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   JMenuItem invertColSel = new JMenuItem();\r
 140 \r
 141   public GAlignFrame()\r
 142   {\r
 143 \r
 144 \r
 145     try\r
 146     {\r
 147       jbInit();\r
 148       setJMenuBar(alignFrameMenuBar);\r
 149 \r
 150       // dynamically fill save as menu with available formats\r
 151       for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
 152       {\r
 153         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 154                              elementAt(\r
 155                                  i));\r
 156         item.addActionListener(new java.awt.event.ActionListener()\r
 157         {\r
 158           public void actionPerformed(ActionEvent e)\r
 159           {\r
 160             outputText_actionPerformed(e);\r
 161           }\r
 162         });\r
 163 \r
 164         outputTextboxMenu.add(item);\r
 165       }\r
 166     }\r
 167     catch (Exception e)\r
 168     {\r
 169     }\r
 170 \r
 171 \r
 172     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 173     {\r
 174       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 175           getUserColourSchemes().keys();\r
 176 \r
 177       while (userColours.hasMoreElements())\r
 178       {\r
 179         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 180             nextElement().toString());\r
 181         radioItem.setName("USER_DEFINED");\r
 182         radioItem.addMouseListener(new MouseAdapter()\r
 183             {\r
 184               public void mousePressed(MouseEvent evt)\r
 185               {\r
 186                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 187                 {\r
 188                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 189 \r
 190                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 191                       "Remove from default list?",\r
 192                       "Remove user defined colour",\r
 193                       JOptionPane.YES_NO_OPTION);\r
 194                   if(option == JOptionPane.YES_OPTION)\r
 195                   {\r
 196                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 197                     colourMenu.remove(radioItem);\r
 198                   }\r
 199                   else\r
 200                     radioItem.addActionListener(new ActionListener()\r
 201                     {\r
 202                       public void actionPerformed(ActionEvent evt)\r
 203                       {\r
 204                         userDefinedColour_actionPerformed(evt);\r
 205                       }\r
 206                     });\r
 207                 }\r
 208               }\r
 209             });\r
 210         radioItem.addActionListener(new ActionListener()\r
 211         {\r
 212           public void actionPerformed(ActionEvent evt)\r
 213           {\r
 214             userDefinedColour_actionPerformed(evt);\r
 215           }\r
 216         });\r
 217         colourMenu.insert(radioItem, 15);\r
 218         colours.add(radioItem);\r
 219       }\r
 220     }\r
 221     colours.add(noColourmenuItem);\r
 222     colours.add(clustalColour);\r
 223     colours.add(zappoColour);\r
 224     colours.add(taylorColour);\r
 225     colours.add(hydrophobicityColour);\r
 226     colours.add(helixColour);\r
 227     colours.add(strandColour);\r
 228     colours.add(turnColour);\r
 229     colours.add(buriedColour);\r
 230     colours.add(userDefinedColour);\r
 231     colours.add(PIDColour);\r
 232     colours.add(BLOSUM62Colour);\r
 233     colours.add(nucleotideColour);\r
 234 \r
 235     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 236 \r
 237 \r
 238   }\r
 239 \r
 240   public void setColourSelected(String defaultColour)\r
 241   {\r
 242 \r
 243     if (defaultColour != null)\r
 244     {\r
 245       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 246 \r
 247       switch (index)\r
 248       {\r
 249         case ColourSchemeProperty.NONE:\r
 250               noColourmenuItem.setSelected(true);\r
 251               break;\r
 252         case ColourSchemeProperty.CLUSTAL:\r
 253           clustalColour.setSelected(true);\r
 254 \r
 255           break;\r
 256 \r
 257         case ColourSchemeProperty.BLOSUM:\r
 258           BLOSUM62Colour.setSelected(true);\r
 259 \r
 260           break;\r
 261 \r
 262         case ColourSchemeProperty.PID:\r
 263           PIDColour.setSelected(true);\r
 264 \r
 265           break;\r
 266 \r
 267         case ColourSchemeProperty.ZAPPO:\r
 268           zappoColour.setSelected(true);\r
 269 \r
 270           break;\r
 271 \r
 272         case ColourSchemeProperty.TAYLOR:\r
 273           taylorColour.setSelected(true);\r
 274           break;\r
 275 \r
 276         case ColourSchemeProperty.HYDROPHOBIC:\r
 277           hydrophobicityColour.setSelected(true);\r
 278 \r
 279           break;\r
 280 \r
 281         case ColourSchemeProperty.HELIX:\r
 282           helixColour.setSelected(true);\r
 283 \r
 284           break;\r
 285 \r
 286         case ColourSchemeProperty.STRAND:\r
 287           strandColour.setSelected(true);\r
 288 \r
 289           break;\r
 290 \r
 291         case ColourSchemeProperty.TURN:\r
 292           turnColour.setSelected(true);\r
 293 \r
 294           break;\r
 295 \r
 296         case ColourSchemeProperty.BURIED:\r
 297           buriedColour.setSelected(true);\r
 298 \r
 299           break;\r
 300 \r
 301         case ColourSchemeProperty.NUCLEOTIDE:\r
 302           nucleotideColour.setSelected(true);\r
 303 \r
 304           break;\r
 305 \r
 306         case ColourSchemeProperty.USER_DEFINED:\r
 307           userDefinedColour.setSelected(true);\r
 308 \r
 309           break;\r
 310       }\r
 311     }\r
 312 \r
 313   }\r
 314 \r
 315   private void jbInit()\r
 316       throws Exception\r
 317   {\r
 318     fileMenu.setMnemonic('F');\r
