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     public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  50     public 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     public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  78     public 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     public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  84     JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  85     public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  86     JMenuItem printMenuItem = new JMenuItem();\r
  87     public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  88     JMenuItem findMenuItem = new JMenuItem();\r
  89     JMenu searchMenu = new JMenu();\r
  90     public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  91     public 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     public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 101     JMenuItem createPNG = new JMenuItem();\r
 102     protected JMenuItem font = new JMenuItem();\r
 103     public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
 104     JMenuItem epsFile = new JMenuItem();\r
 105     JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 106     JMenuItem jnet = 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     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 \r
 225     private void jbInit() throws Exception {\r
 226         fileMenu.setMnemonic('F');\r
 227         fileMenu.setText("File");\r
 228         saveAlignmentMenu.setMnemonic('L');\r
 229         saveAlignmentMenu.setText("Save As");\r
 230         saveAlignmentMenu.addActionListener(new ActionListener() {\r
 231                 public void actionPerformed(ActionEvent e) {\r
 232                     saveAlignmentMenu_actionPerformed(e);\r
 233                 }\r
 234             });\r
 235         closeMenuItem.setMnemonic('C');\r
 236         closeMenuItem.setText("Close");\r
 237         closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 238                 public void actionPerformed(ActionEvent e) {\r
 239                     closeMenuItem_actionPerformed(e);\r
 240                 }\r
 241             });\r
 242         editMenu.setText("Edit");\r
 243         viewMenu.setText("View");\r
 244         colourMenu.setText("Colour");\r
 245         calculateMenu.setText("Calculate");\r
 246         webService.setText("Web Service");\r
 247         selectAllSequenceMenuItem.setText("Select all");\r
 248         selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 249                 java.awt.event.KeyEvent.VK_A,\r
 250                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 251         selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 252                 public void actionPerformed(ActionEvent e) {\r
 253                     selectAllSequenceMenuItem_actionPerformed(e);\r
 254                 }\r
 255             });\r
 256         deselectAllSequenceMenuItem.setText("Deselect All");\r
 257         deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 258                 java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 259         deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 260                 public void actionPerformed(ActionEvent e) {\r
 261                     deselectAllSequenceMenuItem_actionPerformed(e);\r
 262                 }\r
 263             });\r
 264         invertSequenceMenuItem.setText("Invert Selection");\r
 265         invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 266                 public void actionPerformed(ActionEvent e) {\r
 267                     invertSequenceMenuItem_actionPerformed(e);\r
 268                 }\r
 269             });\r
 270         remove2LeftMenuItem.setText("Remove Left");\r
 271         remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 272                 public void actionPerformed(ActionEvent e) {\r
 273                     remove2LeftMenuItem_actionPerformed(e);\r
 274                 }\r
 275             });\r
 276         remove2RightMenuItem.setText("Remove Right");\r
 277         remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 278                 public void actionPerformed(ActionEvent e) {\r
 279                     remove2RightMenuItem_actionPerformed(e);\r
 280                 }\r
 281             });\r
 282         removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 283         removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 284                 public void actionPerformed(ActionEvent e) {\r
 285                     removeGappedColumnMenuItem_actionPerformed(e);\r
 286                 }\r
