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   BorderLayout borderLayout1 = new BorderLayout();\r
  62   public JLabel statusBar = new JLabel();\r
  63   protected JMenuItem saveAs = new JMenuItem();\r
  64   protected JMenu outputTextboxMenu = new JMenu();\r
  65   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  66   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  69       JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  74   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  75   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  76   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  77   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  78   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  79   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  80   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  81   JMenuItem htmlMenuItem = new JMenuItem();\r
  82   JMenuItem overviewMenuItem = new JMenuItem();\r
  83   protected JMenuItem undoMenuItem = new JMenuItem();\r
  84   protected JMenuItem redoMenuItem = new JMenuItem();\r
  85   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  86   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  87   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  88   JMenuItem printMenuItem = new JMenuItem();\r
  89   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  90   JMenuItem findMenuItem = new JMenuItem();\r
  91   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  92   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
  93   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  94   JMenuItem deleteGroups = new JMenuItem();\r
  95   JMenuItem delete = new JMenuItem();\r
  96   JMenuItem copy = new JMenuItem();\r
  97   JMenuItem cut = new JMenuItem();\r
  98   JMenu pasteMenu = new JMenu();\r
  99   JMenuItem pasteNew = new JMenuItem();\r
 100   JMenuItem pasteThis = new JMenuItem();\r
 101   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 102   JMenuItem createPNG = new JMenuItem();\r
 103   protected JMenuItem font = new JMenuItem();\r
 104   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
 105   JMenuItem epsFile = new JMenuItem();\r
 106   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 107   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 108   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 109   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 110   protected JMenuItem modifyPID = new JMenuItem();\r
 111   protected JMenuItem modifyConservation = new JMenuItem();\r
 112   protected JMenu sortByTreeMenu = new JMenu();\r
 113   protected JMenu sort = new JMenu();\r
 114   JMenu calculate = new JMenu();\r
 115   JMenu jMenu2 = new JMenu();\r
 116   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
 117   protected ButtonGroup colours = new ButtonGroup();\r
 118   JMenuItem vamsasStore = new JMenuItem();\r
 119   protected JMenuItem showTranslation = new JMenuItem();\r
 120   public JMenuItem featureSettings = new JMenuItem();\r
 121   JMenuItem fetchSequence = new JMenuItem();\r
 122   JMenuItem annotationColour = new JMenuItem();\r
 123   JMenuItem associatedData = new JMenuItem();\r
 124   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
 125   JMenu addSequenceMenu = new JMenu();\r
 126   JMenuItem addFromFile = new JMenuItem();\r
 127   JMenuItem addFromText = new JMenuItem();\r
 128   JMenuItem addFromURL = new JMenuItem();\r
 129   JMenuItem exportAnnotations = new JMenuItem();\r
 130   JMenuItem exportFeatures = new JMenuItem();\r
 131   protected JPanel statusPanel = new JPanel();\r
 132   GridLayout gridLayout1 = new GridLayout();\r
 133   JMenu jMenu3 = new JMenu();\r
 134   JMenuItem showAllSeqs = new JMenuItem();\r
 135   JMenuItem showAllColumns = new JMenuItem();\r
 136   JMenu hideMenu = new JMenu();\r
 137   JMenuItem hideSelSequences = new JMenuItem();\r
 138   JMenuItem hideSelColumns = new JMenuItem();\r
 139   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
 140   JMenuItem invertColSel = new JMenuItem();\r
 141   protected JTabbedPane tabbedPane = new JTabbedPane();\r
 142   JMenuItem save = new JMenuItem();\r
 143   JMenuItem jMenuItem1 = new JMenuItem();\r
 144   protected JMenuItem reload = new JMenuItem();\r
 145   JMenuItem newView = new JMenuItem();\r
 146   JMenuItem textColour = new JMenuItem();\r
 147   JMenu jMenu1 = new JMenu();\r
 148   JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();\r
 149   JMenu jMenu4 = new JMenu();\r
 150   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
 151   public GAlignFrame()\r
 152   {\r
 153     try\r
 154     {\r
 155       jbInit();\r
 156       setJMenuBar(alignFrameMenuBar);\r
 157 \r
 158       // dynamically fill save as menu with available formats\r
 159       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 160       {\r
 161         JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
 162 \r
 163         item.addActionListener(new java.awt.event.ActionListener()\r
 164         {\r
 165           public void actionPerformed(ActionEvent e)\r
 166           {\r
 167             outputText_actionPerformed(e);\r
 168           }\r
 169         });\r
 170 \r
 171         outputTextboxMenu.add(item);\r
 172       }\r
 173     }\r
 174     catch (Exception e)\r
 175     {\r
 176     }\r
 177 \r
 178     if (!System.getProperty("os.name").startsWith("Mac"))\r
 179     {\r
 180       closeMenuItem.setMnemonic('C');\r
 181       outputTextboxMenu.setMnemonic('T');\r
 182       undoMenuItem.setMnemonic('Z');\r
 183       redoMenuItem.setMnemonic('0');\r
 184       copy.setMnemonic('C');\r
 185       cut.setMnemonic('U');\r
 186       pasteMenu.setMnemonic('P');\r
 187       reload.setMnemonic('R');\r
 188     }\r
 189 \r
 190 \r
 191     if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
 192     {\r
 193       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 194           getUserColourSchemes().keys();\r
 195 \r
 196       while (userColours.hasMoreElements())\r
 197       {\r
 198         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
 199             nextElement().toString());\r
 200         radioItem.setName("USER_DEFINED");\r
 201         radioItem.addMouseListener(new MouseAdapter()\r
 202             {\r
 203               public void mousePressed(MouseEvent evt)\r
 204               {\r
 205                 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
 206                 {\r
 207                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
 208 \r
 209                   int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
 210                       "Remove from default list?",\r
 211                       "Remove user defined colour",\r
 212                       JOptionPane.YES_NO_OPTION);\r
 213                   if(option == JOptionPane.YES_OPTION)\r
 214                   {\r
 215                     jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
 216                     colourMenu.remove(radioItem);\r
 217                   }\r
 218                   else\r