 319     fileMenu.setText("File");\r
 320     saveAlignmentMenu.setMnemonic('L');\r
 321     saveAlignmentMenu.setText("Save As");\r
 322     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 323         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 324     saveAlignmentMenu.addActionListener(new ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         saveAlignmentMenu_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     closeMenuItem.setMnemonic('C');\r
 332     closeMenuItem.setText("Close");\r
 333     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 334     {\r
 335       public void actionPerformed(ActionEvent e)\r
 336       {\r
 337         closeMenuItem_actionPerformed(e);\r
 338       }\r
 339     });\r
 340     editMenu.setText("Edit");\r
 341     viewMenu.setText("View");\r
 342     colourMenu.setText("Colour");\r
 343     calculateMenu.setText("Calculate");\r
 344     webService.setText("Web Service");\r
 345     selectAllSequenceMenuItem.setText("Select all");\r
 346     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 347         java.awt.event.KeyEvent.VK_A,\r
 348         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 349     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 350                                                 ActionListener()\r
 351     {\r
 352       public void actionPerformed(ActionEvent e)\r
 353       {\r
 354         selectAllSequenceMenuItem_actionPerformed(e);\r
 355       }\r
 356     });\r
 357     deselectAllSequenceMenuItem.setText("Deselect All");\r
 358     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 359                                                getKeyStroke(\r
 360         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 361     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 362                                                   ActionListener()\r
 363     {\r
 364       public void actionPerformed(ActionEvent e)\r
 365       {\r
 366         deselectAllSequenceMenuItem_actionPerformed(e);\r
 367       }\r
 368     });\r
 369     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 370     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 371     {\r
 372       public void actionPerformed(ActionEvent e)\r
 373       {\r
 374         invertSequenceMenuItem_actionPerformed(e);\r
 375       }\r
 376     });\r
 377     remove2LeftMenuItem.setText("Remove Left");\r
 378     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 379     {\r
 380       public void actionPerformed(ActionEvent e)\r
 381       {\r
 382         remove2LeftMenuItem_actionPerformed(e);\r
 383       }\r
 384     });\r
 385     remove2RightMenuItem.setText("Remove Right");\r
 386     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 387     {\r
 388       public void actionPerformed(ActionEvent e)\r
 389       {\r
 390         remove2RightMenuItem_actionPerformed(e);\r
 391       }\r
 392     });\r
 393     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 394     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 395                                                  ActionListener()\r
 396     {\r
 397       public void actionPerformed(ActionEvent e)\r
 398       {\r
 399         removeGappedColumnMenuItem_actionPerformed(e);\r
 400       }\r
 401     });\r
 402     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 403     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 404     {\r
 405       public void actionPerformed(ActionEvent e)\r
 406       {\r
 407         removeAllGapsMenuItem_actionPerformed(e);\r
 408       }\r
 409     });\r
 410     viewBoxesMenuItem.setText("Boxes");\r
 411     viewBoxesMenuItem.setState(true);\r
 412     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 413     {\r
 414       public void actionPerformed(ActionEvent e)\r
 415       {\r
 416         viewBoxesMenuItem_actionPerformed(e);\r
 417       }\r
 418     });\r
 419     viewTextMenuItem.setText("Text");\r
 420     viewTextMenuItem.setState(true);\r
 421     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 422     {\r
 423       public void actionPerformed(ActionEvent e)\r
 424       {\r
 425         viewTextMenuItem_actionPerformed(e);\r
 426       }\r
 427     });\r
 428     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 429     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 430     {\r
 431       public void actionPerformed(ActionEvent e)\r
 432       {\r
 433         sortPairwiseMenuItem_actionPerformed(e);\r
 434       }\r
 435     });\r
 436     sortIDMenuItem.setText("by ID");\r
 437     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 438     {\r
 439       public void actionPerformed(ActionEvent e)\r
 440       {\r
 441         sortIDMenuItem_actionPerformed(e);\r
 442       }\r
 443     });\r
 444     sortGroupMenuItem.setText("by Group");\r
 445     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 446     {\r
 447       public void actionPerformed(ActionEvent e)\r
 448       {\r
 449         sortGroupMenuItem_actionPerformed(e);\r
 450       }\r
 451     });\r
 452     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 453     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 454                                                ActionListener()\r
 455     {\r
 456       public void actionPerformed(ActionEvent e)\r
 457       {\r
 458         removeRedundancyMenuItem_actionPerformed(e);\r
 459       }\r
 460     });\r
 461     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 462     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 463                                                 ActionListener()\r
 464     {\r
 465       public void actionPerformed(ActionEvent e)\r
 466       {\r
 467         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 468       }\r
 469     });\r
 470     PCAMenuItem.setText("Principal Component Analysis");\r