 287             });\r
 288         removeAllGapsMenuItem.setText("Remove All Gaps");\r
 289         removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 290                 public void actionPerformed(ActionEvent e) {\r
 291                     removeAllGapsMenuItem_actionPerformed(e);\r
 292                 }\r
 293             });\r
 294         viewBoxesMenuItem.setText("Boxes");\r
 295         viewBoxesMenuItem.setState(true);\r
 296         viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 297                 public void actionPerformed(ActionEvent e) {\r
 298                     viewBoxesMenuItem_actionPerformed(e);\r
 299                 }\r
 300             });\r
 301         viewTextMenuItem.setText("Text");\r
 302         viewTextMenuItem.setState(true);\r
 303         viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 304                 public void actionPerformed(ActionEvent e) {\r
 305                     viewTextMenuItem_actionPerformed(e);\r
 306                 }\r
 307             });\r
 308         sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 309         sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 310                 public void actionPerformed(ActionEvent e) {\r
 311                     sortPairwiseMenuItem_actionPerformed(e);\r
 312                 }\r
 313             });\r
 314         sortIDMenuItem.setText("by ID");\r
 315         sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 316                 public void actionPerformed(ActionEvent e) {\r
 317                     sortIDMenuItem_actionPerformed(e);\r
 318                 }\r
 319             });\r
 320         sortGroupMenuItem.setText("by Group");\r
 321         sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 322                 public void actionPerformed(ActionEvent e) {\r
 323                     sortGroupMenuItem_actionPerformed(e);\r
 324                 }\r
 325             });\r
 326         removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 327         removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 328                 public void actionPerformed(ActionEvent e) {\r
 329                     removeRedundancyMenuItem_actionPerformed(e);\r
 330                 }\r
 331             });\r
 332         pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 333         pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 334                 public void actionPerformed(ActionEvent e) {\r
 335                     pairwiseAlignmentMenuItem_actionPerformed(e);\r
 336                 }\r
 337             });\r
 338         PCAMenuItem.setText("Principal Component Analysis...");\r
 339         PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 340                 public void actionPerformed(ActionEvent e) {\r
 341                     PCAMenuItem_actionPerformed(e);\r
 342                 }\r
 343             });\r
 344         averageDistanceTreeMenuItem.setText(\r
 345             "Average Distance Using % Identity...");\r
 346         averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 347                 public void actionPerformed(ActionEvent e) {\r
 348                     averageDistanceTreeMenuItem_actionPerformed(e);\r
 349                 }\r
 350             });\r
 351         neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
 352         neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 353                 public void actionPerformed(ActionEvent e) {\r
 354                     neighbourTreeMenuItem_actionPerformed(e);\r
 355                 }\r
 356             });\r
 357         clustalAlignMenuItem.setText("Clustal Alignment...");\r
 358         clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 359                 public void actionPerformed(ActionEvent e) {\r
 360                     clustalAlignMenuItem_actionPerformed(e);\r
 361                 }\r
 362             });\r
 363         this.getContentPane().setLayout(borderLayout1);\r
 364         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 365         alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
 366                 public void ancestorAdded(AncestorEvent event) {\r
 367                     alignFrameMenuBar_ancestorAdded(event);\r
 368                 }\r
 369 \r
 370                 public void ancestorRemoved(AncestorEvent event) {\r
 371                 }\r
 372 \r
 373                 public void ancestorMoved(AncestorEvent event) {\r
 374                 }\r
 375             });\r
 376         statusBar.setBackground(Color.white);\r
