPerformed(e);\r
1034       }\r
1035     });\r
1036     statusPanel.setLayout(gridLayout1);\r
1037     jMenu3.setText("Show");\r
1038     showAllSeqs.setText("All Sequences");\r
1039     showAllSeqs.addActionListener(new ActionListener()\r
1040     {\r
1041       public void actionPerformed(ActionEvent e)\r
1042       {\r
1043         showAllSeqs_actionPerformed(e);\r
1044       }\r
1045     });\r
1046     showAllColumns.setText("All Columns");\r
1047     showAllColumns.addActionListener(new ActionListener()\r
1048     {\r
1049       public void actionPerformed(ActionEvent e)\r
1050       {\r
1051         showAllColumns_actionPerformed(e);\r
1052       }\r
1053     });\r
1054     jMenu4.setText("Hide");\r
1055     hideSelSequences.setText("Selected Sequences");\r
1056     hideSelSequences.addActionListener(new ActionListener()\r
1057     {\r
1058       public void actionPerformed(ActionEvent e)\r
1059       {\r
1060         hideSelSequences_actionPerformed(e);\r
1061       }\r
1062     });\r
1063     hideSelColumns.setText("Selected Columns");\r
1064     hideSelColumns.addActionListener(new ActionListener()\r
1065     {\r
1066       public void actionPerformed(ActionEvent e)\r
1067       {\r
1068         hideSelColumns_actionPerformed(e);\r
1069       }\r
1070     });\r
1071     hiddenMarkers.setText("Hidden Markers");\r
1072     hiddenMarkers.setState(true);\r
1073     hiddenMarkers.addActionListener(new ActionListener()\r
1074     {\r
1075       public void actionPerformed(ActionEvent e)\r
1076       {\r
1077         hiddenMarkers_actionPerformed(e);\r
1078       }\r
1079     });\r
1080 \r
1081     alignFrameMenuBar.add(fileMenu);\r
1082     alignFrameMenuBar.add(editMenu);\r
1083     alignFrameMenuBar.add(searchMenu);\r
1084     alignFrameMenuBar.add(viewMenu);\r
1085     alignFrameMenuBar.add(colourMenu);\r
1086     alignFrameMenuBar.add(calculateMenu);\r
1087     alignFrameMenuBar.add(webService);\r
1088     fileMenu.add(addSequenceMenu);\r
1089     fileMenu.add(fetchSequence);\r
1090     fileMenu.addSeparator();\r
1091     fileMenu.add(vamsasStore);\r
1092     fileMenu.add(saveAlignmentMenu);\r
1093     fileMenu.add(jMenu2);\r
1094     fileMenu.add(outputTextboxMenu);\r
1095     fileMenu.add(printMenuItem);\r
1096     fileMenu.addSeparator();\r
1097     fileMenu.add(exportFeatures);\r
1098     fileMenu.add(exportAnnotations);\r
1099     fileMenu.add(LoadtreeMenuItem);\r
1100     fileMenu.add(associatedData);\r
1101     fileMenu.addSeparator();\r
1102     fileMenu.add(closeMenuItem);\r
1103     editMenu.add(undoMenuItem);\r
1104     editMenu.add(redoMenuItem);\r
1105     editMenu.add(cut);\r
1106     editMenu.add(copy);\r
1107     editMenu.add(jMenu1);\r
1108     editMenu.add(delete);\r
1109     editMenu.addSeparator();\r
1110     editMenu.add(selectAllSequenceMenuItem);\r
1111     editMenu.add(deselectAllSequenceMenuItem);\r
1112     editMenu.add(invertSequenceMenuItem);\r
1113     editMenu.add(deleteGroups);\r
1114     editMenu.addSeparator();\r
1115     editMenu.add(remove2LeftMenuItem);\r
1116     editMenu.add(remove2RightMenuItem);\r
1117     editMenu.add(removeGappedColumnMenuItem);\r
1118     editMenu.add(removeAllGapsMenuItem);\r
1119     editMenu.add(removeRedundancyMenuItem);\r
1120     editMenu.addSeparator();\r
1121     editMenu.add(padGapsMenuitem);\r
1122     searchMenu.add(findMenuItem);\r
1123     viewMenu.add(font);\r
1124     viewMenu.add(smoothFont);\r
1125     viewMenu.addSeparator();\r
1126     viewMenu.add(jMenu3);\r
1127     viewMenu.add(jMenu4);\r
1128     viewMenu.add(hiddenMarkers);\r
1129     viewMenu.addSeparator();\r
1130     viewMenu.add(wrapMenuItem);\r
1131     viewMenu.add(seqLimits);\r
1132     viewMenu.add(scaleAbove);\r
