src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.jbgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 \r
  26 import jalview.schemes.*;\r
  27 import java.awt.BorderLayout;\r
  28 \r
  29 \r
  30 \r
  31 \r
  32 public class GAlignFrame\r
  33     extends JInternalFrame\r
  34 {\r
  35   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  36   protected JMenu fileMenu = new JMenu();\r
  37   protected JMenuItem closeMenuItem = new JMenuItem();\r
  38   protected JMenu editMenu = new JMenu();\r
  39   protected JMenu viewMenu = new JMenu();\r
  40   protected JMenu colourMenu = new JMenu();\r
  41   protected JMenu calculateMenu = new JMenu();\r
  42   protected JMenu webService = new JMenu();\r
  43   protected JMenuItem webServiceNoServices;\r
  44   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  45   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  46   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  47   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  48   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  49   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  50   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  51   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  52   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  53   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  54   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  55   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  56   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  57   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  58   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  59   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  60   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  61   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  62   BorderLayout borderLayout1 = new BorderLayout();\r
  63   public JLabel statusBar = new JLabel();\r
  64   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  65   protected JMenu outputTextboxMenu = new JMenu();\r
  66   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  70       JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  75   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  76   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  77   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  78   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  79   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  80   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  81   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  82   JMenuItem htmlMenuItem = new JMenuItem();\r
  83   JMenuItem overviewMenuItem = new JMenuItem();\r
  84   protected JMenuItem undoMenuItem = new JMenuItem();\r
  85   protected JMenuItem redoMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  87   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  88   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  89   JMenuItem printMenuItem = new JMenuItem();\r
  90   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  91   JMenuItem findMenuItem = new JMenuItem();\r
  92   JMenu searchMenu = new JMenu();\r
  93   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  94   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  95   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  96   JMenuItem deleteGroups = new JMenuItem();\r
  97   JMenuItem delete = new JMenuItem();\r
  98   JMenuItem copy = new JMenuItem();\r
  99   JMenuItem cut = new JMenuItem();\r
 100   JMenu jMenu1 = new JMenu();\r
 101   JMenuItem pasteNew = new JMenuItem();\r
 102   JMenuItem pasteThis = new JMenuItem();\r
 103   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 104   JMenuItem createPNG = new JMenuItem();\r
 105   protected JMenuItem font = new JMenuItem();\r
 106   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 107   JMenuItem epsFile = new JMenuItem();\r
 108   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 109   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 110   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 111   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 112   protected JMenuItem modifyPID = new JMenuItem();\r
 113   protected JMenuItem modifyConservation = new JMenuItem();\r
 114   protected JMenu sortByTreeMenu = new JMenu();\r
 115   protected JMenu sort = new JMenu();\r
 116   JMenu calculate = new JMenu();\r
 117   JMenu jMenu2 = new JMenu();\r
 118   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 119   protected ButtonGroup colours = new ButtonGroup();\r
 120   JMenuItem vamsasStore = new JMenuItem();\r
 121   protected JMenuItem showTranslation = new JMenuItem();\r
 122   public JMenuItem featureSettings = new JMenuItem();\r
 123   JMenuItem fetchSequence = new JMenuItem();\r
 124   protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
 125   JMenuItem annotationColour = new JMenuItem();\r
 126   JMenuItem associatedData = new JMenuItem();\r
 127   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 128   JMenu addSequenceMenu = new JMenu();\r
 129   JMenuItem addFromFile = new JMenuItem();\r
 130   JMenuItem addFromText = new JMenuItem();\r
 131   JMenuItem addFromURL = new JMenuItem();\r
 132   JMenuItem exportAnnotations = new JMenuItem();\r
 133   JMenuItem exportFeatures = new JMenuItem();\r
 134   protected JPanel statusPanel = new JPanel();\r
 135   GridLayout gridLayout1 = new GridLayout();\r
 136   JMenu jMenu3 = new JMenu();\r
 137   JMenuItem showAllSeqs = new JMenuItem();\r
 138   JMenuItem showAllColumns = new JMenuItem();\r
 139   JMenu hideMenu = new JMenu();\r
 140   JMenuItem hideSelSequences = new JMenuItem();\r
 141   JMenuItem hideSelColumns = new JMenuItem();\r
 142   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 143   JMenuItem invertColSel = new JMenuItem();\r
 144   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 145   public GAlignFrame()\r
 146   {\r
 147     try\r
 148     {\r
 149       jbInit();\r
 150       setJMenuBar(alignFrameMenuBar);\r
 151 \r
 152       // dynamically fill save as menu with available formats\r
 153       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 154       {\r
 155         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 156 \r
 157         item.addActionListener(new java.awt.event.ActionListener()\r
 158         {\r
 159           public void actionPerformed(ActionEvent e)\r
 160           {\r
 161             outputText_actionPerformed(e);\r
 162           }\r
 163         });\r
 164 \r
 165         outputTextboxMenu.add(item);\r
 166       }\r
 167     }\r
 168     catch (Exception e)\r
 169     {\r
 170     }\r
 171 \r
 172 \r
 173     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 174     {\r
 175       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 176           getUserColourSchemes().keys();\r
 177 \r