 377         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 378         statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 379         statusBar.setText("Status bar");\r
 380         outputTextboxMenu.setMnemonic('T');\r
 381         outputTextboxMenu.setText("Output to Textbox");\r
 382         clustalColour.setText("Clustalx");\r
 383 \r
 384         clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
 385                 public void actionPerformed(ActionEvent e) {\r
 386                     clustalColour_actionPerformed(e);\r
 387                 }\r
 388             });\r
 389         zappoColour.setText("Zappo");\r
 390         zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
 391                 public void actionPerformed(ActionEvent e) {\r
 392                     zappoColour_actionPerformed(e);\r
 393                 }\r
 394             });\r
 395         taylorColour.setText("Taylor");\r
 396         taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
 397                 public void actionPerformed(ActionEvent e) {\r
 398                     taylorColour_actionPerformed(e);\r
 399                 }\r
 400             });\r
 401         hydrophobicityColour.setText("Hydrophobicity");\r
 402         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
 403                 public void actionPerformed(ActionEvent e) {\r
 404                     hydrophobicityColour_actionPerformed(e);\r
 405                 }\r
 406             });\r
 407         helixColour.setText("Helix Propensity");\r
 408         helixColour.addActionListener(new java.awt.event.ActionListener() {\r
 409                 public void actionPerformed(ActionEvent e) {\r
 410                     helixColour_actionPerformed(e);\r
 411                 }\r
 412             });\r
 413         strandColour.setText("Strand Propensity");\r
 414         strandColour.addActionListener(new java.awt.event.ActionListener() {\r
 415                 public void actionPerformed(ActionEvent e) {\r
 416                     strandColour_actionPerformed(e);\r
 417                 }\r
 418             });\r
 419         turnColour.setText("Turn Propensity");\r
 420         turnColour.addActionListener(new java.awt.event.ActionListener() {\r
 421                 public void actionPerformed(ActionEvent e) {\r
 422                     turnColour_actionPerformed(e);\r
 423                 }\r
 424             });\r
 425         buriedColour.setText("Buried Index");\r
 426         buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
 427                 public void actionPerformed(ActionEvent e) {\r
 428                     buriedColour_actionPerformed(e);\r
 429                 }\r
 430             });\r
 431         userDefinedColour.setText("User Defined...");\r
 432         userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
 433                 public void actionPerformed(ActionEvent e) {\r
 434                     userDefinedColour_actionPerformed(e);\r
 435                 }\r
 436             });\r
 437         PIDColour.setText("Percentage Identity");\r
 438         PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
 439                 public void actionPerformed(ActionEvent e) {\r
 440                     PIDColour_actionPerformed(e);\r
 441                 }\r
 442             });\r
 443         BLOSUM62Colour.setText("BLOSUM62 Score");\r
 444         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
 445                 public void actionPerformed(ActionEvent e) {\r
 446                     BLOSUM62Colour_actionPerformed(e);\r
 447                 }\r
 448             });\r
 449         avDistanceTreeBlosumMenuItem.setText(\r
 450             "Average Distance Using BLOSUM62...");\r
 451         avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 452                 public void actionPerformed(ActionEvent e) {\r
 453                     avTreeBlosumMenuItem_actionPerformed(e);\r
 454                 }\r
 455             });\r
 456         njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
 457         njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 458                 public void actionPerformed(ActionEvent e) {\r
 459                     njTreeBlosumMenuItem_actionPerformed(e);\r
 460                 }\r
 461             });\r
 462         annotationPanelMenuItem.setActionCommand("");\r
 463         annotationPanelMenuItem.setText("Show Annotations");\r
 464         annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
 465         annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 466                 public void actionPerformed(ActionEvent e) {\r
 467                     annotationPanelMenuItem_actionPerformed(e);\r
 468                 }\r