 471     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 472     {\r
 473       public void actionPerformed(ActionEvent e)\r
 474       {\r
 475         PCAMenuItem_actionPerformed(e);\r
 476       }\r
 477     });\r
 478     averageDistanceTreeMenuItem.setText(\r
 479         "Average Distance Using % Identity");\r
 480     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 481                                                   ActionListener()\r
 482     {\r
 483       public void actionPerformed(ActionEvent e)\r
 484       {\r
 485         averageDistanceTreeMenuItem_actionPerformed(e);\r
 486       }\r
 487     });\r
 488     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 489     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 490     {\r
 491       public void actionPerformed(ActionEvent e)\r
 492       {\r
 493         neighbourTreeMenuItem_actionPerformed(e);\r
 494       }\r
 495     });\r
 496     this.getContentPane().setLayout(borderLayout1);\r
 497     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 498     statusBar.setBackground(Color.white);\r
 499     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 500     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 501     statusBar.setText("Status bar");\r
 502     outputTextboxMenu.setMnemonic('T');\r
 503     outputTextboxMenu.setText("Output to Textbox");\r
 504     clustalColour.setText("Clustalx");\r
 505 \r
 506     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 507     {\r
 508       public void actionPerformed(ActionEvent e)\r
 509       {\r
 510         clustalColour_actionPerformed(e);\r
 511       }\r
 512     });\r
 513     zappoColour.setText("Zappo");\r
 514     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 515     {\r
 516       public void actionPerformed(ActionEvent e)\r
 517       {\r
 518         zappoColour_actionPerformed(e);\r
 519       }\r
 520     });\r
 521     taylorColour.setText("Taylor");\r
 522     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         taylorColour_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     hydrophobicityColour.setText("Hydrophobicity");\r
 530     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         hydrophobicityColour_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     helixColour.setText("Helix Propensity");\r
 538     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 539     {\r
 540       public void actionPerformed(ActionEvent e)\r
 541       {\r
 542         helixColour_actionPerformed(e);\r
 543       }\r
 544     });\r
 545     strandColour.setText("Strand Propensity");\r
 546     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 547     {\r
 548       public void actionPerformed(ActionEvent e)\r
 549       {\r
 550         strandColour_actionPerformed(e);\r
 551       }\r
 552     });\r
 553     turnColour.setText("Turn Propensity");\r
 554     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 555     {\r
 556       public void actionPerformed(ActionEvent e)\r
 557       {\r
 558         turnColour_actionPerformed(e);\r
 559       }\r
 560     });\r
 561     buriedColour.setText("Buried Index");\r
 562     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 563     {\r
 564       public void actionPerformed(ActionEvent e)\r
 565       {\r
 566         buriedColour_actionPerformed(e);\r
 567       }\r
 568     });\r
 569     userDefinedColour.setText("User Defined...");\r
 570     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 571     {\r
 572       public void actionPerformed(ActionEvent e)\r
 573       {\r
 574         userDefinedColour_actionPerformed(e);\r
 575       }\r
 576     });\r
 577     PIDColour.setText("Percentage Identity");\r
 578     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent e)\r
 581       {\r
 582         PIDColour_actionPerformed(e);\r
 583       }\r
 584     });\r
 585     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 586     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 587     {\r
 588       public void actionPerformed(ActionEvent e)\r
 589       {\r
 590         BLOSUM62Colour_actionPerformed(e);\r
 591       }\r
 592     });\r
 593     avDistanceTreeBlosumMenuItem.setText(\r
 594         "Average Distance Using BLOSUM62");\r
 595     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 596         ActionListener()\r
 597     {\r
 598       public void actionPerformed(ActionEvent e)\r
 599       {\r
 600         avTreeBlosumMenuItem_actionPerformed(e);\r
 601       }\r
 602     });\r
 603     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 604     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 605     {\r
 606       public void actionPerformed(ActionEvent e)\r
 607       {\r
 608         njTreeBlosumMenuItem_actionPerformed(e);\r
 609       }\r
 610     });\r
 611     annotationPanelMenuItem.setActionCommand("");\r
 612     annotationPanelMenuItem.setText("Show Annotations");\r
 613     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 614     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 615     {\r
 616       public void actionPerformed(ActionEvent e)\r
 617       {\r
 618         annotationPanelMenuItem_actionPerformed(e);\r
 619       }\r
 620     });\r
 621     colourTextMenuItem.setText("Colour Text");\r
 622     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 623     {\r
 624       public void actionPerformed(ActionEvent e)\r
 625       {\r
 626         colourTextMenuItem_actionPerformed(e);\r
 627       }\r
 628     });\r
 629     htmlMenuItem.setText("HTML");\r
 630     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 631     {\r
 632       public void actionPerformed(ActionEvent e)\r
 633       {\r
 634         htmlMenuItem_actionPerformed(e);\r
 635       }\r
 636     });\r
 637     overviewMenuItem.setText("Overview Window");\r
 638     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 639     {\r
