src/jalview/jbgui/GAlignFrame.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 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 jalview.gui.Preferences;\r
  22 \r
  23 import jalview.schemes.ColourSchemeProperty;\r
  24 \r
  25 import java.awt.*;\r
  26 import java.awt.event.*;\r
  27 \r
  28 import javax.swing.*;\r
  29 import javax.swing.event.AncestorEvent;\r
  30 import javax.swing.event.AncestorListener;\r
  31 \r
  32 \r
  33 public class GAlignFrame extends JInternalFrame {\r
  34     protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  35     protected JMenu fileMenu = new JMenu();\r
  36     protected JMenuItem closeMenuItem = new JMenuItem();\r
  37     protected JMenu editMenu = new JMenu();\r
  38     protected JMenu viewMenu = new JMenu();\r
  39     protected JMenu colourMenu = new JMenu();\r
  40     protected JMenu calculateMenu = new JMenu();\r
  41     protected JMenu webService = new JMenu();\r
  42     protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  43     protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  44     protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  45     protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  46     protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  47     protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  48     protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  49     protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  50     protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  51     protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  52     protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  53     protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  54     protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  55     protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  56     protected JMenuItem PCAMenuItem = new JMenuItem();\r
  57     protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  58     protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  59     protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  60     BorderLayout borderLayout1 = new BorderLayout();\r
  61     public JLabel statusBar = new JLabel();\r
  62     protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  63     protected JMenu outputTextboxMenu = new JMenu();\r
  64     protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  65     protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  66     protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  67     protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  68     protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  69     protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  70     protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  71     protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  72     protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  73     protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  74     protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  75     JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  76     JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  77     protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  78     protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  79     JMenuItem htmlMenuItem = new JMenuItem();\r
  80     JMenuItem overviewMenuItem = new JMenuItem();\r
  81     protected JMenuItem undoMenuItem = new JMenuItem();\r
  82     protected JMenuItem redoMenuItem = new JMenuItem();\r
  83     protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  84     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  85     protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  86     JMenuItem printMenuItem = new JMenuItem();\r
  87     protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  88     JMenuItem findMenuItem = new JMenuItem();\r
  89     JMenu searchMenu = new JMenu();\r
  90     protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  91     protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  92     protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  93     JMenuItem deleteGroups = new JMenuItem();\r
  94     JMenuItem delete = new JMenuItem();\r
  95     JMenuItem copy = new JMenuItem();\r
  96     JMenuItem cut = new JMenuItem();\r
  97     JMenu jMenu1 = new JMenu();\r
  98     JMenuItem pasteNew = new JMenuItem();\r
  99     JMenuItem pasteThis = new JMenuItem();\r
 100     protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 101     JMenuItem createPNG = new JMenuItem();\r
 102     protected JMenuItem font = new JMenuItem();\r
 103     protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
 104     JMenuItem epsFile = new JMenuItem();\r
 105     JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 106     JMenuItem jpred = new JMenuItem();\r
 107     protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 108     protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 109     protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 110     JMenuItem modifyPID = new JMenuItem();\r
 111     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     JMenuItem msaAlignMenuItem = new JMenuItem();\r
 116     JMenu jMenu2 = new JMenu();\r
 117     JMenuItem padGapsMenuitem = new JMenuItem();\r
 118     JMenuItem ClustalRealign = new JMenuItem();\r
 119 \r
 120     public GAlignFrame() {\r
 121         ButtonGroup colours = new ButtonGroup();\r
 122         colours.add(noColourmenuItem);\r
 123         colours.add(clustalColour);\r