 219                     radioItem.addActionListener(new ActionListener()\r
 220                     {\r
 221                       public void actionPerformed(ActionEvent evt)\r
 222                       {\r
 223                         userDefinedColour_actionPerformed(evt);\r
 224                       }\r
 225                     });\r
 226                 }\r
 227               }\r
 228             });\r
 229         radioItem.addActionListener(new ActionListener()\r
 230         {\r
 231           public void actionPerformed(ActionEvent evt)\r
 232           {\r
 233             userDefinedColour_actionPerformed(evt);\r
 234           }\r
 235         });\r
 236         colourMenu.insert(radioItem, 15);\r
 237         colours.add(radioItem);\r
 238       }\r
 239     }\r
 240     colours.add(noColourmenuItem);\r
 241     colours.add(clustalColour);\r
 242     colours.add(zappoColour);\r
 243     colours.add(taylorColour);\r
 244     colours.add(hydrophobicityColour);\r
 245     colours.add(helixColour);\r
 246     colours.add(strandColour);\r
 247     colours.add(turnColour);\r
 248     colours.add(buriedColour);\r
 249     colours.add(userDefinedColour);\r
 250     colours.add(PIDColour);\r
 251     colours.add(BLOSUM62Colour);\r
 252     colours.add(nucleotideColour);\r
 253 \r
 254     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 255 \r
 256 \r
 257   }\r
 258 \r
 259   public void setColourSelected(String defaultColour)\r
 260   {\r
 261 \r
 262     if (defaultColour != null)\r
 263     {\r
 264       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 265 \r
 266       switch (index)\r
 267       {\r
 268         case ColourSchemeProperty.NONE:\r
 269               noColourmenuItem.setSelected(true);\r
 270               break;\r
 271         case ColourSchemeProperty.CLUSTAL:\r
 272           clustalColour.setSelected(true);\r
 273 \r
 274           break;\r
 275 \r
 276         case ColourSchemeProperty.BLOSUM:\r
 277           BLOSUM62Colour.setSelected(true);\r
 278 \r
 279           break;\r
 280 \r
 281         case ColourSchemeProperty.PID:\r
 282           PIDColour.setSelected(true);\r
 283 \r
 284           break;\r
 285 \r
 286         case ColourSchemeProperty.ZAPPO:\r
 287           zappoColour.setSelected(true);\r
 288 \r
 289           break;\r
 290 \r
 291         case ColourSchemeProperty.TAYLOR:\r
 292           taylorColour.setSelected(true);\r
 293           break;\r
 294 \r
 295         case ColourSchemeProperty.HYDROPHOBIC:\r
 296           hydrophobicityColour.setSelected(true);\r
 297 \r
 298           break;\r
 299 \r
 300         case ColourSchemeProperty.HELIX:\r
 301           helixColour.setSelected(true);\r
 302 \r
 303           break;\r
 304 \r
 305         case ColourSchemeProperty.STRAND:\r
 306           strandColour.setSelected(true);\r
 307 \r
 308           break;\r
 309 \r
 310         case ColourSchemeProperty.TURN:\r
 311           turnColour.setSelected(true);\r
 312 \r
 313           break;\r
 314 \r
 315         case ColourSchemeProperty.BURIED:\r
 316           buriedColour.setSelected(true);\r
 317 \r
 318           break;\r
 319 \r
 320         case ColourSchemeProperty.NUCLEOTIDE:\r
 321           nucleotideColour.setSelected(true);\r
 322 \r
 323           break;\r
 324 \r
 325         case ColourSchemeProperty.USER_DEFINED:\r
 326           userDefinedColour.setSelected(true);\r
 327 \r
 328           break;\r
 329       }\r
 330     }\r
 331 \r
 332   }\r
 333 \r
 334   private void jbInit()\r
 335       throws Exception\r
 336   {\r
 337     fileMenu.setText("File");\r
 338     saveAs.setText("Save As...");\r
 339     saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 340         KeyEvent.VK_S,\r
 341         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 342     saveAs.addActionListener(new ActionListener()\r
 343     {\r
 344       public void actionPerformed(ActionEvent e)\r
 345       {\r
 346         saveAs_actionPerformed(e);\r
 347       }\r
 348     });\r
 349     closeMenuItem.setText("Close");\r
 350     closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 351         event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 352     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 353     {\r
 354       public void actionPerformed(ActionEvent e)\r
 355       {\r
 356         closeMenuItem_actionPerformed(false);\r
 357       }\r
 358     });\r
 359     editMenu.setText("Edit");\r
 360     viewMenu.setText("View");\r
 361     colourMenu.setText("Colour");\r
 362     calculateMenu.setText("Calculate");\r
 363     webService.setText("Web Service");\r
 364     selectAllSequenceMenuItem.setText("Select All");\r
 365     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 366         java.awt.event.KeyEvent.VK_A,\r
 367         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 368     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 369                                                 ActionListener()\r
 370     {\r
 371       public void actionPerformed(ActionEvent e)\r
 372       {\r
 373         selectAllSequenceMenuItem_actionPerformed(e);\r
 374       }\r
 375     });\r
 376     deselectAllSequenceMenuItem.setText("Deselect All");\r
 377     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 378                                                getKeyStroke(\r
 379         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 380     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 381                                                   ActionListener()\r
 382     {\r
 383       public void actionPerformed(ActionEvent e)\r
 384       {\r
 385         deselectAllSequenceMenuItem_actionPerformed(e);\r
 386       }\r
 387     });\r
 388     invertSequenceMenuItem.setText("Invert Sequence Selection");\r
 389     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 390         java.awt.event.KeyEvent.VK_I,\r
 391         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 392     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 393     {\r
 394       public void actionPerformed(ActionEvent e)\r
 395       {\r
 396         invertSequenceMenuItem_actionPerformed(e);\r
 397       }\r
 398     });\r
 399     remove2LeftMenuItem.setText("Remove Left");\r
 400     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 401         awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 402     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 403     {\r
 404       public void actionPerformed(ActionEvent e)\r
 405       {\r
 406         remove2LeftMenuItem_actionPerformed(e);\r
 407       }\r
 408     });\r
 409     remove2RightMenuItem.setText("Remove Right");\r
 410     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 411         awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 412     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 413     {\r
 414       public void actionPerformed(ActionEvent e)\r
 415       {\r
 416         remove2RightMenuItem_actionPerformed(e);\r
 417       }\r
 418     });\r