 640       public void actionPerformed(ActionEvent e)\r
 641       {\r
 642         overviewMenuItem_actionPerformed(e);\r
 643       }\r
 644     });\r
 645     undoMenuItem.setEnabled(false);\r
 646     undoMenuItem.setMnemonic('Z');\r
 647     undoMenuItem.setText("Undo");\r
 648     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 649         java.awt.event.KeyEvent.VK_Z,\r
 650         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 651     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 652     {\r
 653       public void actionPerformed(ActionEvent e)\r
 654       {\r
 655         undoMenuItem_actionPerformed(e);\r
 656       }\r
 657     });\r
 658     redoMenuItem.setEnabled(false);\r
 659     redoMenuItem.setMnemonic('0');\r
 660     redoMenuItem.setText("Redo");\r
 661     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 662     {\r
 663       public void actionPerformed(ActionEvent e)\r
 664       {\r
 665         redoMenuItem_actionPerformed(e);\r
 666       }\r
 667     });\r
 668     conservationMenuItem.setText("By Conservation");\r
 669     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 670     {\r
 671       public void actionPerformed(ActionEvent e)\r
 672       {\r
 673         conservationMenuItem_actionPerformed(e);\r
 674       }\r
 675     });\r
 676     noColourmenuItem.setText("None");\r
 677     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 678     {\r
 679       public void actionPerformed(ActionEvent e)\r
 680       {\r
 681         noColourmenuItem_actionPerformed(e);\r
 682       }\r
 683     });\r
 684     wrapMenuItem.setText("Wrap");\r
 685     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 686     {\r
 687       public void actionPerformed(ActionEvent e)\r
 688       {\r
 689         wrapMenuItem_actionPerformed(e);\r
 690       }\r
 691     });\r
 692     printMenuItem.setText("Print");\r
 693     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 694     {\r
 695       public void actionPerformed(ActionEvent e)\r
 696       {\r
 697         printMenuItem_actionPerformed(e);\r
 698       }\r
 699     });\r
 700     renderGapsMenuItem.setText("Show Gaps");\r
 701     renderGapsMenuItem.setState(true);\r
 702     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 703     {\r
 704       public void actionPerformed(ActionEvent e)\r
 705       {\r
 706         renderGapsMenuItem_actionPerformed(e);\r
 707       }\r
 708     });\r
 709     findMenuItem.setText("Find...");\r
 710     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 711         java.awt.event.KeyEvent.VK_F,\r
 712         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 713     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 714     {\r
 715       public void actionPerformed(ActionEvent e)\r
 716       {\r
 717         findMenuItem_actionPerformed(e);\r
 718       }\r
 719     });\r
 720     searchMenu.setText("Search");\r
 721 \r
 722     abovePIDThreshold.setText("Above Identity Threshold");\r
 723     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 724     {\r
 725       public void actionPerformed(ActionEvent e)\r
 726       {\r
 727         abovePIDThreshold_actionPerformed(e);\r
 728       }\r
 729     });\r
 730     showSeqFeatures.setText("Show Sequence Features");\r
 731     showSeqFeatures.addActionListener(new ActionListener()\r
 732     {\r
 733       public void actionPerformed(ActionEvent actionEvent)\r
 734       {\r
 735         showSeqFeatures_actionPerformed(actionEvent);\r
 736       }\r
 737     });\r
 738     nucleotideColour.setText("Nucleotide");\r
 739     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 740     {\r
 741       public void actionPerformed(ActionEvent e)\r
 742       {\r
 743         nucleotideColour_actionPerformed(e);\r
 744       }\r
 745     });\r
 746     deleteGroups.setText("Undefine groups");\r
 747     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 748     {\r
 749       public void actionPerformed(ActionEvent e)\r
 750       {\r
 751         deleteGroups_actionPerformed(e);\r
 752       }\r
 753     });\r
 754     copy.setText("Copy");\r
 755     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 756         java.awt.event.KeyEvent.VK_C,\r
 757         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 758     copy.setMnemonic(KeyEvent.VK_C);\r
 759 \r
 760     copy.addActionListener(new java.awt.event.ActionListener()\r
 761     {\r
 762       public void actionPerformed(ActionEvent e)\r
 763       {\r
 764         copy_actionPerformed(e);\r
 765       }\r
 766     });\r
 767     cut.setText("Cut");\r
 768     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 769         java.awt.event.KeyEvent.VK_X,\r
 770         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 771     cut.setMnemonic(KeyEvent.VK_X);\r
 772     cut.addActionListener(new java.awt.event.ActionListener()\r
 773     {\r
 774       public void actionPerformed(ActionEvent e)\r
 775       {\r
 776         cut_actionPerformed(e);\r
 777       }\r
 778     });\r
 779     delete.setText("Delete");\r
 780     delete.addActionListener(new java.awt.event.ActionListener()\r
 781     {\r
 782       public void actionPerformed(ActionEvent e)\r
 783       {\r
 784         delete_actionPerformed(e);\r
 785       }\r
 786     });\r
 787     jMenu1.setMnemonic('V');\r
 788     jMenu1.setText("Paste");\r
 789     pasteNew.setText("To New Alignment");\r
 790     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 791         java.awt.event.KeyEvent.VK_V,\r
 792         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 793     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 794     {\r
 795       public void actionPerformed(ActionEvent e)\r
 796       {\r
 797         pasteNew_actionPerformed(e);\r
 798       }\r
 799     });\r
 800     pasteThis.setText("Add To This Alignment");\r