 124         colours.add(zappoColour);\r
 125         colours.add(taylorColour);\r
 126         colours.add(hydrophobicityColour);\r
 127         colours.add(helixColour);\r
 128         colours.add(strandColour);\r
 129         colours.add(turnColour);\r
 130         colours.add(buriedColour);\r
 131         colours.add(userDefinedColour);\r
 132         colours.add(PIDColour);\r
 133         colours.add(BLOSUM62Colour);\r
 134         colours.add(nucleotideColour);\r
 135 \r
 136         noColourmenuItem.setSelected(true);\r
 137 \r
 138         String defaultColour = Preferences.defaultColour;\r
 139 \r
 140         if (defaultColour != null) {\r
 141             int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 142 \r
 143             switch (index) {\r
 144             case ColourSchemeProperty.CLUSTAL:\r
 145                 clustalColour.setSelected(true);\r
 146 \r
 147                 break;\r
 148 \r
 149             case ColourSchemeProperty.BLOSUM:\r
 150                 BLOSUM62Colour.setSelected(true);\r
 151 \r
 152                 break;\r
 153 \r
 154             case ColourSchemeProperty.PID:\r
 155                 PIDColour.setSelected(true);\r
 156 \r
 157                 break;\r
 158 \r
 159             case ColourSchemeProperty.ZAPPO:\r
 160                 zappoColour.setSelected(true);\r
 161 \r
 162                 break;\r
 163 \r
 164             case ColourSchemeProperty.HYDROPHOBIC:\r
 165                 hydrophobicityColour.setSelected(true);\r
 166 \r
 167                 break;\r
 168 \r
 169             case ColourSchemeProperty.HELIX:\r
 170                 helixColour.setSelected(true);\r
 171 \r
 172                 break;\r
 173 \r
 174             case ColourSchemeProperty.STRAND:\r
 175                 strandColour.setSelected(true);\r
 176 \r
 177                 break;\r
 178 \r
 179             case ColourSchemeProperty.TURN:\r
 180                 turnColour.setSelected(true);\r
 181 \r
 182                 break;\r
 183 \r
 184             case ColourSchemeProperty.BURIED:\r
 185                 buriedColour.setSelected(true);\r
 186 \r
 187                 break;\r
 188 \r
 189             case ColourSchemeProperty.NUCLEOTIDE:\r
 190                 nucleotideColour.setSelected(true);\r
 191 \r
 192                 break;\r
 193 \r
 194             case ColourSchemeProperty.USER_DEFINED:\r
 195                 userDefinedColour.setSelected(true);\r
 196 \r
 197                 break;\r
 198             }\r
 199         }\r
 200 \r
 201         try {\r
 202             jbInit();\r
 203             setJMenuBar(alignFrameMenuBar);\r
 204 \r
 205             JMenuItem item;\r
 206 \r
 207             // dynamically fill save as menu with available formats\r
 208             for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
 209                 item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
 210                             i));\r
 211                 item.addActionListener(new java.awt.event.ActionListener() {\r
 212                         public void actionPerformed(ActionEvent e) {\r
 213                             outputText_actionPerformed(e);\r
 214                         }\r
 215                     });\r
 216 \r
 217                 outputTextboxMenu.add(item);\r
 218             }\r
 219         } catch (Exception e) {\r
 220             e.printStackTrace();\r
 221         }\r
 222     }\r
 223 \r
 224     private void jbInit() throws Exception {\r
 225         fileMenu.setMnemonic('F');\r
 226         fileMenu.setText("File");\r
 227         saveAlignmentMenu.setMnemonic('L');\r
 228         saveAlignmentMenu.setText("Save As");\r
 229         saveAlignmentMenu.addActionListener(new ActionListener() {\r
 230                 public void actionPerformed(ActionEvent e) {\r
 231                     saveAlignmentMenu_actionPerformed(e);\r
 232                 }\r
 233             });\r
 234         closeMenuItem.setMnemonic('C');\r
 235         closeMenuItem.setText("Close");\r
 236         closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 237                 public void actionPerformed(ActionEvent e) {\r
 238                     closeMenuItem_actionPerformed(e);\r
 239                 }\r
 240             });\r
 241         editMenu.setText("Edit");\r
 242         viewMenu.setText("View");\r
 243         colourMenu.setText("Colour");\r
 244         calculateMenu.setText("Calculate");\r
 245         webService.setText("Web Service");\r
 246         selectAllSequenceMenuItem.setText("Select all");\r
 247         selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 248                 java.awt.event.KeyEvent.VK_A,\r
 249                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 250         selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 251                 public void actionPerformed(ActionEvent e) {\r
 252                     selectAllSequenceMenuItem_actionPerformed(e);\r
 253                 }\r
 254             });\r
 255         deselectAllSequenceMenuItem.setText("Deselect All");\r
 256         deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 257                 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 258         deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 259                 public void actionPerformed(ActionEvent e) {\r
 260                     deselectAllSequenceMenuItem_actionPerformed(e);\r
 261                 }\r
 262             });\r
 263         invertSequenceMenuItem.setText("Invert Selection");\r
 264         invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 265                 public void actionPerformed(ActionEvent e) {\r