 469             });\r
 470         colourTextMenuItem.setText("Colour Text");\r
 471         colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 472                 public void actionPerformed(ActionEvent e) {\r
 473                     colourTextMenuItem_actionPerformed(e);\r
 474                 }\r
 475             });\r
 476         htmlMenuItem.setText("HTML");\r
 477         htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 478                 public void actionPerformed(ActionEvent e) {\r
 479                     htmlMenuItem_actionPerformed(e);\r
 480                 }\r
 481             });\r
 482         overviewMenuItem.setText("Overview Window...");\r
 483         overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 484                 public void actionPerformed(ActionEvent e) {\r
 485                     overviewMenuItem_actionPerformed(e);\r
 486                 }\r
 487             });\r
 488         undoMenuItem.setEnabled(false);\r
 489         undoMenuItem.setMnemonic('Z');\r
 490         undoMenuItem.setText("Undo");\r
 491         undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 492                 java.awt.event.KeyEvent.VK_Z,\r
 493                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 494         undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 495                 public void actionPerformed(ActionEvent e) {\r
 496                     undoMenuItem_actionPerformed(e);\r
 497                 }\r
 498             });\r
 499         redoMenuItem.setEnabled(false);\r
 500         redoMenuItem.setMnemonic('0');\r
 501         redoMenuItem.setText("Redo");\r
 502         redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 503                 public void actionPerformed(ActionEvent e) {\r
 504                     redoMenuItem_actionPerformed(e);\r
 505                 }\r
 506             });\r
 507         conservationMenuItem.setText("By Conservation");\r
 508         conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 509                 public void actionPerformed(ActionEvent e) {\r
 510                     conservationMenuItem_actionPerformed(e);\r
 511                 }\r
 512             });\r
 513         noColourmenuItem.setText("None");\r
 514         noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 515                 public void actionPerformed(ActionEvent e) {\r
 516                     noColourmenuItem_actionPerformed(e);\r
 517                 }\r
 518             });\r
 519         wrapMenuItem.setText("Wrap");\r
 520         wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 521                 public void actionPerformed(ActionEvent e) {\r
 522                     wrapMenuItem_actionPerformed(e);\r
 523                 }\r
 524             });\r
 525         printMenuItem.setText("Print");\r
 526         printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 527                 public void actionPerformed(ActionEvent e) {\r
 528                     printMenuItem_actionPerformed(e);\r
 529                 }\r
 530             });\r
 531         renderGapsMenuItem.setText("Show Gaps");\r
 532         renderGapsMenuItem.setState(true);\r
 533         renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 534                 public void actionPerformed(ActionEvent e) {\r
 535                     renderGapsMenuItem_actionPerformed(e);\r
 536                 }\r
 537             });\r
 538         findMenuItem.setText("Find...");\r
 539         findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 540                 java.awt.event.KeyEvent.VK_F,\r
 541                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 542         findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 543                 public void actionPerformed(ActionEvent e) {\r
 544                     findMenuItem_actionPerformed(e);\r
 545                 }\r
 546             });\r
 547         searchMenu.setText("Search");\r
 548 \r
 549         abovePIDThreshold.setText("Above Identity Threshold");\r
 550         abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
 551                 public void actionPerformed(ActionEvent e) {\r
 552                     abovePIDThreshold_actionPerformed(e);\r
 553                 }\r
 554             });\r
 555         sequenceFeatures.setText("Sequence Features");\r
 556         sequenceFeatures.addActionListener(new ActionListener() {\r
 557                 public void actionPerformed(ActionEvent actionEvent) {\r
 558                     sequenceFeatures_actionPerformed(actionEvent);\r
 559                 }\r
 560             });\r