 801     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 802     {\r
 803       public void actionPerformed(ActionEvent e)\r
 804       {\r
 805         pasteThis_actionPerformed(e);\r
 806       }\r
 807     });\r
 808     applyToAllGroups.setText("Apply Colour To All Groups");\r
 809     applyToAllGroups.setState(true);\r
 810     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 811     {\r
 812       public void actionPerformed(ActionEvent e)\r
 813       {\r
 814         applyToAllGroups_actionPerformed(e);\r
 815       }\r
 816     });\r
 817     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 818     {\r
 819       public void actionPerformed(ActionEvent e)\r
 820       {\r
 821         createPNG(null);\r
 822       }\r
 823     });\r
 824     createPNG.setActionCommand("Save As PNG Image");\r
 825     createPNG.setText("PNG");\r
 826     font.setText("Font...");\r
 827     font.addActionListener(new java.awt.event.ActionListener()\r
 828     {\r
 829       public void actionPerformed(ActionEvent e)\r
 830       {\r
 831         font_actionPerformed(e);\r
 832       }\r
 833     });\r
 834 \r
 835     seqLimits.setText("Show Sequence Limits");\r
 836     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 837     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 838     {\r
 839       public void actionPerformed(ActionEvent e)\r
 840       {\r
 841         seqLimit_actionPerformed(e);\r
 842       }\r
 843     });\r
 844     epsFile.setText("EPS");\r
 845     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 846     {\r
 847       public void actionPerformed(ActionEvent e)\r
 848       {\r
 849         createEPS(null);\r
 850       }\r
 851     });\r
 852     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 853     LoadtreeMenuItem.setText("Load Associated Tree");\r
 854     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 855     {\r
 856       public void actionPerformed(ActionEvent e)\r
 857       {\r
 858         LoadtreeMenuItem_actionPerformed(e);\r
 859       }\r
 860     });\r
 861     scaleAbove.setVisible(false);\r
 862     scaleAbove.setText("Scale Above");\r
 863     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 864     {\r
 865       public void actionPerformed(ActionEvent e)\r
 866       {\r
 867         scaleAbove_actionPerformed(e);\r
 868       }\r
 869     });\r
 870     scaleLeft.setVisible(false);\r
 871     scaleLeft.setSelected(true);\r
 872     scaleLeft.setText("Scale Left");\r
 873     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 874     {\r
 875       public void actionPerformed(ActionEvent e)\r
 876       {\r
 877         scaleLeft_actionPerformed(e);\r
 878       }\r
 879     });\r
 880     scaleRight.setVisible(false);\r
 881     scaleRight.setSelected(true);\r
 882     scaleRight.setText("Scale Right");\r
 883     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 884     {\r
 885       public void actionPerformed(ActionEvent e)\r
 886       {\r
 887         scaleRight_actionPerformed(e);\r
 888       }\r
 889     });\r
 890     modifyPID.setText("Modify Identity Threshold...");\r
 891     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 892     {\r
 893       public void actionPerformed(ActionEvent e)\r
 894       {\r
 895         modifyPID_actionPerformed(e);\r
 896       }\r
 897     });\r
 898     modifyConservation.setText("Modify Conservation Threshold...");\r
 899     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 900     {\r
 901       public void actionPerformed(ActionEvent e)\r
 902       {\r
 903         modifyConservation_actionPerformed(e);\r
 904       }\r
 905     });\r
 906     sortByTreeMenu.setText("By Tree Order");\r
 907     sort.setText("Sort");\r
 908     calculate.setText("Calculate Tree");\r
 909 \r
 910     jMenu2.setText("Export");\r
 911     padGapsMenuitem.setText("Pad Gaps");\r
 912     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 913     padGapsMenuitem.addActionListener(new ActionListener()\r
 914     {\r
 915       public void actionPerformed(ActionEvent e)\r
 916       {\r
 917         padGapsMenuitem_actionPerformed(e);\r
 918       }\r
 919     });\r
 920     vamsasStore.setVisible(false);\r
 921     vamsasStore.setText("VAMSAS store");\r
 922     vamsasStore.addActionListener(new ActionListener()\r
 923     {\r
 924       public void actionPerformed(ActionEvent e)\r
 925       {\r
 926         vamsasStore_actionPerformed(e);\r
 927       }\r
 928     });\r
 929     showTranslation.setText("Translate cDNA");\r
 930     showTranslation.addActionListener(new ActionListener()\r
 931     {\r
 932       public void actionPerformed(ActionEvent e)\r
 933       {\r
 934         showTranslation_actionPerformed(e);\r
 935       }\r
 936     });\r
 937 \r
 938    /* tabbedPane.addChangeListener(new ChangeListener()\r
 939         {\r
 940           public void stateChanged(ChangeEvent ece)\r
 941           {\r
 942 \r
 943             tabSelected();\r
 944           }\r
 945         });*/\r
 946     featureSettings.setText("Feature Settings...");\r
 947     featureSettings.addActionListener(new ActionListener()\r
 948     {\r
 949       public void actionPerformed(ActionEvent e)\r
 950       {\r
 951         featureSettings_actionPerformed(e);\r
 952       }\r
 953     });\r
 954     fetchSequence.setText("Fetch Sequence(s)...");\r
 955     fetchSequence.addActionListener(new ActionListener()\r
 956     {\r
 957       public void actionPerformed(ActionEvent e)\r
 958       {\r
 959         fetchSequence_actionPerformed(e);\r
 960       }\r
 961     });\r
 962     smoothFont.setText("Smooth Fonts");\r
 963     smoothFont.addActionListener(new ActionListener()\r
 964     {\r
 965       public void actionPerformed(ActionEvent e)\r
 966       {\r
 967         smoothFont_actionPerformed(e);\r
 968       }\r
 969     });\r
 970     smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