 266                     invertSequenceMenuItem_actionPerformed(e);\r
 267                 }\r
 268             });\r
 269         remove2LeftMenuItem.setText("Remove Left");\r
 270         remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 271                 public void actionPerformed(ActionEvent e) {\r
 272                     remove2LeftMenuItem_actionPerformed(e);\r
 273                 }\r
 274             });\r
 275         remove2RightMenuItem.setText("Remove Right");\r
 276         remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 277                 public void actionPerformed(ActionEvent e) {\r
 278                     remove2RightMenuItem_actionPerformed(e);\r
 279                 }\r
 280             });\r
 281         removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 282         removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 283                 public void actionPerformed(ActionEvent e) {\r
 284                     removeGappedColumnMenuItem_actionPerformed(e);\r
 285                 }\r
 286             });\r
 287         removeAllGapsMenuItem.setText("Remove All Gaps");\r
 288         removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 289                 public void actionPerformed(ActionEvent e) {\r
 290                     removeAllGapsMenuItem_actionPerformed(e);\r
 291                 }\r
 292             });\r
 293         viewBoxesMenuItem.setText("Boxes");\r
 294         viewBoxesMenuItem.setState(true);\r
 295         viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 296                 public void actionPerformed(ActionEvent e) {\r
 297                     viewBoxesMenuItem_actionPerformed(e);\r
 298                 }\r
 299             });\r
 300         viewTextMenuItem.setText("Text");\r
 301         viewTextMenuItem.setState(true);\r
 302         viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 303                 public void actionPerformed(ActionEvent e) {\r
 304                     viewTextMenuItem_actionPerformed(e);\r
 305                 }\r
 306             });\r
 307         sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 308         sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 309                 public void actionPerformed(ActionEvent e) {\r
 310                     sortPairwiseMenuItem_actionPerformed(e);\r
 311                 }\r
 312             });\r
 313         sortIDMenuItem.setText("by ID");\r
 314         sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 315                 public void actionPerformed(ActionEvent e) {\r
 316                     sortIDMenuItem_actionPerformed(e);\r
 317                 }\r
 318             });\r
 319         sortGroupMenuItem.setText("by Group");\r
 320         sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 321                 public void actionPerformed(ActionEvent e) {\r
 322                     sortGroupMenuItem_actionPerformed(e);\r
 323                 }\r
 324             });\r
 325         removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 326         removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 327                 public void actionPerformed(ActionEvent e) {\r
 328                     removeRedundancyMenuItem_actionPerformed(e);\r
 329                 }\r
 330             });\r
 331         pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 332         pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 333                 public void actionPerformed(ActionEvent e) {\r
 334                     pairwiseAlignmentMenuItem_actionPerformed(e);\r
 335                 }\r
 336             });\r
 337         PCAMenuItem.setText("Principal Component Analysis...");\r
 338         PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 339                 public void actionPerformed(ActionEvent e) {\r
 340                     PCAMenuItem_actionPerformed(e);\r
 341                 }\r
 342             });\r
 343         averageDistanceTreeMenuItem.setText(\r
 344             "Average Distance Using % Identity...");\r
 345         averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 346                 public void actionPerformed(ActionEvent e) {\r
 347                     averageDistanceTreeMenuItem_actionPerformed(e);\r
 348                 }\r
 349             });\r
 350         neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
 351         neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 352                 public void actionPerformed(ActionEvent e) {\r
 353                     neighbourTreeMenuItem_actionPerformed(e);\r
 354                 }\r
 355             });\r
 356         clustalAlignMenuItem.setText("Clustal Alignment...");\r
 357         clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 358                 public void actionPerformed(ActionEvent e) {\r
 359                     clustalAlignMenuItem_actionPerformed(e);\r
 360                 }\r
 361             });\r
 362         this.getContentPane().setLayout(borderLayout1);\r
 363         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 364         alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
 365                 public void ancestorAdded(AncestorEvent event) {\r
 366                     alignFrameMenuBar_ancestorAdded(event);\r
 367                 }\r
 368 \r
 369                 public void ancestorRemoved(AncestorEvent event) {\r
 370                 }\r
 371 \r
 372                 public void ancestorMoved(AncestorEvent event) {\r
 373                 }\r
 374             });\r
