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