 178       while (userColours.hasMoreElements())\r
 179       {\r
 180         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 181             nextElement().toString());\r
 182         radioItem.setName("USER_DEFINED");\r
 183         radioItem.addMouseListener(new MouseAdapter()\r
 184             {\r
 185               public void mousePressed(MouseEvent evt)\r
 186               {\r
 187                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 188                 {\r
 189                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 190 \r
 191                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 192                       "Remove from default list?",\r
 193                       "Remove user defined colour",\r
 194                       JOptionPane.YES_NO_OPTION);\r
 195                   if(option == JOptionPane.YES_OPTION)\r
 196                   {\r
 197                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 198                     colourMenu.remove(radioItem);\r
 199                   }\r
 200                   else\r
 201                     radioItem.addActionListener(new ActionListener()\r
 202                     {\r
 203                       public void actionPerformed(ActionEvent evt)\r
 204                       {\r
 205                         userDefinedColour_actionPerformed(evt);\r
 206                       }\r
 207                     });\r
 208                 }\r
 209               }\r
 210             });\r
 211         radioItem.addActionListener(new ActionListener()\r
 212         {\r
 213           public void actionPerformed(ActionEvent evt)\r
 214           {\r
 215             userDefinedColour_actionPerformed(evt);\r
 216           }\r
 217         });\r
 218         colourMenu.insert(radioItem, 15);\r
 219         colours.add(radioItem);\r
 220       }\r
 221     }\r
 222     colours.add(noColourmenuItem);\r
 223     colours.add(clustalColour);\r
 224     colours.add(zappoColour);\r
 225     colours.add(taylorColour);\r
 226     colours.add(hydrophobicityColour);\r
 227     colours.add(helixColour);\r
 228     colours.add(strandColour);\r
 229     colours.add(turnColour);\r
 230     colours.add(buriedColour);\r
 231     colours.add(userDefinedColour);\r
 232     colours.add(PIDColour);\r
 233     colours.add(BLOSUM62Colour);\r
 234     colours.add(nucleotideColour);\r
 235 \r
 236     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 237 \r
 238 \r
 239   }\r
 240 \r
 241   public void setColourSelected(String defaultColour)\r
 242   {\r
 243 \r
 244     if (defaultColour != null)\r
 245     {\r
 246       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 247 \r
 248       switch (index)\r
 249       {\r
 250         case ColourSchemeProperty.NONE:\r
 251               noColourmenuItem.setSelected(true);\r
 252               break;\r
 253         case ColourSchemeProperty.CLUSTAL:\r
 254           clustalColour.setSelected(true);\r
 255 \r
 256           break;\r
 257 \r
 258         case ColourSchemeProperty.BLOSUM:\r
 259           BLOSUM62Colour.setSelected(true);\r
 260 \r
 261           break;\r
 262 \r
 263         case ColourSchemeProperty.PID:\r
 264           PIDColour.setSelected(true);\r
 265 \r
 266           break;\r
 267 \r
 268         case ColourSchemeProperty.ZAPPO:\r
 269           zappoColour.setSelected(true);\r
 270 \r
 271           break;\r
 272 \r
 273         case ColourSchemeProperty.TAYLOR:\r
 274           taylorColour.setSelected(true);\r
 275           break;\r
 276 \r
 277         case ColourSchemeProperty.HYDROPHOBIC:\r
 278           hydrophobicityColour.setSelected(true);\r
 279 \r
 280           break;\r
 281 \r
 282         case ColourSchemeProperty.HELIX:\r
 283           helixColour.setSelected(true);\r
 284 \r
 285           break;\r
 286 \r
 287         case ColourSchemeProperty.STRAND:\r
 288           strandColour.setSelected(true);\r
 289 \r
 290           break;\r
 291 \r
 292         case ColourSchemeProperty.TURN:\r
 293           turnColour.setSelected(true);\r
 294 \r
 295           break;\r
 296 \r
 297         case ColourSchemeProperty.BURIED:\r
 298           buriedColour.setSelected(true);\r
 299 \r
 300           break;\r
 301 \r
 302         case ColourSchemeProperty.NUCLEOTIDE:\r
 303           nucleotideColour.setSelected(true);\r
 304 \r
 305           break;\r
 306 \r
 307         case ColourSchemeProperty.USER_DEFINED:\r
 308           userDefinedColour.setSelected(true);\r
 309 \r
 310           break;\r
 311       }\r
 312     }\r
 313 \r
 314   }\r
 315 \r
 316   private void jbInit()\r
 317       throws Exception\r
 318   {\r
 319     fileMenu.setMnemonic('F');\r
 320     fileMenu.setText("File");\r
 321     saveAlignmentMenu.setMnemonic('L');\r
 322     saveAlignmentMenu.setText("Save As");\r
 323     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 324         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 325     saveAlignmentMenu.addActionListener(new ActionListener()\r
 326     {\r
 327       public void actionPerformed(ActionEvent e)\r
 328       {\r
 329         saveAlignmentMenu_actionPerformed(e);\r
 330       }\r
 331     });\r
 332     closeMenuItem.setMnemonic('C');\r
 333     closeMenuItem.setText("Close");\r
 334     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 335     {\r
 336       public void actionPerformed(ActionEvent e)\r
 337       {\r
 338         closeMenuItem_actionPerformed(e);\r
 339       }\r
 340     });\r
 341     editMenu.setText("Edit");\r
 342     viewMenu.setText("View");\r
 343     colourMenu.setText("Colour");\r
 344     calculateMenu.setText("Calculate");\r
 345     webService.setText("Web Service");\r
 346     selectAllSequenceMenuItem.setText("Select all");\r
 347     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 348         java.awt.event.KeyEvent.VK_A,\r
 349         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 350     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 351                                                 ActionListener()\r
 352     {\r
 353       public void actionPerformed(ActionEvent e)\r
 354       {\r
 355         selectAllSequenceMenuItem_actionPerformed(e);\r
 356       }\r
 357     });\r
 358     deselectAllSequenceMenuItem.setText("Deselect All");\r
 359     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 360                                                getKeyStroke(\r
 361         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 362     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 363                                                   ActionListener()\r
 364     {\r
 365       public void actionPerformed(ActionEvent e)\r
 366       {\r
 367         deselectAllSequenceMenuItem_actionPerformed(e);\r
 368       }\r
 369     });\r
 370     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 371     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 372         java.awt.event.KeyEvent.VK_I,\r