 375         statusBar.setBackground(Color.white);\r
 376         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 377         statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 378         statusBar.setText("Status bar");\r
 379         outputTextboxMenu.setMnemonic('T');\r
 380         outputTextboxMenu.setText("Output to Textbox");\r
 381         clustalColour.setText("Clustalx");\r
 382 \r
 383         clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
 384                 public void actionPerformed(ActionEvent e) {\r
 385                     clustalColour_actionPerformed(e);\r
 386                 }\r
 387             });\r
 388         zappoColour.setText("Zappo");\r
 389         zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
 390                 public void actionPerformed(ActionEvent e) {\r
 391                     zappoColour_actionPerformed(e);\r
 392                 }\r
 393             });\r
 394         taylorColour.setText("Taylor");\r
 395         taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
 396                 public void actionPerformed(ActionEvent e) {\r
 397                     taylorColour_actionPerformed(e);\r
 398                 }\r
 399             });\r
 400         hydrophobicityColour.setText("Hydrophobicity");\r
 401         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
 402                 public void actionPerformed(ActionEvent e) {\r
 403                     hydrophobicityColour_actionPerformed(e);\r
 404                 }\r
 405             });\r
 406         helixColour.setText("Helix Propensity");\r
 407         helixColour.addActionListener(new java.awt.event.ActionListener() {\r
 408                 public void actionPerformed(ActionEvent e) {\r
 409                     helixColour_actionPerformed(e);\r
 410                 }\r
 411             });\r
 412         strandColour.setText("Strand Propensity");\r
 413         strandColour.addActionListener(new java.awt.event.ActionListener() {\r
 414                 public void actionPerformed(ActionEvent e) {\r
 415                     strandColour_actionPerformed(e);\r
 416                 }\r
 417             });\r
 418         turnColour.setText("Turn Propensity");\r
 419         turnColour.addActionListener(new java.awt.event.ActionListener() {\r
 420                 public void actionPerformed(ActionEvent e) {\r
 421                     turnColour_actionPerformed(e);\r
 422                 }\r
 423             });\r
 424         buriedColour.setText("Buried Index");\r
 425         buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
 426                 public void actionPerformed(ActionEvent e) {\r
 427                     buriedColour_actionPerformed(e);\r
 428                 }\r
 429             });\r
 430         userDefinedColour.setText("User Defined...");\r
 431         userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
 432                 public void actionPerformed(ActionEvent e) {\r
 433                     userDefinedColour_actionPerformed(e);\r
 434                 }\r
 435             });\r
 436         PIDColour.setText("Percentage Identity");\r
 437         PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
 438                 public void actionPerformed(ActionEvent e) {\r
 439                     PIDColour_actionPerformed(e);\r
 440                 }\r
 441             });\r
 442         BLOSUM62Colour.setText("BLOSUM62 Score");\r
 443         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
 444                 public void actionPerformed(ActionEvent e) {\r
 445                     BLOSUM62Colour_actionPerformed(e);\r
 446                 }\r
 447             });\r
 448         avDistanceTreeBlosumMenuItem.setText(\r
 449             "Average Distance Using BLOSUM62...");\r
 450         avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 451                 public void actionPerformed(ActionEvent e) {\r
 452                     avTreeBlosumMenuItem_actionPerformed(e);\r
 453                 }\r
 454             });\r
 455         njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
 456         njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 457                 public void actionPerformed(ActionEvent e) {\r
 458                     njTreeBlosumMenuItem_actionPerformed(e);\r
 459                 }\r
 460             });\r
 461         annotationPanelMenuItem.setActionCommand("");\r
 462         annotationPanelMenuItem.setText("Show Annotations");\r
 463         annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
 464         annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 465                 public void actionPerformed(ActionEvent e) {\r
 466                     annotationPanelMenuItem_actionPerformed(e);\r
 467                 }\r
 468             });\r
 469         colourTextMenuItem.setText("Colour Text");\r
 470         colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 471                 public void actionPerformed(ActionEvent e) {\r
 472                     colourTextMenuItem_actionPerformed(e);\r
 473                 }\r
 474             });\r
 475         htmlMenuItem.setText("HTML");\r
 476         htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 477                 public void actionPerformed(ActionEvent e) {\r
 478                     htmlMenuItem_actionPerformed(e);\r
 479                 }\r
 480             });\r
 481         overviewMenuItem.setText("Overview Window...");\r
 482         overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 483                 public void actionPerformed(ActionEvent e) {\r