1133     viewMenu.add(scaleLeft);\r
1134     viewMenu.add(scaleRight);\r
1135     viewMenu.add(viewBoxesMenuItem);\r
1136     viewMenu.add(viewTextMenuItem);\r
1137     viewMenu.add(colourTextMenuItem);\r
1138     viewMenu.add(renderGapsMenuItem);\r
1139     viewMenu.add(annotationPanelMenuItem);\r
1140     viewMenu.addSeparator();\r
1141     viewMenu.add(showSeqFeatures);\r
1142     viewMenu.add(featureSettings);\r
1143     viewMenu.addSeparator();\r
1144     viewMenu.add(overviewMenuItem);\r
1145     colourMenu.add(applyToAllGroups);\r
1146     colourMenu.addSeparator();\r
1147     colourMenu.add(noColourmenuItem);\r
1148     colourMenu.add(clustalColour);\r
1149     colourMenu.add(BLOSUM62Colour);\r
1150     colourMenu.add(PIDColour);\r
1151     colourMenu.add(zappoColour);\r
1152     colourMenu.add(taylorColour);\r
1153     colourMenu.add(hydrophobicityColour);\r
1154     colourMenu.add(helixColour);\r
1155     colourMenu.add(strandColour);\r
1156     colourMenu.add(turnColour);\r
1157     colourMenu.add(buriedColour);\r
1158     colourMenu.add(nucleotideColour);\r
1159     colourMenu.add(userDefinedColour);\r
1160     colourMenu.addSeparator();\r
1161     colourMenu.add(conservationMenuItem);\r
1162     colourMenu.add(modifyConservation);\r
1163     colourMenu.add(abovePIDThreshold);\r
1164     colourMenu.add(modifyPID);\r
1165     colourMenu.add(annotationColour);\r
1166     calculateMenu.add(sort);\r
1167     calculateMenu.add(calculate);\r
1168     calculateMenu.addSeparator();\r
1169     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1170     calculateMenu.add(PCAMenuItem);\r
1171     calculateMenu.addSeparator();\r
1172     calculateMenu.add(showTranslation);\r
1173     calculateMenu.add(autoCalculate);\r
1174     webServiceNoServices=new JMenuItem("<No Services>");\r
1175     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1176     jMenu1.add(pasteThis);\r
1177     sort.add(sortIDMenuItem);\r
1178     sort.add(sortGroupMenuItem);\r
1179     sort.add(sortPairwiseMenuItem);\r
1180     calculate.add(averageDistanceTreeMenuItem);\r
1181     calculate.add(neighbourTreeMenuItem);\r
1182     calculate.add(avDistanceTreeBlosumMenuItem);\r
1183     calculate.add(njTreeBlosumMenuItem);\r
1184     jMenu2.add(htmlMenuItem);\r
1185     jMenu2.add(epsFile);\r
1186     jMenu2.add(createPNG);\r
1187     addSequenceMenu.add(addFromFile);\r
1188     addSequenceMenu.add(addFromText);\r
1189     addSequenceMenu.add(addFromURL);\r
1190     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1191     statusPanel.add(statusBar, null);\r
1192     jMenu3.add(showAllColumns);\r
1193     jMenu3.add(showAllSeqs);\r
1194     jMenu4.add(hideSelColumns);\r
1195     jMenu4.add(hideSelSequences);\r
1196   }\r
1197 \r
1198   protected void outputText_actionPerformed(ActionEvent e)\r
1199   {\r
1200   }\r
1201 \r
1202   public void addFromFile_actionPerformed(ActionEvent e)\r
1203   {\r
1204 \r
1205   }\r
1206 \r
1207   public void addFromText_actionPerformed(ActionEvent e)\r
1208   {\r
1209 \r
1210   }\r
1211 \r
1212   public void addFromURL_actionPerformed(ActionEvent e)\r
1213   {\r
1214 \r
1215   }\r
1216 \r
1217   public void exportFeatures_actionPerformed(ActionEvent e)\r
1218   {\r
1219 \r
1220   }\r
1221 \r
1222   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1223   {\r
1224 \r
1225   }\r
1226 \r
1227   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1228   {\r
1229   }\r
1230 \r
1231   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1232   {\r
1233   }\r
1234 \r
1235   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1236   {\r
1237   }\r
1238 \r
1239   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1240   {\r
1241   }\r
1242 \r