 419     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 420     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 421                                               getKeyStroke(java.awt.event.\r
 422         KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 423     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 424                                                  ActionListener()\r
 425     {\r
 426       public void actionPerformed(ActionEvent e)\r
 427       {\r
 428         removeGappedColumnMenuItem_actionPerformed(e);\r
 429       }\r
 430     });\r
 431     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 432     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 433         java.awt.event.KeyEvent.VK_E,\r
 434         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 435     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 436     {\r
 437       public void actionPerformed(ActionEvent e)\r
 438       {\r
 439         removeAllGapsMenuItem_actionPerformed(e);\r
 440       }\r
 441     });\r
 442     viewBoxesMenuItem.setText("Boxes");\r
 443     viewBoxesMenuItem.setState(true);\r
 444     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 445     {\r
 446       public void actionPerformed(ActionEvent e)\r
 447       {\r
 448         viewBoxesMenuItem_actionPerformed(e);\r
 449       }\r
 450     });\r
 451     viewTextMenuItem.setText("Text");\r
 452     viewTextMenuItem.setState(true);\r
 453     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 454     {\r
 455       public void actionPerformed(ActionEvent e)\r
 456       {\r
 457         viewTextMenuItem_actionPerformed(e);\r
 458       }\r
 459     });\r
 460     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 461     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 462     {\r
 463       public void actionPerformed(ActionEvent e)\r
 464       {\r
 465         sortPairwiseMenuItem_actionPerformed(e);\r
 466       }\r
 467     });\r
 468     sortIDMenuItem.setText("by ID");\r
 469     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 470     {\r
 471       public void actionPerformed(ActionEvent e)\r
 472       {\r
 473         sortIDMenuItem_actionPerformed(e);\r
 474       }\r
 475     });\r
 476     sortGroupMenuItem.setText("by Group");\r
 477     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 478     {\r
 479       public void actionPerformed(ActionEvent e)\r
 480       {\r
 481         sortGroupMenuItem_actionPerformed(e);\r
 482       }\r
 483     });\r
 484     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 485     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 486         java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 487     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 488                                                ActionListener()\r
 489     {\r
 490       public void actionPerformed(ActionEvent e)\r
 491       {\r
 492         removeRedundancyMenuItem_actionPerformed(e);\r
 493       }\r
 494     });\r
 495     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 496     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 497                                                 ActionListener()\r
 498     {\r
 499       public void actionPerformed(ActionEvent e)\r
 500       {\r
 501         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 502       }\r
 503     });\r
 504     PCAMenuItem.setText("Principal Component Analysis");\r
 505     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 506     {\r
 507       public void actionPerformed(ActionEvent e)\r
 508       {\r
 509         PCAMenuItem_actionPerformed(e);\r
 510       }\r
 511     });\r
 512     averageDistanceTreeMenuItem.setText(\r
 513         "Average Distance Using % Identity");\r
 514     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 515                                                   ActionListener()\r
 516     {\r
 517       public void actionPerformed(ActionEvent e)\r
 518       {\r
 519         averageDistanceTreeMenuItem_actionPerformed(e);\r
 520       }\r
 521     });\r
 522     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 523     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 524     {\r
 525       public void actionPerformed(ActionEvent e)\r
 526       {\r
 527         neighbourTreeMenuItem_actionPerformed(e);\r
 528       }\r
 529     });\r
 530     this.getContentPane().setLayout(borderLayout1);\r
 531     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 532     statusBar.setBackground(Color.white);\r
 533     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 534     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 535     statusBar.setText("Status bar");\r
 536     outputTextboxMenu.setText("Output to Textbox");\r
 537     clustalColour.setText("Clustalx");\r
 538 \r
 539     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 540     {\r
 541       public void actionPerformed(ActionEvent e)\r
 542       {\r
 543         clustalColour_actionPerformed(e);\r
 544       }\r
 545     });\r
 546     zappoColour.setText("Zappo");\r
 547     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 548     {\r
 549       public void actionPerformed(ActionEvent e)\r
 550       {\r
 551         zappoColour_actionPerformed(e);\r
 552       }\r
 553     });\r
 554     taylorColour.setText("Taylor");\r
 555     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 556     {\r
 557       public void actionPerformed(ActionEvent e)\r
 558       {\r
 559         taylorColour_actionPerformed(e);\r
 560       }\r
 561     });\r
 562     hydrophobicityColour.setText("Hydrophobicity");\r
 563     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 564     {\r
 565       public void actionPerformed(ActionEvent e)\r
 566       {\r
 567         hydrophobicityColour_actionPerformed(e);\r
 568       }\r
 569     });\r
 570     helixColour.setText("Helix Propensity");\r
 571     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 572     {\r
 573       public void actionPerformed(ActionEvent e)\r
 574       {\r
 575         helixColour_actionPerformed(e);\r
 576       }\r
 577     });\r
 578     strandColour.setText("Strand Propensity");\r
 579     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent e)\r
 582       {\r
 583         strandColour_actionPerformed(e);\r
 584       }\r
 585     });\r
 586     turnColour.setText("Turn Propensity");\r
 587     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent e)\r
 590       {\r
 591         turnColour_actionPerformed(e);\r
 592       }\r
 593     });\r
 594     buriedColour.setText("Buried Index");\r
 595     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 596     {\r
 597       public void actionPerformed(ActionEvent e)\r
 598       {\r
 599         buriedColour_actionPerformed(e);\r
 600       }\r
 601     });\r
 602     userDefinedColour.setText("User Defined...");\r
 603     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 604     {\r
 605       public void actionPerformed(ActionEvent e)\r
 606       {\r
 607         userDefinedColour_actionPerformed(e);\r
 608       }\r
 609     });\r
 610     PIDColour.setText("Percentage Identity");\r