 484                     overviewMenuItem_actionPerformed(e);\r
 485                 }\r
 486             });\r
 487         undoMenuItem.setEnabled(false);\r
 488         undoMenuItem.setMnemonic('Z');\r
 489         undoMenuItem.setText("Undo");\r
 490         undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 491                 java.awt.event.KeyEvent.VK_Z,\r
 492                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 493         undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 494                 public void actionPerformed(ActionEvent e) {\r
 495                     undoMenuItem_actionPerformed(e);\r
 496                 }\r
 497             });\r
 498         redoMenuItem.setEnabled(false);\r
 499         redoMenuItem.setMnemonic('0');\r
 500         redoMenuItem.setText("Redo");\r
 501         redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 502                 public void actionPerformed(ActionEvent e) {\r
 503                     redoMenuItem_actionPerformed(e);\r
 504                 }\r
 505             });\r
 506         conservationMenuItem.setText("By Conservation");\r
 507         conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 508                 public void actionPerformed(ActionEvent e) {\r
 509                     conservationMenuItem_actionPerformed(e);\r
 510                 }\r
 511             });\r
 512         noColourmenuItem.setText("None");\r
 513         noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 514                 public void actionPerformed(ActionEvent e) {\r
 515                     noColourmenuItem_actionPerformed(e);\r
 516                 }\r
 517             });\r
 518         wrapMenuItem.setText("Wrap");\r
 519         wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 520                 public void actionPerformed(ActionEvent e) {\r
 521                     wrapMenuItem_actionPerformed(e);\r
 522                 }\r
 523             });\r
 524         printMenuItem.setText("Print");\r
 525         printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 526                 public void actionPerformed(ActionEvent e) {\r
 527                     printMenuItem_actionPerformed(e);\r
 528                 }\r
 529             });\r
 530         renderGapsMenuItem.setText("Show Gaps");\r
 531         renderGapsMenuItem.setState(true);\r
 532         renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 533                 public void actionPerformed(ActionEvent e) {\r
 534                     renderGapsMenuItem_actionPerformed(e);\r
 535                 }\r
 536             });\r
 537         findMenuItem.setText("Find...");\r
 538         findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 539                 java.awt.event.KeyEvent.VK_F,\r
 540                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 541         findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 542                 public void actionPerformed(ActionEvent e) {\r
 543                     findMenuItem_actionPerformed(e);\r
 544                 }\r
 545             });\r
 546         searchMenu.setText("Search");\r
 547 \r
 548         abovePIDThreshold.setText("Above Identity Threshold");\r
 549         abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 550                 public void actionPerformed(ActionEvent e) {\r
 551                     abovePIDThreshold_actionPerformed(e);\r
 552                 }\r
 553             });\r
 554         sequenceFeatures.setText("Sequence Features");\r
 555         sequenceFeatures.addActionListener(new ActionListener() {\r
 556                 public void actionPerformed(ActionEvent actionEvent) {\r
 557                     sequenceFeatures_actionPerformed(actionEvent);\r
 558                 }\r
 559             });\r
 560         nucleotideColour.setText("Nucleotide");\r
 561         nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
 562                 public void actionPerformed(ActionEvent e) {\r
 563                     nucleotideColour_actionPerformed(e);\r
 564                 }\r
 565             });\r
 566         deleteGroups.setText("Undefine groups");\r
 567         deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
 568                 public void actionPerformed(ActionEvent e) {\r
 569                     deleteGroups_actionPerformed(e);\r
 570                 }\r
 571             });\r
 572         copy.setText("Copy");\r
 573         copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 574                 java.awt.event.KeyEvent.VK_C,\r
 575                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 576         copy.setMnemonic(KeyEvent.VK_C);\r
 577 \r
 578         copy.addActionListener(new java.awt.event.ActionListener() {\r
 579                 public void actionPerformed(ActionEvent e) {\r
 580                     copy_actionPerformed(e);\r
 581                 }\r
 582             });\r
 583         cut.setText("Cut");\r
 584         cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 585                 java.awt.event.KeyEvent.VK_X,\r
 586                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 587         cut.setMnemonic(KeyEvent.VK_X);\r
 588         cut.addActionListener(new java.awt.event.ActionListener() {\r
 589                 public void actionPerformed(ActionEvent e) {\r
 590                     cut_actionPerformed(e);\r
 591                 }\r
 592             });\r
 593         delete.setText("Delete");\r
 594         delete.addActionListener(new java.awt.event.ActionListener() {\r
 595                 public void actionPerformed(ActionEvent e) {\r