1243   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1244   {\r
1245   }\r
1246 \r
1247   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1248   {\r
1249   }\r
1250 \r
1251   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1252   {\r
1253   }\r
1254 \r
1255   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1256   {\r
1257   }\r
1258 \r
1259   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1260   {\r
1261   }\r
1262 \r
1263   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1264   {\r
1265   }\r
1266 \r
1267   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1268   {\r
1269   }\r
1270 \r
1271   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1272   {\r
1273   }\r
1274 \r
1275   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1276   {\r
1277   }\r
1278 \r
1279   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1280   {\r
1281   }\r
1282 \r
1283   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1284   {\r
1285   }\r
1286 \r
1287   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1288   {\r
1289   }\r
1290 \r
1291   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1292   {\r
1293   }\r
1294 \r
1295   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1296   {\r
1297   }\r
1298 \r
1299   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1300   {\r
1301   }\r
1302 \r
1303   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1304   {\r
1305   }\r
1306 \r
1307   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1308   {\r
1309   }\r
1310 \r
1311   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1312   {\r
1313   }\r
1314 \r
1315   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1316   {\r
1317   }\r
1318 \r
1319   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1320   {\r
1321   }\r
1322 \r
1323   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1324   {\r
1325   }\r
1326 \r
1327   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1328   {\r
1329   }\r
1330 \r
1331   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1332   {\r
1333   }\r
1334 \r
1335   protected void clustalColour_actionPerformed(ActionEvent e)\r
1336   {\r
1337   }\r
1338 \r
1339   protected void zappoColour_actionPerformed(ActionEvent e)\r
1340   {\r
1341   }\r
1342 \r
1343   protected void taylorColour_actionPerformed(ActionEvent e)\r
1344   {\r
1345   }\r
1346 \r
1347   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1348   {\r
1349   }\r
1350 \r
1351   protected void helixColour_actionPerformed(ActionEvent e)\r
1352   {\r
1353   }\r
1354 \r
1355   protected void strandColour_actionPerformed(ActionEvent e)\r
1356   {\r
1357   }\r
1358 \r
1359   protected void turnColour_actionPerformed(ActionEvent e)\r
1360   {\r
1361   }\r
1362 \r
1363   protected void buriedColour_actionPerformed(ActionEvent e)\r
1364   {\r
1365   }\r
1366 \r
1367   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1368   {\r
1369   }\r
1370 \r
1371   protected void PIDColour_actionPerformed(ActionEvent e)\r
1372   {\r
1373   }\r
1374 \r
1375   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1376   {\r
1377   }\r
1378 \r
1379   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1380   {\r
1381   }\r
1382 \r
1383   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1384   {\r
1385   }\r
1386 \r
1387   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1388   {\r
1389   }\r
1390 \r
1391   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1392   {\r
1393   }\r
1394 \r
1395   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1396   {\r
1397   }\r
1398 \r
1399   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1400   {\r
1401   }\r
1402 \r
1403   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1404   {\r
1405   }\r
1406 \r