 611     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 612     {\r
 613       public void actionPerformed(ActionEvent e)\r
 614       {\r
 615         PIDColour_actionPerformed(e);\r
 616       }\r
 617     });\r
 618     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 619     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 620     {\r
 621       public void actionPerformed(ActionEvent e)\r
 622       {\r
 623         BLOSUM62Colour_actionPerformed(e);\r
 624       }\r
 625     });\r
 626     avDistanceTreeBlosumMenuItem.setText(\r
 627         "Average Distance Using BLOSUM62");\r
 628     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 629         ActionListener()\r
 630     {\r
 631       public void actionPerformed(ActionEvent e)\r
 632       {\r
 633         avTreeBlosumMenuItem_actionPerformed(e);\r
 634       }\r
 635     });\r
 636     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 637     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 638     {\r
 639       public void actionPerformed(ActionEvent e)\r
 640       {\r
 641         njTreeBlosumMenuItem_actionPerformed(e);\r
 642       }\r
 643     });\r
 644     annotationPanelMenuItem.setActionCommand("");\r
 645     annotationPanelMenuItem.setText("Show Annotations");\r
 646     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 647     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 648     {\r
 649       public void actionPerformed(ActionEvent e)\r
 650       {\r
 651         annotationPanelMenuItem_actionPerformed(e);\r
 652       }\r
 653     });\r
 654     colourTextMenuItem.setText("Colour Text");\r
 655     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 656     {\r
 657       public void actionPerformed(ActionEvent e)\r
 658       {\r
 659         colourTextMenuItem_actionPerformed(e);\r
 660       }\r
 661     });\r
 662     htmlMenuItem.setText("HTML");\r
 663     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 664     {\r
 665       public void actionPerformed(ActionEvent e)\r
 666       {\r
 667         htmlMenuItem_actionPerformed(e);\r
 668       }\r
 669     });\r
 670     overviewMenuItem.setText("Overview Window");\r
 671     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 672     {\r
 673       public void actionPerformed(ActionEvent e)\r
 674       {\r
 675         overviewMenuItem_actionPerformed(e);\r
 676       }\r
 677     });\r
 678     undoMenuItem.setEnabled(false);\r
 679     undoMenuItem.setText("Undo");\r
 680     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 681         java.awt.event.KeyEvent.VK_Z,\r
 682         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 683     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 684     {\r
 685       public void actionPerformed(ActionEvent e)\r
 686       {\r
 687         undoMenuItem_actionPerformed(e);\r
 688       }\r
 689     });\r
 690     redoMenuItem.setEnabled(false);\r
 691     redoMenuItem.setText("Redo");\r
 692     redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 693         event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 694     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 695     {\r
 696       public void actionPerformed(ActionEvent e)\r
 697       {\r
 698         redoMenuItem_actionPerformed(e);\r
 699       }\r
 700     });\r
 701     conservationMenuItem.setText("By Conservation");\r
 702     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 703     {\r
 704       public void actionPerformed(ActionEvent e)\r
 705       {\r
 706         conservationMenuItem_actionPerformed(e);\r
 707       }\r
 708     });\r
 709     noColourmenuItem.setText("None");\r
 710     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 711     {\r
 712       public void actionPerformed(ActionEvent e)\r
 713       {\r
 714         noColourmenuItem_actionPerformed(e);\r
 715       }\r
 716     });\r
 717     wrapMenuItem.setText("Wrap");\r
 718     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 719     {\r
 720       public void actionPerformed(ActionEvent e)\r
 721       {\r
 722         wrapMenuItem_actionPerformed(e);\r
 723       }\r
 724     });\r
 725     printMenuItem.setText("Print");\r
 726     printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 727         event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 728     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 729     {\r
 730       public void actionPerformed(ActionEvent e)\r
 731       {\r
 732         printMenuItem_actionPerformed(e);\r
 733       }\r
 734     });\r
 735     renderGapsMenuItem.setText("Show Gaps");\r
 736     renderGapsMenuItem.setState(true);\r
 737     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 738     {\r
 739       public void actionPerformed(ActionEvent e)\r
 740       {\r
 741         renderGapsMenuItem_actionPerformed(e);\r
 742       }\r
 743     });\r
 744     findMenuItem.setText("Find...");\r
 745     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 746         java.awt.event.KeyEvent.VK_F,\r
 747         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 748     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 749     {\r
 750       public void actionPerformed(ActionEvent e)\r
 751       {\r
 752         findMenuItem_actionPerformed(e);\r
 753       }\r
 754     });\r
 755     abovePIDThreshold.setText("Above Identity Threshold");\r
 756     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 757     {\r
 758       public void actionPerformed(ActionEvent e)\r
 759       {\r
 760         abovePIDThreshold_actionPerformed(e);\r
 761       }\r
 762     });\r
 763     showSeqFeatures.setText("Show Sequence Features");\r
 764     showSeqFeatures.addActionListener(new ActionListener()\r
 765     {\r
 766       public void actionPerformed(ActionEvent actionEvent)\r
 767       {\r
 768         showSeqFeatures_actionPerformed(actionEvent);\r
 769       }\r
 770     });\r
 771     nucleotideColour.setText("Nucleotide");\r
 772     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 773     {\r
 774       public void actionPerformed(ActionEvent e)\r
 775       {\r
 776         nucleotideColour_actionPerformed(e);\r
 777       }\r
 778     });\r
 779     deleteGroups.setText("Undefine groups");\r
 780     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
 781         event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 782     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 783     {\r
 784       public void actionPerformed(ActionEvent e)\r
 785       {\r
 786         deleteGroups_actionPerformed(e);\r
 787       }\r
 788     });\r
 789     copy.setText("Copy");\r
 790     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 791         java.awt.event.KeyEvent.VK_C,\r
 792         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 793 \r
 794     copy.addActionListener(new java.awt.event.ActionListener()\r
 795     {\r
 796       public void actionPerformed(ActionEvent e)\r
 797       {\r
 798         copy_actionPerformed(e);\r
 799       }\r
 800     });\r
 801     cut.setText("Cut");\r