 373         java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 374     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 375     {\r
 376       public void actionPerformed(ActionEvent e)\r
 377       {\r
 378         invertSequenceMenuItem_actionPerformed(e);\r
 379       }\r
 380     });\r
 381     remove2LeftMenuItem.setText("Remove Left");\r
 382     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 383         awt.event.KeyEvent.VK_L, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 384     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 385     {\r
 386       public void actionPerformed(ActionEvent e)\r
 387       {\r
 388         remove2LeftMenuItem_actionPerformed(e);\r
 389       }\r
 390     });\r
 391     remove2RightMenuItem.setText("Remove Right");\r
 392     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 393         awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 394     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 395     {\r
 396       public void actionPerformed(ActionEvent e)\r
 397       {\r
 398         remove2RightMenuItem_actionPerformed(e);\r
 399       }\r
 400     });\r
 401     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 402     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 403                                               getKeyStroke(java.awt.event.\r
 404         KeyEvent.VK_E, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 405     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 406                                                  ActionListener()\r
 407     {\r
 408       public void actionPerformed(ActionEvent e)\r
 409       {\r
 410         removeGappedColumnMenuItem_actionPerformed(e);\r
 411       }\r
 412     });\r
 413     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 414     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 415         java.awt.event.KeyEvent.VK_G, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 416     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 417     {\r
 418       public void actionPerformed(ActionEvent e)\r
 419       {\r
 420         removeAllGapsMenuItem_actionPerformed(e);\r
 421       }\r
 422     });\r
 423     viewBoxesMenuItem.setText("Boxes");\r
 424     viewBoxesMenuItem.setState(true);\r
 425     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 426     {\r
 427       public void actionPerformed(ActionEvent e)\r
 428       {\r
 429         viewBoxesMenuItem_actionPerformed(e);\r
 430       }\r
 431     });\r
 432     viewTextMenuItem.setText("Text");\r
 433     viewTextMenuItem.setState(true);\r
 434     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 435     {\r
 436       public void actionPerformed(ActionEvent e)\r
 437       {\r
 438         viewTextMenuItem_actionPerformed(e);\r
 439       }\r
 440     });\r
 441     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 442     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 443     {\r
 444       public void actionPerformed(ActionEvent e)\r
 445       {\r
 446         sortPairwiseMenuItem_actionPerformed(e);\r
 447       }\r
 448     });\r
 449     sortIDMenuItem.setText("by ID");\r
 450     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 451     {\r
 452       public void actionPerformed(ActionEvent e)\r
 453       {\r
 454         sortIDMenuItem_actionPerformed(e);\r
 455       }\r
 456     });\r
 457     sortGroupMenuItem.setText("by Group");\r
 458     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         sortGroupMenuItem_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 466     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 467         java.awt.event.KeyEvent.VK_R, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 468     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 469                                                ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         removeRedundancyMenuItem_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 477     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 478                                                 ActionListener()\r
 479     {\r
 480       public void actionPerformed(ActionEvent e)\r
 481       {\r
 482         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 483       }\r
 484     });\r
 485     PCAMenuItem.setText("Principal Component Analysis");\r
 486     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 487     {\r
 488       public void actionPerformed(ActionEvent e)\r
 489       {\r
 490         PCAMenuItem_actionPerformed(e);\r
 491       }\r
 492     });\r
 493     averageDistanceTreeMenuItem.setText(\r
 494         "Average Distance Using % Identity");\r
 495     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 496                                                   ActionListener()\r
 497     {\r
 498       public void actionPerformed(ActionEvent e)\r
 499       {\r
 500         averageDistanceTreeMenuItem_actionPerformed(e);\r
 501       }\r
 502     });\r
 503     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 504     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 505     {\r
 506       public void actionPerformed(ActionEvent e)\r
 507       {\r
 508         neighbourTreeMenuItem_actionPerformed(e);\r
 509       }\r
 510     });\r
 511     this.getContentPane().setLayout(borderLayout1);\r
 512     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 513     statusBar.setBackground(Color.white);\r
 514     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 515     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 516     statusBar.setText("Status bar");\r
 517     outputTextboxMenu.setMnemonic('T');\r
 518     outputTextboxMenu.setText("Output to Textbox");\r
 519     clustalColour.setText("Clustalx");\r
 520 \r
 521     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 522     {\r
 523       public void actionPerformed(ActionEvent e)\r
 524       {\r
 525         clustalColour_actionPerformed(e);\r
 526       }\r
 527     });\r
 528     zappoColour.setText("Zappo");\r
 529     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 530     {\r
 531       public void actionPerformed(ActionEvent e)\r
 532       {\r
 533         zappoColour_actionPerformed(e);\r
 534       }\r
 535     });\r
 536     taylorColour.setText("Taylor");\r
 537     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 538     {\r
 539       public void actionPerformed(ActionEvent e)\r
 540       {\r
 541         taylorColour_actionPerformed(e);\r
 542       }\r
 543     });\r
 544     hydrophobicityColour.setText("Hydrophobicity");\r
 545     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 546     {\r
 547       public void actionPerformed(ActionEvent e)\r
 548       {\r
 549         hydrophobicityColour_actionPerformed(e);\r
 550       }\r
 551     });\r