 596                     delete_actionPerformed(e);\r
 597                 }\r
 598             });\r
 599         jMenu1.setMnemonic('V');\r
 600         jMenu1.setText("Paste");\r
 601         pasteNew.setText("To New Alignment");\r
 602         pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 603                 java.awt.event.KeyEvent.VK_V,\r
 604                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 605         pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
 606                 public void actionPerformed(ActionEvent e) {\r
 607                     pasteNew_actionPerformed(e);\r
 608                 }\r
 609             });\r
 610         pasteThis.setText("Add To This Alignment");\r
 611         pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
 612                 public void actionPerformed(ActionEvent e) {\r
 613                     pasteThis_actionPerformed(e);\r
 614                 }\r
 615             });\r
 616         applyToAllGroups.setText("Apply Colour To All Groups");\r
 617         applyToAllGroups.setState(true);\r
 618         applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {\r
 619                 public void actionPerformed(ActionEvent e) {\r
 620                     applyToAllGroups_actionPerformed(e);\r
 621                 }\r
 622             });\r
 623         createPNG.addActionListener(new java.awt.event.ActionListener() {\r
 624                 public void actionPerformed(ActionEvent e) {\r
 625                     createPNG_actionPerformed(e);\r
 626                 }\r
 627             });\r
 628         createPNG.setActionCommand("Save As PNG Image");\r
 629         createPNG.setText("PNG");\r
 630         font.setText("Font...");\r
 631         font.addActionListener(new java.awt.event.ActionListener() {\r
 632                 public void actionPerformed(ActionEvent e) {\r
 633                     font_actionPerformed(e);\r
 634                 }\r
 635             });\r
 636         fullSeqId.setText("Show Full Sequence ID");\r
 637         fullSeqId.setState(true);\r
 638         fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
 639                 public void actionPerformed(ActionEvent e) {\r
 640                     fullSeqId_actionPerformed(e);\r
 641                 }\r
 642             });\r
 643         epsFile.setText("EPS");\r
 644         epsFile.addActionListener(new java.awt.event.ActionListener() {\r
 645                 public void actionPerformed(ActionEvent e) {\r
 646                     epsFile_actionPerformed(e);\r
 647                 }\r
 648             });\r
 649         LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 650         LoadtreeMenuItem.setText("Load Assocated Tree");\r
 651         LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 652                 public void actionPerformed(ActionEvent e) {\r
 653                     LoadtreeMenuItem_actionPerformed(e);\r
 654                 }\r
 655             });\r
 656         jpred.setText("JPred...");\r
 657         jpred.addActionListener(new java.awt.event.ActionListener() {\r
 658                 public void actionPerformed(ActionEvent e) {\r
 659                     jpred_actionPerformed(e);\r
 660                 }\r
 661             });\r
 662         scaleAbove.setVisible(false);\r
 663         scaleAbove.setText("Scale Above");\r
 664         scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
 665                 public void actionPerformed(ActionEvent e) {\r
 666                     scaleAbove_actionPerformed(e);\r
 667                 }\r
 668             });\r
 669         scaleLeft.setVisible(false);\r
 670         scaleLeft.setSelected(true);\r
 671         scaleLeft.setText("Scale Left");\r
 672         scaleLeft.addActionListener(new java.awt.event.ActionListener() {\r
 673                 public void actionPerformed(ActionEvent e) {\r
 674                     scaleLeft_actionPerformed(e);\r
 675                 }\r
 676             });\r
 677         scaleRight.setVisible(false);\r
 678         scaleRight.setSelected(true);\r
 679         scaleRight.setText("Scale Right");\r
 680         scaleRight.addActionListener(new java.awt.event.ActionListener() {\r
 681                 public void actionPerformed(ActionEvent e) {\r
 682                     scaleRight_actionPerformed(e);\r
 683                 }\r
 684             });\r
 685         modifyPID.setText("Modify Identity Threshold...");\r
 686         modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
 687                 public void actionPerformed(ActionEvent e) {\r
 688                     modifyPID_actionPerformed(e);\r
 689                 }\r
 690             });\r
 691         modifyConservation.setText("Modify Conservation Threshold...");\r
 692         modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
 693                 public void actionPerformed(ActionEvent e) {\r
 694                     modifyConservation_actionPerformed(e);\r
 695                 }\r
 696             });\r
 697         sortByTreeMenu.setText("By Tree Order");\r
 698         sort.setText("Sort");\r
 699         calculate.setText("Calculate Tree");\r
 700         msaAlignMenuItem.setText("Muscle Alignment...");\r
 701         msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 702                 public void actionPerformed(ActionEvent e) {\r
 703                     msaAlignMenuItem_actionPerformed(e);\r
 704                 }\r
 705             });\r
 706         jMenu2.setText("Export");\r
 707         padGapsMenuitem.setText("Pad Gaps");\r