 802     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 803         java.awt.event.KeyEvent.VK_X,\r
 804         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 805     cut.addActionListener(new java.awt.event.ActionListener()\r
 806     {\r
 807       public void actionPerformed(ActionEvent e)\r
 808       {\r
 809         cut_actionPerformed(e);\r
 810       }\r
 811     });\r
 812     delete.setText("Delete");\r
 813     delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
 814         KeyEvent.VK_BACK_SPACE, 0, false));\r
 815     delete.addActionListener(new java.awt.event.ActionListener()\r
 816     {\r
 817       public void actionPerformed(ActionEvent e)\r
 818       {\r
 819         delete_actionPerformed(e);\r
 820       }\r
 821     });\r
 822     pasteMenu.setText("Paste");\r
 823     pasteNew.setText("To New Alignment");\r
 824     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 825         java.awt.event.KeyEvent.VK_V,\r
 826         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));\r
 827     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 828     {\r
 829       public void actionPerformed(ActionEvent e)\r
 830       {\r
 831         pasteNew_actionPerformed(e);\r
 832       }\r
 833     });\r
 834     pasteThis.setText("Add To This Alignment");\r
 835     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 836         java.awt.event.KeyEvent.VK_V,\r
 837         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 838     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 839     {\r
 840       public void actionPerformed(ActionEvent e)\r
 841       {\r
 842         pasteThis_actionPerformed(e);\r
 843       }\r
 844     });\r
 845     applyToAllGroups.setText("Apply Colour To All Groups");\r
 846     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 847     {\r
 848       public void actionPerformed(ActionEvent e)\r
 849       {\r
 850         applyToAllGroups_actionPerformed(e);\r
 851       }\r
 852     });\r
 853     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 854     {\r
 855       public void actionPerformed(ActionEvent e)\r
 856       {\r
 857         createPNG(null);\r
 858       }\r
 859     });\r
 860     createPNG.setActionCommand("Save As PNG Image");\r
 861     createPNG.setText("PNG");\r
 862     font.setText("Font...");\r
 863     font.addActionListener(new java.awt.event.ActionListener()\r
 864     {\r
 865       public void actionPerformed(ActionEvent e)\r
 866       {\r
 867         font_actionPerformed(e);\r
 868       }\r
 869     });\r
 870 \r
 871     seqLimits.setText("Show Sequence Limits");\r
 872     seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
 873     seqLimits.addActionListener(new java.awt.event.ActionListener()\r
 874     {\r
 875       public void actionPerformed(ActionEvent e)\r
 876       {\r
 877         seqLimit_actionPerformed(e);\r
 878       }\r
 879     });\r
 880     epsFile.setText("EPS");\r
 881     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 882     {\r
 883       public void actionPerformed(ActionEvent e)\r
 884       {\r
 885         createEPS(null);\r
 886       }\r
 887     });\r
 888     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 889     LoadtreeMenuItem.setText("Load Associated Tree");\r
 890     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 891     {\r
 892       public void actionPerformed(ActionEvent e)\r
 893       {\r
 894         LoadtreeMenuItem_actionPerformed(e);\r
 895       }\r
 896     });\r
 897     scaleAbove.setVisible(false);\r
 898     scaleAbove.setText("Scale Above");\r
 899     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 900     {\r
 901       public void actionPerformed(ActionEvent e)\r
 902       {\r
 903         scaleAbove_actionPerformed(e);\r
 904       }\r
 905     });\r
 906     scaleLeft.setVisible(false);\r
 907     scaleLeft.setSelected(true);\r
 908     scaleLeft.setText("Scale Left");\r
 909     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 910     {\r
 911       public void actionPerformed(ActionEvent e)\r
 912       {\r
 913         scaleLeft_actionPerformed(e);\r
 914       }\r
 915     });\r
 916     scaleRight.setVisible(false);\r
 917     scaleRight.setSelected(true);\r
 918     scaleRight.setText("Scale Right");\r
 919     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 920     {\r
 921       public void actionPerformed(ActionEvent e)\r
 922       {\r
 923         scaleRight_actionPerformed(e);\r
 924       }\r
 925     });\r
 926     modifyPID.setText("Modify Identity Threshold...");\r
 927     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 928     {\r
 929       public void actionPerformed(ActionEvent e)\r
 930       {\r
 931         modifyPID_actionPerformed(e);\r
 932       }\r
 933     });\r
 934     modifyConservation.setText("Modify Conservation Threshold...");\r
 935     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 936     {\r
 937       public void actionPerformed(ActionEvent e)\r
 938       {\r
 939         modifyConservation_actionPerformed(e);\r
 940       }\r
 941     });\r
 942     sortByTreeMenu.setText("By Tree Order");\r
 943     sort.setText("Sort");\r
 944     calculate.setText("Calculate Tree");\r
 945 \r
 946     jMenu2.setText("Export Image");\r
 947     padGapsMenuitem.setText("Pad Gaps");\r
 948     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
 949     padGapsMenuitem.addActionListener(new ActionListener()\r
 950     {\r
 951       public void actionPerformed(ActionEvent e)\r
 952       {\r
 953         padGapsMenuitem_actionPerformed(e);\r
 954       }\r
 955     });\r
 956     vamsasStore.setVisible(false);\r
 957     vamsasStore.setText("VAMSAS store");\r
 958     vamsasStore.addActionListener(new ActionListener()\r
 959     {\r
 960       public void actionPerformed(ActionEvent e)\r
 961       {\r
 962         vamsasStore_actionPerformed(e);\r
 963       }\r
 964     });\r
 965     showTranslation.setText("Translate cDNA");\r
 966     showTranslation.addActionListener(new ActionListener()\r
 967     {\r
 968       public void actionPerformed(ActionEvent e)\r
 969       {\r
 970         showTranslation_actionPerformed(e);\r
 971       }\r
 972     });\r
 973 \r
 974 \r
 975     featureSettings.setText("Feature Settings...");\r
 976     featureSettings.addActionListener(new ActionListener()\r
 977     {\r
 978       public void actionPerformed(ActionEvent e)\r
 979       {\r
 980         featureSettings_actionPerformed(e);\r
 981       }\r
 982     });\r
 983     fetchSequence.setText("Fetch Sequence(s)...");\r
 984     fetchSequence.addActionListener(new ActionListener()\r
 985     {\r
 986       public void actionPerformed(ActionEvent e)\r
 987       {\r
 988         fetchSequence_actionPerformed(e);\r
 989       }\r
 990     });\r
 991 \r
 992     annotationColour.setText("By Annotation...");\r
 993     annotationColour.addActionListener(new ActionListener()\r
 994     {\r
 995       public void actionPerformed(ActionEvent e)\r
 996       {\r
 997         annotationColour_actionPerformed(e);\r
 998       }\r