 552     helixColour.setText("Helix Propensity");\r
 553     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 554     {\r
 555       public void actionPerformed(ActionEvent e)\r
 556       {\r
 557         helixColour_actionPerformed(e);\r
 558       }\r
 559     });\r
 560     strandColour.setText("Strand Propensity");\r
 561     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 562     {\r
 563       public void actionPerformed(ActionEvent e)\r
 564       {\r
 565         strandColour_actionPerformed(e);\r
 566       }\r
 567     });\r
 568     turnColour.setText("Turn Propensity");\r
 569     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 570     {\r
 571       public void actionPerformed(ActionEvent e)\r
 572       {\r
 573         turnColour_actionPerformed(e);\r
 574       }\r
 575     });\r
 576     buriedColour.setText("Buried Index");\r
 577     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 578     {\r
 579       public void actionPerformed(ActionEvent e)\r
 580       {\r
 581         buriedColour_actionPerformed(e);\r
 582       }\r
 583     });\r
 584     userDefinedColour.setText("User Defined...");\r
 585     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 586     {\r
 587       public void actionPerformed(ActionEvent e)\r
 588       {\r
 589         userDefinedColour_actionPerformed(e);\r
 590       }\r
 591     });\r
 592     PIDColour.setText("Percentage Identity");\r
 593     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 594     {\r
 595       public void actionPerformed(ActionEvent e)\r
 596       {\r
 597         PIDColour_actionPerformed(e);\r
 598       }\r
 599     });\r
 600     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 601     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 602     {\r
 603       public void actionPerformed(ActionEvent e)\r
 604       {\r
 605         BLOSUM62Colour_actionPerformed(e);\r
 606       }\r
 607     });\r
 608     avDistanceTreeBlosumMenuItem.setText(\r
 609         "Average Distance Using BLOSUM62");\r
 610     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 611         ActionListener()\r
 612     {\r
 613       public void actionPerformed(ActionEvent e)\r
 614       {\r
 615         avTreeBlosumMenuItem_actionPerformed(e);\r
 616       }\r
 617     });\r
 618     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 619     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 620     {\r
 621       public void actionPerformed(ActionEvent e)\r
 622       {\r
 623         njTreeBlosumMenuItem_actionPerformed(e);\r
 624       }\r
 625     });\r
 626     annotationPanelMenuItem.setActionCommand("");\r
 627     annotationPanelMenuItem.setText("Show Annotations");\r
 628     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 629     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 630     {\r
 631       public void actionPerformed(ActionEvent e)\r
 632       {\r
 633         annotationPanelMenuItem_actionPerformed(e);\r
 634       }\r
 635     });\r
 636     colourTextMenuItem.setText("Colour Text");\r
 637     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 638     {\r
 639       public void actionPerformed(ActionEvent e)\r
 640       {\r
 641         colourTextMenuItem_actionPerformed(e);\r
 642       }\r
 643     });\r
 644     htmlMenuItem.setText("HTML");\r
 645     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 646     {\r
 647       public void actionPerformed(ActionEvent e)\r
 648       {\r
 649         htmlMenuItem_actionPerformed(e);\r
 650       }\r
 651     });\r
 652     overviewMenuItem.setText("Overview Window");\r
 653     overviewMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 654         event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 655     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 656     {\r
 657       public void actionPerformed(ActionEvent e)\r
 658       {\r
 659         overviewMenuItem_actionPerformed(e);\r
 660       }\r
 661     });\r
 662     undoMenuItem.setEnabled(false);\r
 663     undoMenuItem.setMnemonic('Z');\r
 664     undoMenuItem.setText("Undo");\r
 665     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 666         java.awt.event.KeyEvent.VK_Z,\r
 667         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 668     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 669     {\r
 670       public void actionPerformed(ActionEvent e)\r
 671       {\r
 672         undoMenuItem_actionPerformed(e);\r
 673       }\r
 674     });\r
 675     redoMenuItem.setEnabled(false);\r
 676     redoMenuItem.setMnemonic('0');\r
 677     redoMenuItem.setText("Redo");\r
 678     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 679         event.KeyEvent.VK_Y, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 680     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 681     {\r
 682       public void actionPerformed(ActionEvent e)\r
 683       {\r
 684         redoMenuItem_actionPerformed(e);\r
 685       }\r
 686     });\r
 687     conservationMenuItem.setText("By Conservation");\r
 688     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 689     {\r
 690       public void actionPerformed(ActionEvent e)\r
 691       {\r
 692         conservationMenuItem_actionPerformed(e);\r
 693       }\r
 694     });\r
 695     noColourmenuItem.setText("None");\r
 696     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 697     {\r
 698       public void actionPerformed(ActionEvent e)\r
 699       {\r
 700         noColourmenuItem_actionPerformed(e);\r
 701       }\r
 702     });\r
 703     wrapMenuItem.setText("Wrap");\r
 704     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 705     {\r
 706       public void actionPerformed(ActionEvent e)\r
 707       {\r
 708         wrapMenuItem_actionPerformed(e);\r
 709       }\r
 710     });\r
 711     printMenuItem.setText("Print");\r
 712     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 713     {\r
 714       public void actionPerformed(ActionEvent e)\r
 715       {\r
 716         printMenuItem_actionPerformed(e);\r
 717       }\r
 718     });\r
 719     renderGapsMenuItem.setText("Show Gaps");\r
 720     renderGapsMenuItem.setState(true);\r
 721     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 722     {\r
 723       public void actionPerformed(ActionEvent e)\r
 724       {\r
 725         renderGapsMenuItem_actionPerformed(e);\r
 726       }\r
 727     });\r
 728     findMenuItem.setText("Find...");\r
 729     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 730         java.awt.event.KeyEvent.VK_F,\r
 731         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 732     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 733     {\r
 734       public void actionPerformed(ActionEvent e)\r
 735       {\r
 736         findMenuItem_actionPerformed(e);\r
 737       }\r
 738     });\r
 739     searchMenu.setText("Search");\r
 740 \r