 561         nucleotideColour.setText("Nucleotide");\r
 562         nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
 563                 public void actionPerformed(ActionEvent e) {\r
 564                     nucleotideColour_actionPerformed(e);\r
 565                 }\r
 566             });\r
 567         deleteGroups.setText("Undefine groups");\r
 568         deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
 569                 public void actionPerformed(ActionEvent e) {\r
 570                     deleteGroups_actionPerformed(e);\r
 571                 }\r
 572             });\r
 573         copy.setText("Copy");\r
 574         copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 575                 java.awt.event.KeyEvent.VK_C,\r
 576                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 577         copy.setMnemonic(KeyEvent.VK_C);\r
 578 \r
 579         copy.addActionListener(new java.awt.event.ActionListener() {\r
 580                 public void actionPerformed(ActionEvent e) {\r
 581                     copy_actionPerformed(e);\r
 582                 }\r
 583             });\r
 584         cut.setText("Cut");\r
 585         cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 586                 java.awt.event.KeyEvent.VK_X,\r
 587                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 588         cut.setMnemonic(KeyEvent.VK_X);\r
 589         cut.addActionListener(new java.awt.event.ActionListener() {\r
 590                 public void actionPerformed(ActionEvent e) {\r
 591                     cut_actionPerformed(e);\r
 592                 }\r
 593             });\r
 594         delete.setText("Delete");\r
 595         delete.addActionListener(new java.awt.event.ActionListener() {\r
 596                 public void actionPerformed(ActionEvent e) {\r
 597                     delete_actionPerformed(e);\r
 598                 }\r
 599             });\r
 600         jMenu1.setMnemonic('V');\r
 601         jMenu1.setText("Paste");\r
 602         pasteNew.setText("To New Alignment");\r
 603         pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 604                 java.awt.event.KeyEvent.VK_V,\r
 605                 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 606         pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
 607                 public void actionPerformed(ActionEvent e) {\r
 608                     pasteNew_actionPerformed(e);\r
 609                 }\r
 610             });\r
 611         pasteThis.setText("Add To This Alignment");\r
 612         pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
 613                 public void actionPerformed(ActionEvent e) {\r
 614                     pasteThis_actionPerformed(e);\r
 615                 }\r
 616             });\r
 617         applyToAllGroups.setText("Apply Colour To All Groups");\r
 618         applyToAllGroups.setState(true);\r
 619         applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {\r
 620                 public void actionPerformed(ActionEvent e) {\r
 621                     applyToAllGroups_actionPerformed(e);\r
 622                 }\r
 623             });\r
 624         createPNG.addActionListener(new java.awt.event.ActionListener() {\r
 625                 public void actionPerformed(ActionEvent e) {\r
 626                     createPNG_actionPerformed(e);\r
 627                 }\r
 628             });\r
 629         createPNG.setActionCommand("Save As PNG Image");\r
 630         createPNG.setText("PNG");\r
 631         font.setText("Font...");\r
 632         font.addActionListener(new java.awt.event.ActionListener() {\r
 633                 public void actionPerformed(ActionEvent e) {\r
 634                     font_actionPerformed(e);\r
 635                 }\r
 636             });\r
 637         fullSeqId.setText("Show Full Sequence ID");\r
 638         fullSeqId.setState(true);\r
 639         fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
 640                 public void actionPerformed(ActionEvent e) {\r
 641                     fullSeqId_actionPerformed(e);\r
 642                 }\r
 643             });\r
 644         epsFile.setText("EPS");\r
 645         epsFile.addActionListener(new java.awt.event.ActionListener() {\r
 646                 public void actionPerformed(ActionEvent e) {\r
 647                     epsFile_actionPerformed(e);\r
 648                 }\r
 649             });\r
 650         LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 651         LoadtreeMenuItem.setText("Load Assocated Tree");\r
 652         LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 653                 public void actionPerformed(ActionEvent e) {\r