 971     annotationColour.setText("By Annotation...");\r
 972     annotationColour.addActionListener(new ActionListener()\r
 973     {\r
 974       public void actionPerformed(ActionEvent e)\r
 975       {\r
 976         annotationColour_actionPerformed(e);\r
 977       }\r
 978     });\r
 979     associatedData.setText("Load Features / Annotations");\r
 980     associatedData.addActionListener(new ActionListener()\r
 981     {\r
 982       public void actionPerformed(ActionEvent e)\r
 983       {\r
 984         associatedData_actionPerformed(e);\r
 985       }\r
 986     });\r
 987     autoCalculate.setText("Autocalculate Consensus");\r
 988     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
 989     autoCalculate.addActionListener(new ActionListener()\r
 990     {\r
 991       public void actionPerformed(ActionEvent e)\r
 992       {\r
 993         autoCalculate_actionPerformed(e);\r
 994       }\r
 995     });\r
 996     addSequenceMenu.setText("Add Sequences");\r
 997     addFromFile.setText("From File");\r
 998     addFromFile.addActionListener(new ActionListener()\r
 999     {\r
1000       public void actionPerformed(ActionEvent e)\r
1001       {\r
1002         addFromFile_actionPerformed(e);\r
1003       }\r
1004     });\r
1005     addFromText.setText("From Textbox");\r
1006     addFromText.addActionListener(new ActionListener()\r
1007     {\r
1008       public void actionPerformed(ActionEvent e)\r
1009       {\r
1010         addFromText_actionPerformed(e);\r
1011       }\r
1012     });\r
1013     addFromURL.setText("From URL");\r
1014     addFromURL.addActionListener(new ActionListener()\r
1015     {\r
1016       public void actionPerformed(ActionEvent e)\r
1017       {\r
1018         addFromURL_actionPerformed(e);\r
1019       }\r
1020     });\r
1021     exportFeatures.setText("Export Features...");\r
1022     exportFeatures.addActionListener(new ActionListener()\r
1023     {\r
1024       public void actionPerformed(ActionEvent e)\r
1025       {\r
1026         exportFeatures_actionPerformed(e);\r
1027       }\r
1028     });\r
1029     exportAnnotations.setText("Export Annotations...");\r
1030     exportAnnotations.addActionListener(new ActionListener()\r
1031     {\r
1032       public void actionPerformed(ActionEvent e)\r
1033       {\r
1034         exportAnnotations_actionPerformed(e);\r
1035       }\r
1036     });\r
1037     statusPanel.setLayout(gridLayout1);\r
1038     jMenu3.setText("Show");\r
1039     showAllSeqs.setText("All Sequences");\r
1040     showAllSeqs.addActionListener(new ActionListener()\r
1041     {\r
1042       public void actionPerformed(ActionEvent e)\r
1043       {\r
1044         showAllSeqs_actionPerformed(e);\r
1045       }\r
1046     });\r
1047     showAllColumns.setText("All Columns");\r
1048     showAllColumns.addActionListener(new ActionListener()\r
1049     {\r
1050       public void actionPerformed(ActionEvent e)\r
1051       {\r
1052         showAllColumns_actionPerformed(e);\r
1053       }\r
1054     });\r
1055     jMenu4.setText("Hide");\r
1056     hideSelSequences.setText("Selected Sequences");\r
1057     hideSelSequences.addActionListener(new ActionListener()\r
1058     {\r
1059       public void actionPerformed(ActionEvent e)\r
1060       {\r
1061         hideSelSequences_actionPerformed(e);\r
1062       }\r
1063     });\r
1064     hideSelColumns.setText("Selected Columns");\r
1065     hideSelColumns.addActionListener(new ActionListener()\r
1066     {\r
1067       public void actionPerformed(ActionEvent e)\r
1068       {\r
1069         hideSelColumns_actionPerformed(e);\r
1070       }\r
1071     });\r
1072     hiddenMarkers.setText("Hidden Markers");\r
1073     hiddenMarkers.setState(true);\r
1074     hiddenMarkers.addActionListener(new ActionListener()\r
1075     {\r
1076       public void actionPerformed(ActionEvent e)\r
1077       {\r
1078         hiddenMarkers_actionPerformed(e);\r
1079       }\r
1080     });\r
1081     invertColSel.setText("Invert Column Selection");\r
1082     invertColSel.addActionListener(new ActionListener()\r
1083     {\r
1084       public void actionPerformed(ActionEvent e)\r
1085       {\r
1086         invertColSel_actionPerformed(e);\r
1087       }\r
1088     });\r
1089 \r
1090     alignFrameMenuBar.add(fileMenu);\r
1091     alignFrameMenuBar.add(editMenu);\r
1092     alignFrameMenuBar.add(searchMenu);\r
1093     alignFrameMenuBar.add(viewMenu);\r
1094     alignFrameMenuBar.add(colourMenu);\r
1095     alignFrameMenuBar.add(calculateMenu);\r
1096     alignFrameMenuBar.add(webService);\r
1097     fileMenu.add(addSequenceMenu);\r
1098     fileMenu.add(fetchSequence);\r
1099     fileMenu.addSeparator();\r
1100     fileMenu.add(vamsasStore);\r
1101     fileMenu.add(saveAlignmentMenu);\r
1102     fileMenu.add(jMenu2);\r
1103     fileMenu.add(outputTextboxMenu);\r
1104     fileMenu.add(printMenuItem);\r
1105     fileMenu.addSeparator();\r
1106     fileMenu.add(exportFeatures);\r
1107     fileMenu.add(exportAnnotations);\r
1108     fileMenu.add(LoadtreeMenuItem);\r
1109     fileMenu.add(associatedData);\r
1110     fileMenu.addSeparator();\r
1111     fileMenu.add(closeMenuItem);\r
1112     editMenu.add(undoMenuItem);\r
1113     editMenu.add(redoMenuItem);\r
1114     editMenu.add(cut);\r
1115     editMenu.add(copy);\r
1116     editMenu.add(jMenu1);\r
1117     editMenu.add(delete);\r
1118     editMenu.addSeparator();\r
1119     editMenu.add(selectAllSequenceMenuItem);\r
1120     editMenu.add(deselectAllSequenceMenuItem);\r
1121     editMenu.add(invertSequenceMenuItem);\r
1122     editMenu.add(invertColSel);\r
1123     editMenu.add(deleteGroups);\r
1124     editMenu.addSeparator();\r
1125     editMenu.add(remove2LeftMenuItem);\r
1126     editMenu.add(remove2RightMenuItem);\r
1127     editMenu.add(removeGappedColumnMenuItem);\r
1128     editMenu.add(removeAllGapsMenuItem);\r
1129     editMenu.add(removeRedundancyMenuItem);\r
