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