1407   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1408   {\r
1409   }\r
1410 \r
1411   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1412   {\r
1413   }\r
1414 \r
1415   protected void copy_actionPerformed(ActionEvent e)\r
1416   {\r
1417   }\r
1418 \r
1419   protected void cut_actionPerformed(ActionEvent e)\r
1420   {\r
1421   }\r
1422 \r
1423   protected void delete_actionPerformed(ActionEvent e)\r
1424   {\r
1425   }\r
1426 \r
1427   protected void pasteNew_actionPerformed(ActionEvent e)\r
1428   {\r
1429   }\r
1430 \r
1431   protected void pasteThis_actionPerformed(ActionEvent e)\r
1432   {\r
1433   }\r
1434 \r
1435   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1436   {\r
1437   }\r
1438 \r
1439   public void createPNG(java.io.File f)\r
1440   {\r
1441   }\r
1442 \r
1443   protected void font_actionPerformed(ActionEvent e)\r
1444   {\r
1445   }\r
1446 \r
1447   protected void seqLimit_actionPerformed(ActionEvent e)\r
1448   {\r
1449   }\r
1450 \r
1451   public void seqDBRef_actionPerformed(ActionEvent e)\r
1452   {\r
1453 \r
1454   }\r
1455 \r
1456 \r
1457   public void createEPS(java.io.File f)\r
1458   {\r
1459   }\r
1460 \r
1461   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1462   {\r
1463   }\r
1464 \r
1465   protected void jpred_actionPerformed(ActionEvent e)\r
1466   {\r
1467   }\r
1468 \r
1469   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1470   {\r
1471   }\r
1472 \r
1473   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1474   {\r
1475   }\r
1476 \r
1477   protected void scaleRight_actionPerformed(ActionEvent e)\r
1478   {\r
1479   }\r
1480 \r
1481   protected void modifyPID_actionPerformed(ActionEvent e)\r
1482   {\r
1483   }\r
1484 \r
1485   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1486   {\r
1487   }\r
1488 \r
1489 \r
1490 \r
1491   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1492   {\r
1493   }\r
1494 \r
1495   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1496   {\r
1497   }\r
1498 \r
1499 \r
1500   public void vamsasStore_actionPerformed(ActionEvent e)\r
1501   {\r
1502 \r
1503   }\r
1504 \r
1505   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1506   {\r
1507 \r
1508   }\r
1509 \r
1510   public void showTranslation_actionPerformed(ActionEvent e)\r
1511   {\r
1512 \r
1513   }\r
1514 \r
1515   public void featureSettings_actionPerformed(ActionEvent e)\r
1516   {\r
1517 \r
1518   }\r
1519 \r
1520   public void fetchSequence_actionPerformed(ActionEvent e)\r
1521   {\r
1522 \r
1523   }\r
1524 \r
1525   public void smoothFont_actionPerformed(ActionEvent e)\r
1526   {\r
1527 \r
1528   }\r
1529 \r
1530   public void annotationColour_actionPerformed(ActionEvent e)\r
1531   {\r
1532 \r
1533   }\r
1534 \r
1535 \r
1536   public void associatedData_actionPerformed(ActionEvent e)\r
1537   {\r
1538 \r
1539   }\r
1540 \r
1541   public void autoCalculate_actionPerformed(ActionEvent e)\r
1542   {\r
1543 \r
1544   }\r
1545 \r
1546   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1547   {\r
1548 \r
1549   }\r
1550 \r
1551   public void showAllColumns_actionPerformed(ActionEvent e)\r
1552   {\r
1553 \r
1554   }\r
1555 \r
1556   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1557   {\r
1558 \r
1559   }\r
1560 \r
1561   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1562   {\r
1563 \r
1564   }\r
1565 \r
1566   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1567   {\r
1568 \r
1569   }\r
1570 \r
1571   public void findPdbId_actionPerformed(ActionEvent e)\r
1572   {\r
1573 \r
1574   }\r
1575 \r
1576   public void enterPdbId_actionPerformed(ActionEvent e)\r
1577   {\r
1578 \r
1579   }\r
1580 \r
1581   public void pdbFile_actionPerformed(ActionEvent e)\r
1582   {\r
1583 \r
1584   }\r
1585 }\r