1130     editMenu.addSeparator();\r
1131     editMenu.add(padGapsMenuitem);\r
1132     searchMenu.add(findMenuItem);\r
1133     viewMenu.add(font);\r
1134     viewMenu.add(smoothFont);\r
1135     viewMenu.addSeparator();\r
1136     viewMenu.add(jMenu3);\r
1137     viewMenu.add(jMenu4);\r
1138     viewMenu.add(hiddenMarkers);\r
1139     viewMenu.addSeparator();\r
1140     viewMenu.add(wrapMenuItem);\r
1141     viewMenu.add(seqLimits);\r
1142     viewMenu.add(scaleAbove);\r
1143     viewMenu.add(scaleLeft);\r
1144     viewMenu.add(scaleRight);\r
1145     viewMenu.add(viewBoxesMenuItem);\r
1146     viewMenu.add(viewTextMenuItem);\r
1147     viewMenu.add(colourTextMenuItem);\r
1148     viewMenu.add(renderGapsMenuItem);\r
1149     viewMenu.add(annotationPanelMenuItem);\r
1150     viewMenu.addSeparator();\r
1151     viewMenu.add(showSeqFeatures);\r
1152     viewMenu.add(featureSettings);\r
1153     viewMenu.addSeparator();\r
1154     viewMenu.add(overviewMenuItem);\r
1155     colourMenu.add(applyToAllGroups);\r
1156     colourMenu.addSeparator();\r
1157     colourMenu.add(noColourmenuItem);\r
1158     colourMenu.add(clustalColour);\r
1159     colourMenu.add(BLOSUM62Colour);\r
1160     colourMenu.add(PIDColour);\r
1161     colourMenu.add(zappoColour);\r
1162     colourMenu.add(taylorColour);\r
1163     colourMenu.add(hydrophobicityColour);\r
1164     colourMenu.add(helixColour);\r
1165     colourMenu.add(strandColour);\r
1166     colourMenu.add(turnColour);\r
1167     colourMenu.add(buriedColour);\r
1168     colourMenu.add(nucleotideColour);\r
1169     colourMenu.add(userDefinedColour);\r
1170     colourMenu.addSeparator();\r
1171     colourMenu.add(conservationMenuItem);\r
1172     colourMenu.add(modifyConservation);\r
1173     colourMenu.add(abovePIDThreshold);\r
1174     colourMenu.add(modifyPID);\r
1175     colourMenu.add(annotationColour);\r
1176     calculateMenu.add(sort);\r
1177     calculateMenu.add(calculate);\r
1178     calculateMenu.addSeparator();\r
1179     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1180     calculateMenu.add(PCAMenuItem);\r
1181     calculateMenu.addSeparator();\r
1182     calculateMenu.add(showTranslation);\r
1183     calculateMenu.add(autoCalculate);\r
1184     webServiceNoServices=new JMenuItem("<No Services>");\r
1185     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1186     jMenu1.add(pasteThis);\r
1187     sort.add(sortIDMenuItem);\r
1188     sort.add(sortGroupMenuItem);\r
1189     sort.add(sortPairwiseMenuItem);\r
1190     calculate.add(averageDistanceTreeMenuItem);\r
1191     calculate.add(neighbourTreeMenuItem);\r
1192     calculate.add(avDistanceTreeBlosumMenuItem);\r
1193     calculate.add(njTreeBlosumMenuItem);\r
1194     jMenu2.add(htmlMenuItem);\r
1195     jMenu2.add(epsFile);\r
1196     jMenu2.add(createPNG);\r
1197     addSequenceMenu.add(addFromFile);\r
1198     addSequenceMenu.add(addFromText);\r
1199     addSequenceMenu.add(addFromURL);\r
1200     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1201     statusPanel.add(statusBar, null);\r
1202     jMenu3.add(showAllColumns);\r
1203     jMenu3.add(showAllSeqs);\r
1204     jMenu4.add(hideSelColumns);\r
1205     jMenu4.add(hideSelSequences);\r
1206   }\r
1207 \r
1208   protected void outputText_actionPerformed(ActionEvent e)\r
1209   {\r
1210   }\r
1211 \r
1212   public void addFromFile_actionPerformed(ActionEvent e)\r
1213   {\r
1214 \r
1215   }\r
1216 \r
1217   public void addFromText_actionPerformed(ActionEvent e)\r
1218   {\r
1219 \r
1220   }\r
1221 \r
1222   public void addFromURL_actionPerformed(ActionEvent e)\r
1223   {\r
1224 \r
1225   }\r
1226 \r
1227   public void exportFeatures_actionPerformed(ActionEvent e)\r
1228   {\r
1229 \r
1230   }\r
1231 \r
1232   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1233   {\r
1234 \r
1235   }\r
1236 \r
1237   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1238   {\r
1239   }\r
1240 \r
1241   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1242   {\r
1243   }\r
1244 \r
1245   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1246   {\r
1247   }\r
1248 \r
1249   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1250   {\r
1251   }\r
1252 \r
1253   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1254   {\r
1255   }\r
1256 \r
1257   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1258   {\r
1259   }\r
1260 \r
1261   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1262   {\r
1263   }\r
1264 \r
1265   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1266   {\r
1267   }\r
1268 \r
1269   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1270   {\r
1271   }\r
1272 \r
1273   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1274   {\r
1275   }\r
1276 \r
1277   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1278   {\r
1279   }\r
1280 \r
1281   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1282   {\r
1283   }\r
1284 \r
1285   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1286   {\r
1287   }\r
1288 \r
1289   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1290   {\r
1291   }\r
1292 \r
1293   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1294   {\r
1295   }\r
1296 \r
1297   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1298   {\r
1299   }\r
1300 \r
1301   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1302   {\r
1303   }\r
1304 \r
1305   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1306   {\r
1307   }\r
1308 \r
1309   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1310   {\r
1311   }\r
1312 \r
1313   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1314   {\r
1315   }\r
1316 \r
1317   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1318   {\r
1319   }\r
1320 \r
1321   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1322   {\r
1323   }\r
1324 \r
1325   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1326   {\r
1327   }\r