 999     });\r
1000     associatedData.setText("Load Features / Annotations");\r
1001     associatedData.addActionListener(new ActionListener()\r
1002     {\r
1003       public void actionPerformed(ActionEvent e)\r
1004       {\r
1005         associatedData_actionPerformed(e);\r
1006       }\r
1007     });\r
1008     autoCalculate.setText("Autocalculate Consensus");\r
1009     autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
1010     autoCalculate.addActionListener(new ActionListener()\r
1011     {\r
1012       public void actionPerformed(ActionEvent e)\r
1013       {\r
1014         autoCalculate_actionPerformed(e);\r
1015       }\r
1016     });\r
1017     addSequenceMenu.setText("Add Sequences");\r
1018     addFromFile.setText("From File");\r
1019     addFromFile.addActionListener(new ActionListener()\r
1020     {\r
1021       public void actionPerformed(ActionEvent e)\r
1022       {\r
1023         addFromFile_actionPerformed(e);\r
1024       }\r
1025     });\r
1026     addFromText.setText("From Textbox");\r
1027     addFromText.addActionListener(new ActionListener()\r
1028     {\r
1029       public void actionPerformed(ActionEvent e)\r
1030       {\r
1031         addFromText_actionPerformed(e);\r
1032       }\r
1033     });\r
1034     addFromURL.setText("From URL");\r
1035     addFromURL.addActionListener(new ActionListener()\r
1036     {\r
1037       public void actionPerformed(ActionEvent e)\r
1038       {\r
1039         addFromURL_actionPerformed(e);\r
1040       }\r
1041     });\r
1042     exportFeatures.setText("Export Features...");\r
1043     exportFeatures.addActionListener(new ActionListener()\r
1044     {\r
1045       public void actionPerformed(ActionEvent e)\r
1046       {\r
1047         exportFeatures_actionPerformed(e);\r
1048       }\r
1049     });\r
1050     exportAnnotations.setText("Export Annotations...");\r
1051     exportAnnotations.addActionListener(new ActionListener()\r
1052     {\r
1053       public void actionPerformed(ActionEvent e)\r
1054       {\r
1055         exportAnnotations_actionPerformed(e);\r
1056       }\r
1057     });\r
1058     statusPanel.setLayout(gridLayout1);\r
1059     jMenu3.setText("Show");\r
1060     showAllSeqs.setText("All Sequences");\r
1061     showAllSeqs.addActionListener(new ActionListener()\r
1062     {\r
1063       public void actionPerformed(ActionEvent e)\r
1064       {\r
1065         showAllSeqs_actionPerformed(e);\r
1066       }\r
1067     });\r
1068     showAllColumns.setText("All Columns");\r
1069     showAllColumns.addActionListener(new ActionListener()\r
1070     {\r
1071       public void actionPerformed(ActionEvent e)\r
1072       {\r
1073         showAllColumns_actionPerformed(e);\r
1074       }\r
1075     });\r
1076     hideMenu.setText("Hide");\r
1077     hideSelSequences.setText("Selected Sequences");\r
1078     hideSelSequences.addActionListener(new ActionListener()\r
1079     {\r
1080       public void actionPerformed(ActionEvent e)\r
1081       {\r
1082         hideSelSequences_actionPerformed(e);\r
1083       }\r
1084     });\r
1085     hideSelColumns.setText("Selected Columns");\r
1086     hideSelColumns.addActionListener(new ActionListener()\r
1087     {\r
1088       public void actionPerformed(ActionEvent e)\r
1089       {\r
1090         hideSelColumns_actionPerformed(e);\r
1091       }\r
1092     });\r
1093     hiddenMarkers.setText("Show Hidden Markers");\r
1094     hiddenMarkers.addActionListener(new ActionListener()\r
1095     {\r
1096       public void actionPerformed(ActionEvent e)\r
1097       {\r
1098         hiddenMarkers_actionPerformed(e);\r
1099       }\r
1100     });\r
1101     invertColSel.setText("Invert Column Selection");\r
1102     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
1103         event.KeyEvent.VK_I,\r
1104         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
1105         |java.awt.event.KeyEvent.ALT_MASK,\r
1106         false));\r
1107     invertColSel.addActionListener(new ActionListener()\r
1108     {\r
1109       public void actionPerformed(ActionEvent e)\r
1110       {\r
1111         invertColSel_actionPerformed(e);\r
1112       }\r
1113     });\r
1114     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
1115     {\r
1116         public void stateChanged(ChangeEvent evt)\r
1117         {\r
1118             JTabbedPane pane = (JTabbedPane)evt.getSource();\r
1119             int sel = pane.getSelectedIndex();\r
1120             tabSelectionChanged(sel);\r
1121         }\r
1122     });\r
1123     tabbedPane.addMouseListener(new MouseAdapter()\r
1124     {\r
1125       public void mousePressed(MouseEvent e)\r
1126       {\r
1127         tabbedPane_mousePressed(e);\r
1128       }\r
1129     });\r
1130     tabbedPane.addFocusListener(new FocusAdapter()\r
1131     {\r
1132       public void focusGained(FocusEvent e)\r
1133       {\r
1134         tabbedPane_focusGained(e);\r
1135       }\r
1136     });\r
1137     save.setText("Save");\r
1138     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1139         KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1140     save.addActionListener(new ActionListener()\r
1141     {\r
1142       public void actionPerformed(ActionEvent e)\r
1143       {\r
1144         save_actionPerformed(e);\r
1145       }\r
1146     });\r
1147     reload.setEnabled(false);\r
1148     reload.setText("Reload");\r
1149     reload.addActionListener(new ActionListener()\r
1150     {\r
1151       public void actionPerformed(ActionEvent e)\r
1152       {\r
1153         reload_actionPerformed(e);\r
1154       }\r
1155     });\r
1156     newView.setText("New View");\r
1157     newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
1158         KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
1159     newView.addActionListener(new ActionListener()\r
1160     {\r
1161       public void actionPerformed(ActionEvent e)\r
1162       {\r
1163         newView_actionPerformed(e);\r
1164       }\r
1165     });\r
1166     tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
1167                               +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
1168     textColour.setText("Text Colour");\r
1169     textColour.addActionListener(new ActionListener()\r
1170     {\r
1171       public void actionPerformed(ActionEvent e)\r
1172       {\r
1173         textColour_actionPerformed(e);\r
1174       }\r
1175     });\r
1176     jMenu1.setText("Format");\r
1177     jCheckBoxMenuItem1.setText("Right Align Ids");\r
1178     jMenu4.setText("Select");\r
1179     idRightAlign.setText("Right Align Sequence Id");\r
1180     idRightAlign.addActionListener(new ActionListener()\r
1181     {\r
1182       public void actionPerformed(ActionEvent e)\r
1183       {\r
1184         idRightAlign_actionPerformed(e);\r
1185       }\r
1186     });\r
1187 \r
1188     alignFrameMenuBar.add(fileMenu);\r
1189     alignFrameMenuBar.add(editMenu);\r
1190     alignFrameMenuBar.add(jMenu4);\r
1191     alignFrameMenuBar.add(viewMenu);\r
1192     alignFrameMenuBar.add(jMenu1);\r
1193     alignFrameMenuBar.add(colourMenu);\r
1194     alignFrameMenuBar.add(calculateMenu);\r