 741     abovePIDThreshold.setText("Above Identity Threshold");\r
 742     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 743     {\r
 744       public void actionPerformed(ActionEvent e)\r
 745       {\r
 746         abovePIDThreshold_actionPerformed(e);\r
 747       }\r
 748     });\r
 749     showSeqFeatures.setText("Show Sequence Features");\r
 750     showSeqFeatures.addActionListener(new ActionListener()\r
 751     {\r
 752       public void actionPerformed(ActionEvent actionEvent)\r
 753       {\r
 754         showSeqFeatures_actionPerformed(actionEvent);\r
 755       }\r
 756     });\r
 757     nucleotideColour.setText("Nucleotide");\r
 758     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 759     {\r
 760       public void actionPerformed(ActionEvent e)\r
 761       {\r
 762         nucleotideColour_actionPerformed(e);\r
 763       }\r
 764     });\r
 765     deleteGroups.setText("Undefine groups");\r
 766     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 767         event.KeyEvent.VK_U, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 768     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 769     {\r
 770       public void actionPerformed(ActionEvent e)\r
 771       {\r
 772         deleteGroups_actionPerformed(e);\r
 773       }\r
 774     });\r
 775     copy.setText("Copy");\r
 776     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 777         java.awt.event.KeyEvent.VK_C,\r
 778         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 779     copy.setMnemonic(KeyEvent.VK_C);\r
 780 \r
 781     copy.addActionListener(new java.awt.event.ActionListener()\r
 782     {\r
 783       public void actionPerformed(ActionEvent e)\r
 784       {\r
 785         copy_actionPerformed(e);\r
 786       }\r
 787     });\r
 788     cut.setText("Cut");\r
 789     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 790         java.awt.event.KeyEvent.VK_X,\r
 791         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 792     cut.setMnemonic(KeyEvent.VK_X);\r
 793     cut.addActionListener(new java.awt.event.ActionListener()\r
 794     {\r
 795       public void actionPerformed(ActionEvent e)\r
 796       {\r
 797         cut_actionPerformed(e);\r
 798       }\r
 799     });\r
 800     delete.setText("Delete");\r
 801     delete.addActionListener(new java.awt.event.ActionListener()\r
 802     {\r
 803       public void actionPerformed(ActionEvent e)\r
 804       {\r
 805         delete_actionPerformed(e);\r
 806       }\r
 807     });\r
 808     jMenu1.setMnemonic('V');\r
 809     jMenu1.setText("Paste");\r
 810     pasteNew.setText("To New Alignment");\r
 811     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 812         java.awt.event.KeyEvent.VK_V,\r
 813         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 814     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 815     {\r
 816       public void actionPerformed(ActionEvent e)\r
 817       {\r
 818         pasteNew_actionPerformed(e);\r
 819       }\r
 820     });\r
 821     pasteThis.setText("Add To This Alignment");\r
 822     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 823     {\r
 824       public void actionPerformed(ActionEvent e)\r
 825       {\r
 826         pasteThis_actionPerformed(e);\r
 827       }\r
 828     });\r
 829     applyToAllGroups.setText("Apply Colour To All Groups");\r
 830     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 831     {\r
 832       public void actionPerformed(ActionEvent e)\r
 833       {\r
 834         applyToAllGroups_actionPerformed(e);\r
 835       }\r
 836     });\r
 837     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 838     {\r
 839       public void actionPerformed(ActionEvent e)\r
 840       {\r
 841         createPNG(null);\r
 842       }\r
 843     });\r
 844     createPNG.setActionCommand("Save As PNG Image");\r
 845     createPNG.setText("PNG");\r
 846     font.setText("Font...");\r
 847     font.addActionListener(new java.awt.event.ActionListener()\r
 848     {\r
 849       public void actionPerformed(ActionEvent e)\r
 850       {\r
 851         font_actionPerformed(e);\r
 852       }\r
 853     });\r
 854 \r
 855     seqLimits.setText("Show Sequence Limits");\r
 856     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 857     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 858     {\r
 859       public void actionPerformed(ActionEvent e)\r
 860       {\r
 861         seqLimit_actionPerformed(e);\r
 862       }\r
 863     });\r
 864     epsFile.setText("EPS");\r
 865     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 866     {\r
 867       public void actionPerformed(ActionEvent e)\r
 868       {\r
 869         createEPS(null);\r
 870       }\r
 871     });\r
 872     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 873     LoadtreeMenuItem.setText("Load Associated Tree");\r
 874     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 875     {\r
 876       public void actionPerformed(ActionEvent e)\r
 877       {\r
 878         LoadtreeMenuItem_actionPerformed(e);\r
 879       }\r
 880     });\r
 881     scaleAbove.setVisible(false);\r
 882     scaleAbove.setText("Scale Above");\r
 883     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 884     {\r
 885       public void actionPerformed(ActionEvent e)\r
 886       {\r
 887         scaleAbove_actionPerformed(e);\r
 888       }\r
 889     });\r
 890     scaleLeft.setVisible(false);\r
 891     scaleLeft.setSelected(true);\r
 892     scaleLeft.setText("Scale Left");\r
 893     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 894     {\r
 895       public void actionPerformed(ActionEvent e)\r
 896       {\r
 897         scaleLeft_actionPerformed(e);\r
 898       }\r
 899     });\r
 900     scaleRight.setVisible(false);\r
 901     scaleRight.setSelected(true);\r
 902     scaleRight.setText("Scale Right");\r
 903     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 904     {\r
 905       public void actionPerformed(ActionEvent e)\r
 906       {\r
 907         scaleRight_actionPerformed(e);\r
 908       }\r
 909     });\r
 910     modifyPID.setText("Modify Identity Threshold...");\r
 911     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 912     {\r
 913       public void actionPerformed(ActionEvent e)\r
 914       {\r
 915         modifyPID_actionPerformed(e);\r
 916       }\r
 917     });\r
 918     modifyConservation.setText("Modify Conservation Threshold...");\r
 919     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 920     {\r
 921       public void actionPerformed(ActionEvent e)\r
 922       {\r
 923         modifyConservation_actionPerformed(e);\r
 924       }\r
 925     });\r
 926     sortByTreeMenu.setText("By Tree Order");\r
 927     sort.setText("Sort");\r
 928     calculate.setText("Calculate Tree");\r
 929 \r
 930     jMenu2.setText("Export");\r
 931     padGapsMenuitem.setText("Pad Gaps");\r