1328 \r
1329   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1330   {\r
1331   }\r
1332 \r
1333   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1334   {\r
1335   }\r
1336 \r
1337   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1338   {\r
1339   }\r
1340 \r
1341   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1342   {\r
1343   }\r
1344 \r
1345   protected void clustalColour_actionPerformed(ActionEvent e)\r
1346   {\r
1347   }\r
1348 \r
1349   protected void zappoColour_actionPerformed(ActionEvent e)\r
1350   {\r
1351   }\r
1352 \r
1353   protected void taylorColour_actionPerformed(ActionEvent e)\r
1354   {\r
1355   }\r
1356 \r
1357   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1358   {\r
1359   }\r
1360 \r
1361   protected void helixColour_actionPerformed(ActionEvent e)\r
1362   {\r
1363   }\r
1364 \r
1365   protected void strandColour_actionPerformed(ActionEvent e)\r
1366   {\r
1367   }\r
1368 \r
1369   protected void turnColour_actionPerformed(ActionEvent e)\r
1370   {\r
1371   }\r
1372 \r
1373   protected void buriedColour_actionPerformed(ActionEvent e)\r
1374   {\r
1375   }\r
1376 \r
1377   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1378   {\r
1379   }\r
1380 \r
1381   protected void PIDColour_actionPerformed(ActionEvent e)\r
1382   {\r
1383   }\r
1384 \r
1385   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1386   {\r
1387   }\r
1388 \r
1389   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1390   {\r
1391   }\r
1392 \r
1393   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1394   {\r
1395   }\r
1396 \r
1397   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1398   {\r
1399   }\r
1400 \r
1401   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1402   {\r
1403   }\r
1404 \r
1405   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1406   {\r
1407   }\r
1408 \r
1409   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1410   {\r
1411   }\r
1412 \r
1413   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1414   {\r
1415   }\r
1416 \r
1417   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1418   {\r
1419   }\r
1420 \r
1421   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1422   {\r
1423   }\r
1424 \r
1425   protected void copy_actionPerformed(ActionEvent e)\r
1426   {\r
1427   }\r
1428 \r
1429   protected void cut_actionPerformed(ActionEvent e)\r
1430   {\r
1431   }\r
1432 \r
1433   protected void delete_actionPerformed(ActionEvent e)\r
1434   {\r
1435   }\r
1436 \r
1437   protected void pasteNew_actionPerformed(ActionEvent e)\r
1438   {\r
1439   }\r
1440 \r
1441   protected void pasteThis_actionPerformed(ActionEvent e)\r
1442   {\r
1443   }\r
1444 \r
1445   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1446   {\r
1447   }\r
1448 \r
1449   public void createPNG(java.io.File f)\r
1450   {\r
1451   }\r
1452 \r
1453   protected void font_actionPerformed(ActionEvent e)\r
1454   {\r
1455   }\r
1456 \r
1457   protected void seqLimit_actionPerformed(ActionEvent e)\r
1458   {\r
1459   }\r
1460 \r
1461   public void seqDBRef_actionPerformed(ActionEvent e)\r
1462   {\r
1463 \r
1464   }\r
1465 \r
1466 \r
1467   public void createEPS(java.io.File f)\r
1468   {\r
1469   }\r
1470 \r
1471   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1472   {\r
1473   }\r
1474 \r
1475   protected void jpred_actionPerformed(ActionEvent e)\r
1476   {\r
1477   }\r
1478 \r
1479   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1480   {\r
1481   }\r
1482 \r
1483   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1484   {\r
1485   }\r
1486 \r
1487   protected void scaleRight_actionPerformed(ActionEvent e)\r
1488   {\r
1489   }\r
1490 \r
1491   protected void modifyPID_actionPerformed(ActionEvent e)\r
1492   {\r
1493   }\r
1494 \r
1495   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1496   {\r
1497   }\r
1498 \r
1499 \r
1500 \r
1501   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1502   {\r
1503   }\r
1504 \r
1505   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1506   {\r
1507   }\r
1508 \r
1509 \r
1510   public void vamsasStore_actionPerformed(ActionEvent e)\r
1511   {\r
1512 \r
1513   }\r
1514 \r
1515   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1516   {\r
1517 \r
1518   }\r
1519 \r
1520   public void showTranslation_actionPerformed(ActionEvent e)\r
1521   {\r
1522 \r
1523   }\r
1524 \r
1525   public void featureSettings_actionPerformed(ActionEvent e)\r
1526   {\r
1527 \r
1528   }\r
1529 \r
1530   public void fetchSequence_actionPerformed(ActionEvent e)\r
1531   {\r
1532 \r
1533   }\r
1534 \r
1535   public void smoothFont_actionPerformed(ActionEvent e)\r
1536   {\r
1537 \r
1538   }\r
1539 \r
1540   public void annotationColour_actionPerformed(ActionEvent e)\r
1541   {\r
1542 \r
1543   }\r
1544 \r
1545 \r
1546   public void associatedData_actionPerformed(ActionEvent e)\r
1547   {\r
1548 \r
1549   }\r
1550 \r
1551   public void autoCalculate_actionPerformed(ActionEvent e)\r
1552   {\r
1553 \r
1554   }\r
1555 \r
1556   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1557   {\r
1558 \r
1559   }\r
1560 \r
1561   public void showAllColumns_actionPerformed(ActionEvent e)\r
1562   {\r
1563 \r
1564   }\r
1565 \r
1566   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1567   {\r
1568 \r
1569   }\r
1570 \r
1571   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1572   {\r
1573 \r
1574   }\r
1575 \r
1576   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1577   {\r
1578 \r
1579   }\r
1580 \r
1581   public void findPdbId_actionPerformed(ActionEvent e)\r
1582   {\r
1583 \r
1584   }\r
1585 \r
1586   public void enterPdbId_actionPerformed(ActionEvent e)\r
1587   {\r
1588 \r
1589   }\r
1590 \r
1591   public void pdbFile_actionPerformed(ActionEvent e)\r
1592   {\r
1593 \r
1594   }\r
1595 \r
1596   public void invertColSel_actionPerformed(ActionEvent e)\r
1597   {\r
1598 \r
1599   }\r
1600 }\r