1195     alignFrameMenuBar.add(webService);\r
1196     fileMenu.add(fetchSequence);\r
1197     fileMenu.add(addSequenceMenu);\r
1198     fileMenu.add(reload);\r
1199     fileMenu.addSeparator();\r
1200     fileMenu.add(vamsasStore);\r
1201     fileMenu.add(save);\r
1202     fileMenu.add(saveAs);\r
1203     fileMenu.add(outputTextboxMenu);\r
1204     fileMenu.add(printMenuItem);\r
1205     fileMenu.addSeparator();\r
1206     fileMenu.add(jMenu2);\r
1207     fileMenu.add(exportFeatures);\r
1208     fileMenu.add(exportAnnotations);\r
1209     fileMenu.add(LoadtreeMenuItem);\r
1210     fileMenu.add(associatedData);\r
1211     fileMenu.addSeparator();\r
1212     fileMenu.add(closeMenuItem);\r
1213     editMenu.add(undoMenuItem);\r
1214     editMenu.add(redoMenuItem);\r
1215     editMenu.add(cut);\r
1216     editMenu.add(copy);\r
1217     editMenu.add(pasteMenu);\r
1218     editMenu.add(delete);\r
1219     editMenu.addSeparator();\r
1220     editMenu.add(remove2LeftMenuItem);\r
1221     editMenu.add(remove2RightMenuItem);\r
1222     editMenu.add(removeGappedColumnMenuItem);\r
1223     editMenu.add(removeAllGapsMenuItem);\r
1224     editMenu.add(removeRedundancyMenuItem);\r
1225     editMenu.addSeparator();\r
1226     editMenu.add(padGapsMenuitem);\r
1227     viewMenu.add(newView);\r
1228     viewMenu.addSeparator();\r
1229     viewMenu.add(jMenu3);\r
1230     viewMenu.add(hideMenu);\r
1231     viewMenu.addSeparator();\r
1232     viewMenu.add(annotationPanelMenuItem);\r
1233     viewMenu.addSeparator();\r
1234     viewMenu.add(showSeqFeatures);\r
1235     viewMenu.add(featureSettings);\r
1236     viewMenu.addSeparator();\r
1237     viewMenu.add(overviewMenuItem);\r
1238     colourMenu.add(applyToAllGroups);\r
1239     colourMenu.add(textColour);\r
1240     colourMenu.addSeparator();\r
1241     colourMenu.add(noColourmenuItem);\r
1242     colourMenu.add(clustalColour);\r
1243     colourMenu.add(BLOSUM62Colour);\r
1244     colourMenu.add(PIDColour);\r
1245     colourMenu.add(zappoColour);\r
1246     colourMenu.add(taylorColour);\r
1247     colourMenu.add(hydrophobicityColour);\r
1248     colourMenu.add(helixColour);\r
1249     colourMenu.add(strandColour);\r
1250     colourMenu.add(turnColour);\r
1251     colourMenu.add(buriedColour);\r
1252     colourMenu.add(nucleotideColour);\r
1253     colourMenu.add(userDefinedColour);\r
1254     colourMenu.addSeparator();\r
1255     colourMenu.add(conservationMenuItem);\r
1256     colourMenu.add(modifyConservation);\r
1257     colourMenu.add(abovePIDThreshold);\r
1258     colourMenu.add(modifyPID);\r
1259     colourMenu.add(annotationColour);\r
1260     calculateMenu.add(sort);\r
1261     calculateMenu.add(calculate);\r
1262     calculateMenu.addSeparator();\r
1263     calculateMenu.add(pairwiseAlignmentMenuItem);\r
1264     calculateMenu.add(PCAMenuItem);\r
1265     calculateMenu.addSeparator();\r
1266     calculateMenu.add(showTranslation);\r
1267     calculateMenu.add(autoCalculate);\r
1268     webServiceNoServices=new JMenuItem("<No Services>");\r
1269     webService.add(webServiceNoServices);pasteMenu.add(pasteNew);\r
1270     pasteMenu.add(pasteThis);\r
1271     sort.add(sortIDMenuItem);\r
1272     sort.add(sortGroupMenuItem);\r
1273     sort.add(sortPairwiseMenuItem);\r
1274     calculate.add(averageDistanceTreeMenuItem);\r
1275     calculate.add(neighbourTreeMenuItem);\r
1276     calculate.add(avDistanceTreeBlosumMenuItem);\r
1277     calculate.add(njTreeBlosumMenuItem);\r
1278     jMenu2.add(htmlMenuItem);\r
1279     jMenu2.add(epsFile);\r
1280     jMenu2.add(createPNG);\r
1281     addSequenceMenu.add(addFromFile);\r
1282     addSequenceMenu.add(addFromText);\r
1283     addSequenceMenu.add(addFromURL);\r
1284     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
1285     statusPanel.add(statusBar, null);\r
1286     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
1287     jMenu3.add(showAllColumns);\r
1288     jMenu3.add(showAllSeqs);\r
1289     hideMenu.add(hideSelColumns);\r
1290     hideMenu.add(hideSelSequences);\r
1291     jMenu1.add(font);\r
1292     jMenu1.addSeparator();\r
1293     jMenu1.add(wrapMenuItem);\r
1294     jMenu1.add(scaleAbove);\r
1295     jMenu1.add(scaleLeft);\r
1296     jMenu1.add(scaleRight);\r
1297     jMenu1.add(seqLimits);\r
1298     jMenu1.add(idRightAlign);\r
1299     jMenu1.add(hiddenMarkers);\r
1300     jMenu1.add(viewBoxesMenuItem);\r
1301     jMenu1.add(viewTextMenuItem);\r
1302     jMenu1.add(colourTextMenuItem);\r
1303     jMenu1.add(renderGapsMenuItem);\r
1304     jMenu4.add(findMenuItem);\r
1305     jMenu4.addSeparator();\r
1306     jMenu4.add(selectAllSequenceMenuItem);\r
1307     jMenu4.add(deselectAllSequenceMenuItem);\r
1308     jMenu4.add(invertSequenceMenuItem);\r
1309     jMenu4.add(invertColSel);\r
1310     jMenu4.add(deleteGroups);\r
1311   }\r
1312 \r
1313   protected void outputText_actionPerformed(ActionEvent e)\r
1314   {\r
1315   }\r
1316 \r
1317   public void addFromFile_actionPerformed(ActionEvent e)\r
1318   {\r
1319 \r
1320   }\r
1321 \r
1322   public void addFromText_actionPerformed(ActionEvent e)\r
1323   {\r
1324 \r
1325   }\r
1326 \r
1327   public void addFromURL_actionPerformed(ActionEvent e)\r
1328   {\r
1329 \r
1330   }\r
1331 \r
1332   public void exportFeatures_actionPerformed(ActionEvent e)\r
1333   {\r
1334 \r
1335   }\r
1336 \r
1337   public void exportAnnotations_actionPerformed(ActionEvent e)\r
1338   {\r
1339 \r
1340   }\r
1341 \r
1342   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
1343   {\r
1344   }\r
1345 \r
1346   protected void closeMenuItem_actionPerformed(boolean b)\r
1347   {\r
1348   }\r
1349 \r
1350   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1351   {\r
1352   }\r
1353 \r
1354   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1355   {\r
1356   }\r
1357 \r
1358   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1359   {\r
1360   }\r
1361 \r
1362   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1363   {\r
1364   }\r
1365 \r
1366   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1367   {\r
1368   }\r
1369 \r
1370   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1371   {\r
1372   }\r
1373 \r
1374   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1375   {\r
1376   }\r
1377 \r
1378   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1379   {\r
1380   }\r
1381 \r
1382   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1383   {\r
1384   }\r
1385 \r
1386   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1387   {\r
1388   }\r
1389 \r
1390   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1391   {\r
1392   }\r
1393 \r
1394   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1395   {\r
1396   }\r
1397 \r
1398   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1399   {\r
1400   }\r
1401 \r
1402   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1403   {\r
1404   }\r
1405 \r
1406   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1407   {\r
1408   }\r
1409 \r
1410   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1411   {\r
1412   }\r
1413 \r
1414   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1415   {\r