 708         padGapsMenuitem.addActionListener(new ActionListener() {\r
 709                 public void actionPerformed(ActionEvent e) {\r
 710                     padGapsMenuitem_actionPerformed(e);\r
 711                 }\r
 712             });\r
 713         ClustalRealign.setText("Clustal Realign...");\r
 714         ClustalRealign.addActionListener(new ActionListener() {\r
 715                 public void actionPerformed(ActionEvent e) {\r
 716                     ClustalRealign_actionPerformed(e);\r
 717                 }\r
 718             });\r
 719         alignFrameMenuBar.add(fileMenu);\r
 720         alignFrameMenuBar.add(editMenu);\r
 721         alignFrameMenuBar.add(searchMenu);\r
 722         alignFrameMenuBar.add(viewMenu);\r
 723         alignFrameMenuBar.add(colourMenu);\r
 724         alignFrameMenuBar.add(calculateMenu);\r
 725         fileMenu.add(saveAlignmentMenu);\r
 726         fileMenu.add(jMenu2);\r
 727         fileMenu.add(outputTextboxMenu);\r
 728         fileMenu.add(printMenuItem);\r
 729         fileMenu.addSeparator();\r
 730         fileMenu.add(LoadtreeMenuItem);\r
 731         fileMenu.addSeparator();\r
 732         fileMenu.add(closeMenuItem);\r
 733         editMenu.add(undoMenuItem);\r
 734         editMenu.add(redoMenuItem);\r
 735         editMenu.add(cut);\r
 736         editMenu.add(copy);\r
 737         editMenu.add(jMenu1);\r
 738         editMenu.add(delete);\r
 739         editMenu.addSeparator();\r
 740         editMenu.add(selectAllSequenceMenuItem);\r
 741         editMenu.add(deselectAllSequenceMenuItem);\r
 742         editMenu.add(invertSequenceMenuItem);\r
 743         editMenu.add(deleteGroups);\r
 744         editMenu.addSeparator();\r
 745         editMenu.add(remove2LeftMenuItem);\r
 746         editMenu.add(remove2RightMenuItem);\r
 747         editMenu.add(removeGappedColumnMenuItem);\r
 748         editMenu.add(removeAllGapsMenuItem);\r
 749         editMenu.add(removeRedundancyMenuItem);\r
 750         editMenu.addSeparator();\r
 751         editMenu.add(padGapsMenuitem);\r
 752         searchMenu.add(findMenuItem);\r
 753         viewMenu.add(font);\r
 754         viewMenu.addSeparator();\r
 755         viewMenu.add(wrapMenuItem);\r
 756         viewMenu.add(fullSeqId);\r
 757         viewMenu.add(scaleAbove);\r
 758         viewMenu.add(scaleLeft);\r
 759         viewMenu.add(scaleRight);\r
 760         viewMenu.add(viewBoxesMenuItem);\r
 761         viewMenu.add(viewTextMenuItem);\r
 762         viewMenu.add(colourTextMenuItem);\r
 763         viewMenu.add(renderGapsMenuItem);\r
 764         viewMenu.add(annotationPanelMenuItem);\r
 765         viewMenu.add(sequenceFeatures);\r
 766         viewMenu.addSeparator();\r
 767         viewMenu.add(overviewMenuItem);\r
 768         colourMenu.add(applyToAllGroups);\r
 769         colourMenu.addSeparator();\r
 770         colourMenu.add(noColourmenuItem);\r
 771         colourMenu.add(clustalColour);\r
 772         colourMenu.add(BLOSUM62Colour);\r
 773         colourMenu.add(PIDColour);\r
 774         colourMenu.add(zappoColour);\r
 775         colourMenu.add(taylorColour);\r
 776         colourMenu.add(hydrophobicityColour);\r
 777         colourMenu.add(helixColour);\r
 778         colourMenu.add(strandColour);\r
 779         colourMenu.add(turnColour);\r
 780         colourMenu.add(buriedColour);\r
 781         colourMenu.add(nucleotideColour);\r
 782         colourMenu.add(userDefinedColour);\r
 783         colourMenu.addSeparator();\r
 784         colourMenu.add(conservationMenuItem);\r
 785         colourMenu.add(modifyConservation);\r
 786         colourMenu.add(abovePIDThreshold);\r
 787         colourMenu.add(modifyPID);\r
 788         calculateMenu.add(sort);\r
 789         calculateMenu.add(calculate);\r
 790         calculateMenu.addSeparator();\r
 791         calculateMenu.add(pairwiseAlignmentMenuItem);\r
 792         calculateMenu.add(PCAMenuItem);\r
 793         calculateMenu.addSeparator();\r
 794         calculateMenu.add(webService);\r
 795         webService.add(clustalAlignMenuItem);\r
 796         webService.add(msaAlignMenuItem);\r
 797         webService.add(jpred);\r
 798         webService.add(ClustalRealign);\r
 799         this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 800         jMenu1.add(pasteNew);\r
 801         jMenu1.add(pasteThis);\r
 802         sort.add(sortIDMenuItem);\r
 803         sort.add(sortGroupMenuItem);\r
 804         sort.add(sortPairwiseMenuItem);\r
 805         calculate.add(averageDistanceTreeMenuItem);\r
 806         calculate.add(neighbourTreeMenuItem);\r
 807         calculate.add(avDistanceTreeBlosumMenuItem);\r
 808         calculate.add(njTreeBlosumMenuItem);\r
 809         jMenu2.add(htmlMenuItem);\r
 810         jMenu2.add(epsFile);\r
 811         jMenu2.add(createPNG);\r
 812     }\r
 813 \r
 814     protected void outputText_actionPerformed(ActionEvent e) {\r
 815     }\r
 816 \r
 817     protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
 818     }\r
 819 \r
 820     protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
 821     }\r
 822 \r
 823     protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
 824     }\r
 825 \r
 826     protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
 827     }\r
 828 \r
 829     protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 830     }\r
 831 \r
 832     protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 833     }\r
 834 \r
 835     protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 836     }\r
 837 \r
 838     protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