 654                     LoadtreeMenuItem_actionPerformed(e);\r
 655                 }\r
 656             });\r
 657         jnet.setText("JNet...");\r
 658         jnet.addActionListener(new java.awt.event.ActionListener() {\r
 659                 public void actionPerformed(ActionEvent e) {\r
 660                     jpred_actionPerformed(e);\r
 661                 }\r
 662             });\r
 663         scaleAbove.setVisible(false);\r
 664         scaleAbove.setText("Scale Above");\r
 665         scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
 666                 public void actionPerformed(ActionEvent e) {\r
 667                     scaleAbove_actionPerformed(e);\r
 668                 }\r
 669             });\r
 670         scaleLeft.setVisible(false);\r
 671         scaleLeft.setSelected(true);\r
 672         scaleLeft.setText("Scale Left");\r
 673         scaleLeft.addActionListener(new java.awt.event.ActionListener() {\r
 674                 public void actionPerformed(ActionEvent e) {\r
 675                     scaleLeft_actionPerformed(e);\r
 676                 }\r
 677             });\r
 678         scaleRight.setVisible(false);\r
 679         scaleRight.setSelected(true);\r
 680         scaleRight.setText("Scale Right");\r
 681         scaleRight.addActionListener(new java.awt.event.ActionListener() {\r
 682                 public void actionPerformed(ActionEvent e) {\r
 683                     scaleRight_actionPerformed(e);\r
 684                 }\r
 685             });\r
 686         modifyPID.setText("Modify Identity Threshold...");\r
 687         modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
 688                 public void actionPerformed(ActionEvent e) {\r
 689                     modifyPID_actionPerformed(e);\r
 690                 }\r
 691             });\r
 692         modifyConservation.setText("Modify Conservation Threshold...");\r
 693         modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
 694                 public void actionPerformed(ActionEvent e) {\r
 695                     modifyConservation_actionPerformed(e);\r
 696                 }\r
 697             });\r
 698         sortByTreeMenu.setText("By Tree Order");\r
 699         sort.setText("Sort");\r
 700         calculate.setText("Calculate Tree");\r
 701         msaAlignMenuItem.setText("Muscle Alignment...");\r
 702         msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 703                 public void actionPerformed(ActionEvent e) {\r
 704                     msaAlignMenuItem_actionPerformed(e);\r
 705                 }\r
 706             });\r
 707         jMenu2.setText("Export");\r
 708         padGapsMenuitem.setText("Pad Gaps");\r
 709         padGapsMenuitem.addActionListener(new ActionListener() {\r
 710                 public void actionPerformed(ActionEvent e) {\r
 711                     padGapsMenuitem_actionPerformed(e);\r
 712                 }\r
 713             });\r
 714         ClustalRealign.setText("Clustal Realign...");\r
 715         ClustalRealign.addActionListener(new ActionListener() {\r
 716                 public void actionPerformed(ActionEvent e) {\r
 717                     ClustalRealign_actionPerformed(e);\r
 718                 }\r
 719             });\r
 720         alignFrameMenuBar.add(fileMenu);\r
 721         alignFrameMenuBar.add(editMenu);\r
 722         alignFrameMenuBar.add(searchMenu);\r
 723         alignFrameMenuBar.add(viewMenu);\r
 724         alignFrameMenuBar.add(colourMenu);\r
 725         alignFrameMenuBar.add(calculateMenu);\r
 726         fileMenu.add(saveAlignmentMenu);\r
 727         fileMenu.add(jMenu2);\r
 728         fileMenu.add(outputTextboxMenu);\r
 729         fileMenu.add(printMenuItem);\r
 730         fileMenu.addSeparator();\r
 731         fileMenu.add(LoadtreeMenuItem);\r
 732         fileMenu.addSeparator();\r
 733         fileMenu.add(closeMenuItem);\r
 734         editMenu.add(undoMenuItem);\r
 735         editMenu.add(redoMenuItem);\r
 736         editMenu.add(cut);\r
 737         editMenu.add(copy);\r
 738         editMenu.add(jMenu1);\r
 739         editMenu.add(delete);\r
 740         editMenu.addSeparator();\r
 741         editMenu.add(selectAllSequenceMenuItem);\r
 742         editMenu.add(deselectAllSequenceMenuItem);\r
 743         editMenu.add(invertSequenceMenuItem);\r
 744         editMenu.add(deleteGroups);\r
 745         editMenu.addSeparator();\r
 746         editMenu.add(remove2LeftMenuItem);\r
 747         editMenu.add(remove2RightMenuItem);\r
 748         editMenu.add(removeGappedColumnMenuItem);\r
 749         editMenu.add(removeAllGapsMenuItem);\r