 932     padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 933         event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 934     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 935     padGapsMenuitem.addActionListener(new ActionListener()\r
 936     {\r
 937       public void actionPerformed(ActionEvent e)\r
 938       {\r
 939         padGapsMenuitem_actionPerformed(e);\r
 940       }\r
 941     });\r
 942     vamsasStore.setVisible(false);\r
 943     vamsasStore.setText("VAMSAS store");\r
 944     vamsasStore.addActionListener(new ActionListener()\r
 945     {\r
 946       public void actionPerformed(ActionEvent e)\r
 947       {\r
 948         vamsasStore_actionPerformed(e);\r
 949       }\r
 950     });\r
 951     showTranslation.setText("Translate cDNA");\r
 952     showTranslation.addActionListener(new ActionListener()\r
 953     {\r
 954       public void actionPerformed(ActionEvent e)\r
 955       {\r
 956         showTranslation_actionPerformed(e);\r
 957       }\r
 958     });\r
 959 \r
 960 \r
 961     featureSettings.setText("Feature Settings...");\r
 962     featureSettings.addActionListener(new ActionListener()\r
 963     {\r
 964       public void actionPerformed(ActionEvent e)\r
 965       {\r
 966         featureSettings_actionPerformed(e);\r
 967       }\r
 968     });\r
 969     fetchSequence.setText("Fetch Sequence(s)...");\r
 970     fetchSequence.addActionListener(new ActionListener()\r
 971     {\r
 972       public void actionPerformed(ActionEvent e)\r
 973       {\r
 974         fetchSequence_actionPerformed(e);\r
 975       }\r
 976     });\r
 977     smoothFont.setText("Smooth Fonts");\r
 978     smoothFont.addActionListener(new ActionListener()\r
 979     {\r
 980       public void actionPerformed(ActionEvent e)\r
 981       {\r
 982         smoothFont_actionPerformed(e);\r
 983       }\r
 984     });\r
 985 \r
 986     annotationColour.setText("By Annotation...");\r
 987     annotationColour.addActionListener(new ActionListener()\r
 988     {\r
 989       public void actionPerformed(ActionEvent e)\r
 990       {\r
 991         annotationColour_actionPerformed(e);\r
 992       }\r
 993     });\r
 994     associatedData.setText("Load Features / Annotations");\r
 995     associatedData.addActionListener(new ActionListener()\r
 996     {\r
 997       public void actionPerformed(ActionEvent e)\r
 998       {\r
 999         associatedData_actionPerformed(e);\r
1000       }\r
1001     });\r
1002     autoCalculate.setText("Autocalculate Consensus");\r
1003     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1004     autoCalculate.addActionListener(new ActionListener()\r
1005     {\r
1006       public void actionPerformed(ActionEvent e)\r
1007       {\r
1008         autoCalculate_actionPerformed(e);\r
1009       }\r
1010     });\r
1011     addSequenceMenu.setText("Add Sequences");\r
1012     addFromFile.setText("From File");\r
1013     addFromFile.addActionListener(new ActionListener()\r
1014     {\r
1015       public void actionPerformed(ActionEvent e)\r
1016       {\r
1017         addFromFile_actionPerformed(e);\r
1018       }\r
1019     });\r
1020     addFromText.setText("From Textbox");\r
1021     addFromText.addActionListener(new ActionListener()\r
1022     {\r
1023       public void actionPerformed(ActionEvent e)\r
1024       {\r
1025         addFromText_actionPerformed(e);\r
1026       }\r
1027     });\r
1028     addFromURL.setText("From URL");\r
1029     addFromURL.addActionListener(new ActionListener()\r
1030     {\r
1031       public void actionPerformed(ActionEvent e)\r
1032       {\r
1033         addFromURL_actionPerformed(e);\r
1034       }\r
1035     });\r
1036     exportFeatures.setText("Export Features...");\r
1037     exportFeatures.addActionListener(new ActionListener()\r
1038     {\r
1039       public void actionPerformed(ActionEvent e)\r
1040       {\r
1041         exportFeatures_actionPerformed(e);\r
1042       }\r
1043     });\r
1044     exportAnnotations.setText("Export Annotations...");\r
1045     exportAnnotations.addActionListener(new ActionListener()\r
1046     {\r
1047       public void actionPerformed(ActionEvent e)\r
1048       {\r
1049         exportAnnotations_actionPerformed(e);\r
1050       }\r
1051     });\r
1052     statusPanel.setLayout(gridLayout1);\r
1053     jMenu3.setText("Show");\r
1054     showAllSeqs.setText("All Sequences");\r
1055     showAllSeqs.addActionListener(new ActionListener()\r
1056     {\r
1057       public void actionPerformed(ActionEvent e)\r
1058       {\r
1059         showAllSeqs_actionPerformed(e);\r
1060       }\r
1061     });\r
1062     showAllColumns.setText("All Columns");\r
1063     showAllColumns.addActionListener(new ActionListener()\r
1064     {\r
1065       public void actionPerformed(ActionEvent e)\r
1066       {\r
1067         showAllColumns_actionPerformed(e);\r
1068       }\r
1069     });\r
1070     hideMenu.setText("Hide");\r
1071     hideSelSequences.setText("Selected Sequences");\r
1072     hideSelSequences.addActionListener(new ActionListener()\r
1073     {\r
1074       public void actionPerformed(ActionEvent e)\r
1075       {\r
1076         hideSelSequences_actionPerformed(e);\r
1077       }\r
1078     });\r
1079     hideSelColumns.setText("Selected Columns");\r
1080     hideSelColumns.addActionListener(new ActionListener()\r
1081     {\r
1082       public void actionPerformed(ActionEvent e)\r
1083       {\r
1084         hideSelColumns_actionPerformed(e);\r
1085       }\r
1086     });\r
1087     hiddenMarkers.setText("Hidden Markers");\r
1088     hiddenMarkers.addActionListener(new ActionListener()\r
1089     {\r
1090       public void actionPerformed(ActionEvent e)\r
1091       {\r
1092         hiddenMarkers_actionPerformed(e);\r
1093       }\r
1094     });\r
1095     invertColSel.setText("Invert Column Selection");\r
1096     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1097         event.KeyEvent.VK_I, java.awt.event.KeyEvent.CTRL_MASK, false));\r
1098     invertColSel.addActionListener(new ActionListener()\r
1099     {\r
1100       public void actionPerformed(ActionEvent e)\r
1101       {\r
1102         invertColSel_actionPerformed(e);\r
1103       }\r
1104     });\r
1105     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1106     {\r
1107         public void stateChanged(ChangeEvent evt)\r
1108         {\r
1109             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1110             int sel = pane.getSelectedIndex();\r
1111             tabSelectionChanged(sel);\r
1112         }\r
1113     });\r
1114     tabbedPane.addMouseListener(new MouseAdapter()\r
1115     {\r
1116       public void mousePressed(MouseEvent e)\r
1117       {\r
1118         tabbedPane_mousePressed(e);\r
1119       }\r
1120     });\r
1121     tabbedPane.addFocusListener(new FocusAdapter()\r
1122     {\r
1123       public void focusGained(FocusEvent e)\r
1124       {\r
1125         tabbedPane_focusGained(e);\r
1126       }\r