 839     }\r
 840 \r
 841     protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
 842     }\r
 843 \r
 844     protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
 845     }\r
 846 \r
 847     protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
 848     }\r
 849 \r
 850     protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
 851     }\r
 852 \r
 853     protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
 854     }\r
 855 \r
 856     protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
 857     }\r
 858 \r
 859     protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
 860     }\r
 861 \r
 862     protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
 863     }\r
 864 \r
 865     protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
 866     }\r
 867 \r
 868     protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
 869     }\r
 870 \r
 871     protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
 872     }\r
 873 \r
 874     protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
 875     }\r
 876 \r
 877     protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
 878     }\r
 879 \r
 880     protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
 881     }\r
 882 \r
 883     protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
 884     }\r
 885 \r
 886     protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
 887     }\r
 888 \r
 889     protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
 890     }\r
 891 \r
 892     protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 893     }\r
 894 \r
 895     protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 896     }\r
 897 \r
 898     protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
 899     }\r
 900 \r
 901     protected void clustalColour_actionPerformed(ActionEvent e) {\r
 902     }\r
 903 \r
 904     protected void zappoColour_actionPerformed(ActionEvent e) {\r
 905     }\r
 906 \r
 907     protected void taylorColour_actionPerformed(ActionEvent e) {\r
 908     }\r
 909 \r
 910     protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
 911     }\r
 912 \r
 913     protected void helixColour_actionPerformed(ActionEvent e) {\r
 914     }\r
 915 \r
 916     protected void strandColour_actionPerformed(ActionEvent e) {\r
 917     }\r
 918 \r
 919     protected void turnColour_actionPerformed(ActionEvent e) {\r
 920     }\r
 921 \r
 922     protected void buriedColour_actionPerformed(ActionEvent e) {\r
 923     }\r
 924 \r
 925     protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
 926     }\r
 927 \r
 928     protected void PIDColour_actionPerformed(ActionEvent e) {\r
 929     }\r
 930 \r
 931     protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
 932     }\r
 933 \r
 934     protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
 935     }\r
 936 \r
 937     protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
 938     }\r
 939 \r
 940     protected void printMenuItem_actionPerformed(ActionEvent e) {\r
 941     }\r
 942 \r
 943     protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
 944     }\r
 945 \r
 946     protected void findMenuItem_actionPerformed(ActionEvent e) {\r
 947     }\r
 948 \r
 949     protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
 950     }\r
 951 \r
 952     public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
 953     }\r
 954 \r
 955     protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
 956     }\r
 957 \r
 958     protected void deleteGroups_actionPerformed(ActionEvent e) {\r
 959     }\r
 960 \r
 961     protected void copy_actionPerformed(ActionEvent e) {\r
 962     }\r
 963 \r
 964     protected void cut_actionPerformed(ActionEvent e) {\r
 965     }\r
 966 \r
 967     protected void delete_actionPerformed(ActionEvent e) {\r
 968     }\r
 969 \r
 970     protected void pasteNew_actionPerformed(ActionEvent e) {\r
 971     }\r
 972 \r
 973     protected void pasteThis_actionPerformed(ActionEvent e) {\r
 974     }\r
 975 \r
 976     protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
 977     }\r
 978 \r
 979     protected void createPNG_actionPerformed(ActionEvent e) {\r
 980     }\r
 981 \r
 982     protected void font_actionPerformed(ActionEvent e) {\r
 983     }\r
 984 \r
 985     protected void fullSeqId_actionPerformed(ActionEvent e) {\r
 986     }\r
 987 \r
 988     protected void epsFile_actionPerformed(ActionEvent e) {\r
 989     }\r
 990 \r
 991     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
 992     }\r
 993 \r
 994     protected void jpred_actionPerformed(ActionEvent e) {\r
 995     }\r
 996 \r
 997     protected void scaleAbove_actionPerformed(ActionEvent e) {\r
 998     }\r
 999 \r
1000     protected void scaleLeft_actionPerformed(ActionEvent e) {\r
1001     }\r
1002 \r
1003     protected void scaleRight_actionPerformed(ActionEvent e) {\r
1004     }\r
1005 \r
1006     protected void modifyPID_actionPerformed(ActionEvent e) {\r
1007     }\r
1008 \r
1009     protected void modifyConservation_actionPerformed(ActionEvent e) {\r
1010     }\r
1011 \r
1012     protected void preferences_actionPerformed(ActionEvent e) {\r
1013     }\r
1014 \r
1015     protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
1016     }\r
1017 \r
1018     protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
1019     }\r
1020 \r
1021     protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
1022     }\r
1023 \r
1024     protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
1025     }\r
1026 \r
1027     protected void ClustalRealign_actionPerformed(ActionEvent e) {\r
1028     }\r
1029 }\r