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