1416   }\r
1417 \r
1418   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1419   {\r
1420   }\r
1421 \r
1422   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1423   {\r
1424   }\r
1425 \r
1426   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1427   {\r
1428   }\r
1429 \r
1430   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1431   {\r
1432   }\r
1433 \r
1434   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1435   {\r
1436   }\r
1437 \r
1438   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1439   {\r
1440   }\r
1441 \r
1442   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1443   {\r
1444   }\r
1445 \r
1446   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1447   {\r
1448   }\r
1449 \r
1450   protected void clustalColour_actionPerformed(ActionEvent e)\r
1451   {\r
1452   }\r
1453 \r
1454   protected void zappoColour_actionPerformed(ActionEvent e)\r
1455   {\r
1456   }\r
1457 \r
1458   protected void taylorColour_actionPerformed(ActionEvent e)\r
1459   {\r
1460   }\r
1461 \r
1462   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1463   {\r
1464   }\r
1465 \r
1466   protected void helixColour_actionPerformed(ActionEvent e)\r
1467   {\r
1468   }\r
1469 \r
1470   protected void strandColour_actionPerformed(ActionEvent e)\r
1471   {\r
1472   }\r
1473 \r
1474   protected void turnColour_actionPerformed(ActionEvent e)\r
1475   {\r
1476   }\r
1477 \r
1478   protected void buriedColour_actionPerformed(ActionEvent e)\r
1479   {\r
1480   }\r
1481 \r
1482   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1483   {\r
1484   }\r
1485 \r
1486   protected void PIDColour_actionPerformed(ActionEvent e)\r
1487   {\r
1488   }\r
1489 \r
1490   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1491   {\r
1492   }\r
1493 \r
1494   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1495   {\r
1496   }\r
1497 \r
1498   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1499   {\r
1500   }\r
1501 \r
1502   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1503   {\r
1504   }\r
1505 \r
1506   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1507   {\r
1508   }\r
1509 \r
1510   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1511   {\r
1512   }\r
1513 \r
1514   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1515   {\r
1516   }\r
1517 \r
1518   public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
1519   {\r
1520   }\r
1521 \r
1522   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1523   {\r
1524   }\r
1525 \r
1526   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1527   {\r
1528   }\r
1529 \r
1530   protected void copy_actionPerformed(ActionEvent e)\r
1531   {\r
1532   }\r
1533 \r
1534   protected void cut_actionPerformed(ActionEvent e)\r
1535   {\r
1536   }\r
1537 \r
1538   protected void delete_actionPerformed(ActionEvent e)\r
1539   {\r
1540   }\r
1541 \r
1542   protected void pasteNew_actionPerformed(ActionEvent e)\r
1543   {\r
1544   }\r
1545 \r
1546   protected void pasteThis_actionPerformed(ActionEvent e)\r
1547   {\r
1548   }\r
1549 \r
1550   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1551   {\r
1552   }\r
1553 \r
1554   public void createPNG(java.io.File f)\r
1555   {\r
1556   }\r
1557 \r
1558   protected void font_actionPerformed(ActionEvent e)\r
1559   {\r
1560   }\r
1561 \r
1562   protected void seqLimit_actionPerformed(ActionEvent e)\r
1563   {\r
1564   }\r
1565 \r
1566   public void seqDBRef_actionPerformed(ActionEvent e)\r
1567   {\r
1568 \r
1569   }\r
1570 \r
1571 \r
1572   public void createEPS(java.io.File f)\r
1573   {\r
1574   }\r
1575 \r
1576   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1577   {\r
1578   }\r
1579 \r
1580   protected void jpred_actionPerformed(ActionEvent e)\r
1581   {\r
1582   }\r
1583 \r
1584   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1585   {\r
1586   }\r
1587 \r
1588   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1589   {\r
1590   }\r
1591 \r
1592   protected void scaleRight_actionPerformed(ActionEvent e)\r
1593   {\r
1594   }\r
1595 \r
1596   protected void modifyPID_actionPerformed(ActionEvent e)\r
1597   {\r
1598   }\r
1599 \r
1600   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1601   {\r
1602   }\r
1603 \r
1604 \r
1605 \r
1606   protected void saveAs_actionPerformed(ActionEvent e)\r
1607   {\r
1608   }\r
1609 \r
1610   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1611   {\r
1612   }\r
1613 \r
1614 \r
1615   public void vamsasStore_actionPerformed(ActionEvent e)\r
1616   {\r
1617 \r
1618   }\r
1619 \r
1620   public void vamsasLoad_actionPerformed(ActionEvent e)\r
1621   {\r
1622 \r
1623   }\r
1624 \r
1625   public void showTranslation_actionPerformed(ActionEvent e)\r
1626   {\r
1627 \r
1628   }\r
1629 \r
1630   public void featureSettings_actionPerformed(ActionEvent e)\r
1631   {\r
1632 \r
1633   }\r
1634 \r
1635   public void fetchSequence_actionPerformed(ActionEvent e)\r
1636   {\r
1637 \r
1638   }\r
1639 \r
1640   public void smoothFont_actionPerformed(ActionEvent e)\r
1641   {\r
1642 \r
1643   }\r
1644 \r
1645   public void annotationColour_actionPerformed(ActionEvent e)\r
1646   {\r
1647 \r
1648   }\r
1649 \r
1650 \r
1651   public void associatedData_actionPerformed(ActionEvent e)\r
1652   {\r
1653 \r
1654   }\r
1655 \r
1656   public void autoCalculate_actionPerformed(ActionEvent e)\r
1657   {\r
1658 \r
1659   }\r
1660 \r
1661   public void showAllSeqs_actionPerformed(ActionEvent e)\r
1662   {\r
1663 \r
1664   }\r
1665 \r
1666   public void showAllColumns_actionPerformed(ActionEvent e)\r
1667   {\r
1668 \r
1669   }\r
1670 \r
1671   public void hideSelSequences_actionPerformed(ActionEvent e)\r
1672   {\r
1673 \r
1674   }\r
1675 \r
1676   public void hideSelColumns_actionPerformed(ActionEvent e)\r
1677   {\r
1678 \r
1679   }\r
1680 \r
1681   public void hiddenMarkers_actionPerformed(ActionEvent e)\r
1682   {\r
1683 \r
1684   }\r
1685 \r
1686   public void findPdbId_actionPerformed(ActionEvent e)\r
1687   {\r
1688 \r
1689   }\r
1690 \r
1691   public void enterPdbId_actionPerformed(ActionEvent e)\r
1692   {\r
1693 \r
1694   }\r
1695 \r
1696   public void pdbFile_actionPerformed(ActionEvent e)\r
1697   {\r
1698 \r
1699   }\r
1700 \r
1701   public void invertColSel_actionPerformed(ActionEvent e)\r
1702   {\r
1703 \r
1704   }\r
1705 \r
1706   public void tabSelectionChanged(int sel)\r
1707   {\r
1708 \r
1709   }\r
1710 \r
1711   public void tabbedPane_mousePressed(MouseEvent e)\r
1712   {\r
1713 \r
1714   }\r
1715 \r
1716   public void tabbedPane_focusGained(FocusEvent e)\r
1717   {\r
1718     requestFocus();\r
1719   }\r
1720 \r
1721   public void save_actionPerformed(ActionEvent e)\r
1722   {\r
1723 \r
1724   }\r
1725 \r
1726   public void reload_actionPerformed(ActionEvent e)\r
1727   {\r
1728 \r
1729   }\r
1730 \r
1731   public void newView_actionPerformed(ActionEvent e)\r
1732   {\r
1733 \r
1734   }\r
1735 \r
1736   public void textColour_actionPerformed(ActionEvent e)\r
1737   {\r
1738 \r
1739   }\r
1740 \r
1741   public void idRightAlign_actionPerformed(ActionEvent e)\r
1742   {\r
1743 \r
1744   }\r
1745 }\r