 750         editMenu.add(removeRedundancyMenuItem);\r
 751         editMenu.addSeparator();\r
 752         editMenu.add(padGapsMenuitem);\r
 753         searchMenu.add(findMenuItem);\r
 754         viewMenu.add(font);\r
 755         viewMenu.addSeparator();\r
 756         viewMenu.add(wrapMenuItem);\r
 757         viewMenu.add(fullSeqId);\r
 758         viewMenu.add(scaleAbove);\r
 759         viewMenu.add(scaleLeft);\r
 760         viewMenu.add(scaleRight);\r
 761         viewMenu.add(viewBoxesMenuItem);\r
 762         viewMenu.add(viewTextMenuItem);\r
 763         viewMenu.add(colourTextMenuItem);\r
 764         viewMenu.add(renderGapsMenuItem);\r
 765         viewMenu.add(annotationPanelMenuItem);\r
 766         viewMenu.add(sequenceFeatures);\r
 767         viewMenu.addSeparator();\r
 768         viewMenu.add(overviewMenuItem);\r
 769         colourMenu.add(applyToAllGroups);\r
 770         colourMenu.addSeparator();\r
 771         colourMenu.add(noColourmenuItem);\r
 772         colourMenu.add(clustalColour);\r
 773         colourMenu.add(BLOSUM62Colour);\r
 774         colourMenu.add(PIDColour);\r
 775         colourMenu.add(zappoColour);\r
 776         colourMenu.add(taylorColour);\r
 777         colourMenu.add(hydrophobicityColour);\r
 778         colourMenu.add(helixColour);\r
 779         colourMenu.add(strandColour);\r
 780         colourMenu.add(turnColour);\r
 781         colourMenu.add(buriedColour);\r
 782         colourMenu.add(nucleotideColour);\r
 783         colourMenu.add(userDefinedColour);\r
 784         colourMenu.addSeparator();\r
 785         colourMenu.add(conservationMenuItem);\r
 786         colourMenu.add(modifyConservation);\r
 787         colourMenu.add(abovePIDThreshold);\r
 788         colourMenu.add(modifyPID);\r
 789         calculateMenu.add(sort);\r
 790         calculateMenu.add(calculate);\r
 791         calculateMenu.addSeparator();\r
 792         calculateMenu.add(pairwiseAlignmentMenuItem);\r
 793         calculateMenu.add(PCAMenuItem);\r
 794         calculateMenu.addSeparator();\r
 795         calculateMenu.add(webService);\r
 796         webService.add(clustalAlignMenuItem);\r
 797         webService.add(msaAlignMenuItem);\r
 798         webService.add(jnet);\r
 799         webService.add(ClustalRealign);\r
 800         this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 801         jMenu1.add(pasteNew);\r
 802         jMenu1.add(pasteThis);\r
 803         sort.add(sortIDMenuItem);\r
 804         sort.add(sortGroupMenuItem);\r
 805         sort.add(sortPairwiseMenuItem);\r
 806         calculate.add(averageDistanceTreeMenuItem);\r
 807         calculate.add(neighbourTreeMenuItem);\r
 808         calculate.add(avDistanceTreeBlosumMenuItem);\r
 809         calculate.add(njTreeBlosumMenuItem);\r
 810         jMenu2.add(htmlMenuItem);\r
 811         jMenu2.add(epsFile);\r
 812         jMenu2.add(createPNG);\r
 813     }\r
 814 \r
 815     protected void outputText_actionPerformed(ActionEvent e) {\r
 816     }\r
 817 \r
 818     protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
 819     }\r
 820 \r
 821     protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
 822     }\r
 823 \r
 824     protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
 825     }\r
 826 \r
 827     protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
 828     }\r
 829 \r
 830     protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 831     }\r
 832 \r
 833     protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 834     }\r
 835 \r
 836     protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 837     }\r
 838 \r
 839     protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
 840     }\r
 841 \r
 842     protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
 843     }\r
 844 \r
 845     protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
 846     }\r
 847 \r
 848     protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
 849     }\r
 850 \r
 851     protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
 852     }\r
 853 \r
 854     protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
 855     }\r
 856 \r
 857     protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
 858     }\r
 859 \r
 860     protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
 861     }\r
 862 \r
 863     protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
 864     }\r
 865 \r
 866     protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
 867     }\r
 868 \r
 869     protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
 870     }\r
 871 \r
 872     protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