1127     });\r
1128 \r
1129     alignFrameMenuBar.add(fileMenu);\r
1130     alignFrameMenuBar.add(editMenu);\r
1131     alignFrameMenuBar.add(searchMenu);\r
1132     alignFrameMenuBar.add(viewMenu);\r
1133     alignFrameMenuBar.add(colourMenu);\r
1134     alignFrameMenuBar.add(calculateMenu);\r
1135     alignFrameMenuBar.add(webService);\r
1136     fileMenu.add(addSequenceMenu);\r
1137     fileMenu.add(fetchSequence);\r
1138     fileMenu.addSeparator();\r
1139     fileMenu.add(vamsasStore);\r
1140     fileMenu.add(saveAlignmentMenu);\r
1141     fileMenu.add(jMenu2);\r
1142     fileMenu.add(outputTextboxMenu);\r
1143     fileMenu.add(printMenuItem);\r
1144     fileMenu.addSeparator();\r
1145     fileMenu.add(exportFeatures);\r
1146     fileMenu.add(exportAnnotations);\r
1147     fileMenu.add(LoadtreeMenuItem);\r
1148     fileMenu.add(associatedData);\r
1149     fileMenu.addSeparator();\r
1150     fileMenu.add(closeMenuItem);\r
1151     editMenu.add(undoMenuItem);\r
1152     editMenu.add(redoMenuItem);\r
1153     editMenu.add(cut);\r
1154     editMenu.add(copy);\r
1155     editMenu.add(jMenu1);\r
1156     editMenu.add(delete);\r
1157     editMenu.addSeparator();\r
1158     editMenu.add(selectAllSequenceMenuItem);\r
1159     editMenu.add(deselectAllSequenceMenuItem);\r
1160     editMenu.add(invertSequenceMenuItem);\r
1161     editMenu.add(invertColSel);\r
1162     editMenu.add(deleteGroups);\r
1163     editMenu.addSeparator();\r
1164     editMenu.add(remove2LeftMenuItem);\r
1165     editMenu.add(remove2RightMenuItem);\r
1166     editMenu.add(removeGappedColumnMenuItem);\r
1167     editMenu.add(removeAllGapsMenuItem);\r
1168     editMenu.add(removeRedundancyMenuItem);\r
1169     editMenu.addSeparator();\r
1170     editMenu.add(padGapsMenuitem);\r
1171     searchMenu.add(findMenuItem);\r
1172     viewMenu.add(font);\r
1173     viewMenu.add(smoothFont);\r
1174     viewMenu.addSeparator();\r
1175     viewMenu.add(jMenu3);\r
1176     viewMenu.add(hideMenu);\r
1177     viewMenu.add(hiddenMarkers);\r
1178     viewMenu.addSeparator();\r
1179     viewMenu.add(wrapMenuItem);\r
1180     viewMenu.add(seqLimits);\r
1181     viewMenu.add(scaleAbove);\r
1182     viewMenu.add(scaleLeft);\r
1183     viewMenu.add(scaleRight);\r
1184     viewMenu.add(viewBoxesMenuItem);\r
1185     viewMenu.add(viewTextMenuItem);\r
1186     viewMenu.add(colourTextMenuItem);\r
1187     viewMenu.add(renderGapsMenuItem);\r
1188     viewMenu.add(annotationPanelMenuItem);\r
1189     viewMenu.addSeparator();\r
1190     viewMenu.add(showSeqFeatures);\r
1191     viewMenu.add(featureSettings);\r
1192     viewMenu.addSeparator();\r
1193     viewMenu.add(overviewMenuItem);\r
1194     colourMenu.add(applyToAllGroups);\r
1195     colourMenu.addSeparator();\r
1196     colourMenu.add(noColourmenuItem);\r
1197     colourMenu.add(clustalColour);\r
1198     colourMenu.add(BLOSUM62Colour);\r
1199     colourMenu.add(PIDColour);\r
1200     colourMenu.add(zappoColour);\r
1201     colourMenu.add(taylorColour);\r
1202     colourMenu.add(hydrophobicityColour);\r
1203     colourMenu.add(helixColour);\r
1204     colourMenu.add(strandColour);\r
1205     colourMenu.add(turnColour);\r
1206     colourMenu.add(buriedColour);\r
1207     colourMenu.add(nucleotideColour);\r
1208     colourMenu.add(userDefinedColour);\r
1209     colourMenu.addSeparator();\r
1210     colourMenu.add(conservationMenuItem);\r
1211     colourMenu.add(modifyConservation);\r
1212     colourMenu.add(abovePIDThreshold);\r
1213     colourMenu.add(modifyPID);\r
1214     colourMenu.add(annotationColour);\r
1215     calculateMenu.add(sort);\r
1216     calculateMenu.add(calculate);\r
1217     calculateMenu.addSeparator();\r
1218     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1219     calculateMenu.add(PCAMenuItem);\r
1220     calculateMenu.addSeparator();\r
1221     calculateMenu.add(showTranslation);\r
1222     calculateMenu.add(autoCalculate);\r
1223     webServiceNoServices=new JMenuItem("<No Services>");\r
1224     webService.add(webServiceNoServices);jMenu1.add(pasteNew);\r
1225     jMenu1.add(pasteThis);\r
1226     sort.add(sortIDMenuItem);\r
1227     sort.add(sortGroupMenuItem);\r
1228     sort.add(sortPairwiseMenuItem);\r
1229     calculate.add(averageDistanceTreeMenuItem);\r
1230     calculate.add(neighbourTreeMenuItem);\r
1231     calculate.add(avDistanceTreeBlosumMenuItem);\r
1232     calculate.add(njTreeBlosumMenuItem);\r
1233     jMenu2.add(htmlMenuItem);\r
1234     jMenu2.add(epsFile);\r
1235     jMenu2.add(createPNG);\r
1236     addSequenceMenu.add(addFromFile);\r
1237     addSequenceMenu.add(addFromText);\r
1238     addSequenceMenu.add(addFromURL);\r
1239     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1240     statusPanel.add(statusBar, null);\r
1241     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1242     jMenu3.add(showAllColumns);\r
1243     jMenu3.add(showAllSeqs);\r
1244     hideMenu.add(hideSelColumns);\r
1245     hideMenu.add(hideSelSequences);\r
1246   }\r
1247 \r
1248   protected void outputText_actionPerformed(ActionEvent e)\r
1249   {\r
1250   }\r
1251 \r
1252   public void addFromFile_actionPerformed(ActionEvent e)\r
1253   {\r
1254 \r
1255   }\r
1256 \r
1257   public void addFromText_actionPerformed(ActionEvent e)\r
1258   {\r
1259 \r
1260   }\r
1261 \r
1262   public void addFromURL_actionPerformed(ActionEvent e)\r
1263   {\r
1264 \r
1265   }\r
1266 \r
1267   public void exportFeatures_actionPerformed(ActionEvent e)\r
1268   {\r
1269 \r
1270   }\r
1271 \r
1272   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1273   {\r
1274 \r
1275   }\r
1276 \r
1277   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1278   {\r
1279   }\r
1280 \r
1281   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
1282   {\r
1283   }\r
1284 \r
1285   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1286   {\r
1287   }\r
1288 \r
1289   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1290   {\r
1291   }\r
1292 \r
1293   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1294   {\r
1295   }\r
1296 \r
1297   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1298   {\r
1299   }\r
1300 \r
1301   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1302   {\r
1303   }\r
1304 \r
1305   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1306   {\r
1307   }\r
1308 \r
1309   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1310   {\r
1311   }\r
1312 \r
1313   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1314   {\r
1315   }\r
1316 \r
1317   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1318   {\r
1319   }\r
1320 \r
1321   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1322   {\r
1323   }\r
1324 \r
1325   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1326   {\r
1327   }\r
1328 \r
1329   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1330   {\r
1331   }\r
1332 \r
1333   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1334   {\r
