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