 873     }\r
 874 \r
 875     protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
 876     }\r
 877 \r
 878     protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
 879     }\r
 880 \r
 881     protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
 882     }\r
 883 \r
 884     protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
 885     }\r
 886 \r
 887     protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
 888     }\r
 889 \r
 890     protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
 891     }\r
 892 \r
 893     protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 894     }\r
 895 \r
 896     protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 897     }\r
 898 \r
 899     protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
 900     }\r
 901 \r
 902     protected void clustalColour_actionPerformed(ActionEvent e) {\r
 903     }\r
 904 \r
 905     protected void zappoColour_actionPerformed(ActionEvent e) {\r
 906     }\r
 907 \r
 908     protected void taylorColour_actionPerformed(ActionEvent e) {\r
 909     }\r
 910 \r
 911     protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
 912     }\r
 913 \r
 914     protected void helixColour_actionPerformed(ActionEvent e) {\r
 915     }\r
 916 \r
 917     protected void strandColour_actionPerformed(ActionEvent e) {\r
 918     }\r
 919 \r
 920     protected void turnColour_actionPerformed(ActionEvent e) {\r
 921     }\r
 922 \r
 923     protected void buriedColour_actionPerformed(ActionEvent e) {\r
 924     }\r
 925 \r
 926     protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
 927     }\r
 928 \r
 929     protected void PIDColour_actionPerformed(ActionEvent e) {\r
 930     }\r
 931 \r
 932     protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
 933     }\r
 934 \r
 935     protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
 936     }\r
 937 \r
 938     protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
 939     }\r
 940 \r
 941     protected void printMenuItem_actionPerformed(ActionEvent e) {\r
 942     }\r
 943 \r
 944     protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
 945     }\r
 946 \r
 947     protected void findMenuItem_actionPerformed(ActionEvent e) {\r
 948     }\r
 949 \r
 950     protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
 951     }\r
 952 \r
 953     public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
 954     }\r
 955 \r
 956     protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
 957     }\r
 958 \r
 959     protected void deleteGroups_actionPerformed(ActionEvent e) {\r
 960     }\r
 961 \r
 962     protected void copy_actionPerformed(ActionEvent e) {\r
 963     }\r
 964 \r
 965     protected void cut_actionPerformed(ActionEvent e) {\r
 966     }\r
 967 \r
 968     protected void delete_actionPerformed(ActionEvent e) {\r
 969     }\r
 970 \r
 971     protected void pasteNew_actionPerformed(ActionEvent e) {\r
 972     }\r
 973 \r
 974     protected void pasteThis_actionPerformed(ActionEvent e) {\r
 975     }\r
 976 \r
 977     protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
 978     }\r
 979 \r
 980     protected void createPNG_actionPerformed(ActionEvent e) {\r
 981     }\r
 982 \r
 983     protected void font_actionPerformed(ActionEvent e) {\r
 984     }\r
 985 \r
 986     protected void fullSeqId_actionPerformed(ActionEvent e) {\r
 987     }\r
 988 \r
 989     protected void epsFile_actionPerformed(ActionEvent e) {\r
 990     }\r
 991 \r
 992     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
 993     }\r
 994 \r
 995     protected void jpred_actionPerformed(ActionEvent e) {\r
 996     }\r
 997 \r
 998     protected void scaleAbove_actionPerformed(ActionEvent e) {\r
 999     }\r
1000 \r
1001     protected void scaleLeft_actionPerformed(ActionEvent e) {\r
1002     }\r
1003 \r
1004     protected void scaleRight_actionPerformed(ActionEvent e) {\r
1005     }\r
1006 \r
1007     protected void modifyPID_actionPerformed(ActionEvent e) {\r
1008     }\r
1009 \r
1010     protected void modifyConservation_actionPerformed(ActionEvent e) {\r
1011     }\r
1012 \r
1013     protected void preferences_actionPerformed(ActionEvent e) {\r
1014     }\r
1015 \r
1016     protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
1017     }\r
1018 \r
1019     protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
1020     }\r
1021 \r
1022     protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
1023     }\r
1024 \r
1025     protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
1026     }\r
1027 \r
1028     protected void ClustalRealign_actionPerformed(ActionEvent e) {\r
1029     }\r
1030 }\r