1335   }\r
1336 \r
1337   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1338   {\r
1339   }\r
1340 \r
1341   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1342   {\r
1343   }\r
1344 \r
1345   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1346   {\r
1347   }\r
1348 \r
1349   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1350   {\r
1351   }\r
1352 \r
1353   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1354   {\r
1355   }\r
1356 \r
1357   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1358   {\r
1359   }\r
1360 \r
1361   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1362   {\r
1363   }\r
1364 \r
1365   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1366   {\r
1367   }\r
1368 \r
1369   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1370   {\r
1371   }\r
1372 \r
1373   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1374   {\r
1375   }\r
1376 \r
1377   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1378   {\r
1379   }\r
1380 \r
1381   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1382   {\r
1383   }\r
1384 \r
1385   protected void clustalColour_actionPerformed(ActionEvent e)\r
1386   {\r
1387   }\r
1388 \r
1389   protected void zappoColour_actionPerformed(ActionEvent e)\r
1390   {\r
1391   }\r
1392 \r
1393   protected void taylorColour_actionPerformed(ActionEvent e)\r
1394   {\r
1395   }\r
1396 \r
1397   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1398   {\r
1399   }\r
1400 \r
1401   protected void helixColour_actionPerformed(ActionEvent e)\r
1402   {\r
1403   }\r
1404 \r
1405   protected void strandColour_actionPerformed(ActionEvent e)\r
1406   {\r
1407   }\r
1408 \r
1409   protected void turnColour_actionPerformed(ActionEvent e)\r
1410   {\r
1411   }\r
1412 \r
1413   protected void buriedColour_actionPerformed(ActionEvent e)\r
1414   {\r
1415   }\r
1416 \r
1417   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1418   {\r
1419   }\r
1420 \r
1421   protected void PIDColour_actionPerformed(ActionEvent e)\r
1422   {\r
1423   }\r
1424 \r
1425   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1426   {\r
1427   }\r
1428 \r
1429   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1430   {\r
1431   }\r
1432 \r
1433   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1434   {\r
1435   }\r
1436 \r
1437   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1438   {\r
1439   }\r
1440 \r
1441   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1442   {\r
1443   }\r
1444 \r
1445   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1446   {\r
1447   }\r
1448 \r
1449   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1450   {\r
1451   }\r
1452 \r
1453   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1454   {\r
1455   }\r
1456 \r
1457   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1458   {\r
1459   }\r
1460 \r
1461   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1462   {\r
1463   }\r
1464 \r
1465   protected void copy_actionPerformed(ActionEvent e)\r
1466   {\r
1467   }\r
1468 \r
1469   protected void cut_actionPerformed(ActionEvent e)\r
1470   {\r
1471   }\r
1472 \r
1473   protected void delete_actionPerformed(ActionEvent e)\r
1474   {\r
1475   }\r
1476 \r
1477   protected void pasteNew_actionPerformed(ActionEvent e)\r
1478   {\r
1479   }\r
1480 \r
1481   protected void pasteThis_actionPerformed(ActionEvent e)\r
1482   {\r
1483   }\r
1484 \r
1485   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1486   {\r
1487   }\r
1488 \r
1489   public void createPNG(java.io.File f)\r
1490   {\r
1491   }\r
1492 \r
1493   protected void font_actionPerformed(ActionEvent e)\r
1494   {\r
1495   }\r
1496 \r
1497   protected void seqLimit_actionPerformed(ActionEvent e)\r
1498   {\r
1499   }\r
1500 \r
1501   public void seqDBRef_actionPerformed(ActionEvent e)\r
1502   {\r
1503 \r
1504   }\r
1505 \r
1506 \r
1507   public void createEPS(java.io.File f)\r
1508   {\r
1509   }\r
1510 \r
1511   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1512   {\r
1513   }\r
1514 \r
1515   protected void jpred_actionPerformed(ActionEvent e)\r
1516   {\r
1517   }\r
1518 \r
1519   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1520   {\r
1521   }\r
1522 \r
1523   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1524   {\r
1525   }\r
1526 \r
1527   protected void scaleRight_actionPerformed(ActionEvent e)\r
1528   {\r
1529   }\r
1530 \r
1531   protected void modifyPID_actionPerformed(ActionEvent e)\r
1532   {\r
1533   }\r
1534 \r
1535   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1536   {\r
1537   }\r
1538 \r
1539 \r
1540 \r
1541   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1542   {\r
1543   }\r
1544 \r
1545   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1546   {\r
1547   }\r
1548 \r
1549 \r
1550   public void vamsasStore_actionPerformed(ActionEvent e)\r
1551   {\r
1552 \r
1553   }\r
1554 \r
1555   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1556   {\r
1557 \r
1558   }\r
1559 \r
1560   public void showTranslation_actionPerformed(ActionEvent e)\r
1561   {\r
1562 \r
1563   }\r
1564 \r
1565   public void featureSettings_actionPerformed(ActionEvent e)\r
1566   {\r
1567 \r
1568   }\r
1569 \r
1570   public void fetchSequence_actionPerformed(ActionEvent e)\r
1571   {\r
1572 \r
1573   }\r
1574 \r
1575   public void smoothFont_actionPerformed(ActionEvent e)\r
1576   {\r
1577 \r
1578   }\r
1579 \r
1580   public void annotationColour_actionPerformed(ActionEvent e)\r
1581   {\r
1582 \r
1583   }\r
1584 \r
1585 \r
1586   public void associatedData_actionPerformed(ActionEvent e)\r
1587   {\r
1588 \r
1589   }\r
1590 \r
1591   public void autoCalculate_actionPerformed(ActionEvent e)\r
1592   {\r
1593 \r
1594   }\r
1595 \r
1596   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1597   {\r
1598 \r
1599   }\r
1600 \r
1601   public void showAllColumns_actionPerformed(ActionEvent e)\r
1602   {\r
1603 \r
1604   }\r
1605 \r
1606   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1607   {\r
1608 \r
1609   }\r
1610 \r
1611   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1612   {\r
1613 \r
1614   }\r
1615 \r
1616   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1617   {\r
1618 \r
1619   }\r
1620 \r
1621   public void findPdbId_actionPerformed(ActionEvent e)\r
1622   {\r
1623 \r
1624   }\r
1625 \r
1626   public void enterPdbId_actionPerformed(ActionEvent e)\r
1627   {\r
1628 \r
1629   }\r
1630 \r
1631   public void pdbFile_actionPerformed(ActionEvent e)\r
1632   {\r
1633 \r
1634   }\r
1635 \r
1636   public void invertColSel_actionPerformed(ActionEvent e)\r
1637   {\r
1638 \r
1639   }\r
1640 \r
1641   public void tabSelectionChanged(int sel)\r
1642   {\r
1643 \r
1644   }\r
1645 \r
1646   public void tabbedPane_mousePressed(MouseEvent e)\r
1647   {\r
1648 \r
1649   }\r
1650 \r
1651   public void tabbedPane_focusGained(FocusEvent e)\r
1652   {\r
1653     requestFocus();\r
1654   }\r
1655 }\r