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 java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 \r
  26 import jalview.gui.*;\r
  27 import jalview.schemes.*;\r
  28 \r
  29 public class GAlignFrame\r
  30     extends JInternalFrame\r
  31 {\r
  32   protected JMenuBar alignFrameMenuBar = new JMenuBar();\r
  33   protected JMenu fileMenu = new JMenu();\r
  34   protected JMenuItem closeMenuItem = new JMenuItem();\r
  35   protected JMenu editMenu = new JMenu();\r
  36   protected JMenu viewMenu = new JMenu();\r
  37   protected JMenu colourMenu = new JMenu();\r
  38   protected JMenu calculateMenu = new JMenu();\r
  39   protected JMenu webService = new JMenu();\r
  40   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
  41   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
  42   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
  43   protected JMenuItem remove2LeftMenuItem = new JMenuItem();\r
  44   protected JMenuItem remove2RightMenuItem = new JMenuItem();\r
  45   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();\r
  46   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();\r
  47   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
  48   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();\r
  49   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();\r
  50   protected JMenuItem sortIDMenuItem = new JMenuItem();\r
  51   protected JMenuItem sortGroupMenuItem = new JMenuItem();\r
  52   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();\r
  53   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();\r
  54   protected JMenuItem PCAMenuItem = new JMenuItem();\r
  55   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
  56   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
  57   protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
  58   BorderLayout borderLayout1 = new BorderLayout();\r
  59   public JLabel statusBar = new JLabel();\r
  60   protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
  61   protected JMenu outputTextboxMenu = new JMenu();\r
  62   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  63   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  64   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  65   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  66       JRadioButtonMenuItem();\r
  67   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  68   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  71   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  73   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  74   JMenuItem njTreeBlosumMenuItem = new JMenuItem();\r
  75   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();\r
  76   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
  77   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();\r
  78   JMenuItem htmlMenuItem = new JMenuItem();\r
  79   JMenuItem overviewMenuItem = new JMenuItem();\r
  80   protected JMenuItem undoMenuItem = new JMenuItem();\r
  81   protected JMenuItem redoMenuItem = new JMenuItem();\r
  82   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  84   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
  85   JMenuItem printMenuItem = new JMenuItem();\r
  86   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
  87   JMenuItem findMenuItem = new JMenuItem();\r
  88   JMenu searchMenu = new JMenu();\r
  89   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
  90   public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
  91   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
  92   JMenuItem deleteGroups = new JMenuItem();\r
  93   JMenuItem delete = new JMenuItem();\r
  94   JMenuItem copy = new JMenuItem();\r
  95   JMenuItem cut = new JMenuItem();\r
  96   JMenu jMenu1 = new JMenu();\r
  97   JMenuItem pasteNew = new JMenuItem();\r
  98   JMenuItem pasteThis = new JMenuItem();\r
  99   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
 100   JMenuItem createPNG = new JMenuItem();\r
 101   protected JMenuItem font = new JMenuItem();\r
 102   public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
 103   JMenuItem epsFile = new JMenuItem();\r
 104   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
 105   JMenuItem jnet = new JMenuItem();\r
 106   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
 107   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
 108   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
 109   JMenuItem modifyPID = new JMenuItem();\r
 110   JMenuItem modifyConservation = new JMenuItem();\r
 111   protected JMenu sortByTreeMenu = new JMenu();\r
 112   protected JMenu sort = new JMenu();\r
 113   JMenu calculate = new JMenu();\r
 114   JMenuItem msaAlignMenuItem = new JMenuItem();\r
 115   JMenu jMenu2 = new JMenu();\r
 116   JMenuItem padGapsMenuitem = new JMenuItem();\r
 117   JMenuItem ClustalRealign = new JMenuItem();\r
 118 \r
 119   public GAlignFrame()\r
 120   {\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     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 137 \r
 138 \r
 139     try\r
 140     {\r
 141       jbInit();\r
 142       setJMenuBar(alignFrameMenuBar);\r
 143 \r
 144       JMenuItem item;\r
 145 \r
 146       // dynamically fill save as menu with available formats\r
 147       for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
 148       {\r
 149         item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
 150                              elementAt(\r
 151                                  i));\r
 152         item.addActionListener(new java.awt.event.ActionListener()\r
 153         {\r
 154           public void actionPerformed(ActionEvent e)\r
 155           {\r
 156             outputText_actionPerformed(e);\r
 157           }\r
 158         });\r
 159 \r
 160         outputTextboxMenu.add(item);\r
 161       }\r
 162     }\r
 163     catch (Exception e)\r
 164     {\r
 165     }\r
 166 \r
 167   }\r
 168 \r
 169   public void setColourSelected(String defaultColour)\r
 170   {\r
 171 \r
 172     if (defaultColour != null)\r
 173     {\r
 174       int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
 175 \r
 176       switch (index)\r
 177       {\r
 178         case ColourSchemeProperty.NONE:\r
 179               noColourmenuItem.setSelected(true);\r
 180               break;\r
 181         case ColourSchemeProperty.CLUSTAL:\r
 182           clustalColour.setSelected(true);\r
 183 \r
 184           break;\r
 185 \r
 186         case ColourSchemeProperty.BLOSUM:\r
 187           BLOSUM62Colour.setSelected(true);\r
 188 \r
 189           break;\r
 190 \r
 191         case ColourSchemeProperty.PID:\r
 192           PIDColour.setSelected(true);\r
 193 \r
 194           break;\r
 195 \r
 196         case ColourSchemeProperty.ZAPPO:\r
 197           zappoColour.setSelected(true);\r
 198 \r
 199           break;\r
 200 \r
 201         case ColourSchemeProperty.TAYLOR:\r
 202           taylorColour.setSelected(true);\r
 203           break;\r
 204 \r
 205         case ColourSchemeProperty.HYDROPHOBIC:\r
 206           hydrophobicityColour.setSelected(true);\r
 207 \r
 208           break;\r
 209 \r
 210         case ColourSchemeProperty.HELIX:\r
 211           helixColour.setSelected(true);\r
 212 \r
 213           break;\r
 214 \r
 215         case ColourSchemeProperty.STRAND:\r
 216           strandColour.setSelected(true);\r
 217 \r
 218           break;\r
 219 \r
 220         case ColourSchemeProperty.TURN:\r
 221           turnColour.setSelected(true);\r
 222 \r
 223           break;\r
 224 \r
 225         case ColourSchemeProperty.BURIED:\r
 226           buriedColour.setSelected(true);\r
 227 \r
 228           break;\r
 229 \r
 230         case ColourSchemeProperty.NUCLEOTIDE:\r
 231           nucleotideColour.setSelected(true);\r
 232 \r
 233           break;\r
 234 \r
 235         case ColourSchemeProperty.USER_DEFINED:\r
 236           userDefinedColour.setSelected(true);\r
 237 \r
 238           break;\r
 239       }\r
 240     }\r
 241 \r
 242   }\r
 243 \r
 244   private void jbInit()\r
 245       throws Exception\r
 246   {\r
 247     fileMenu.setMnemonic('F');\r
 248     fileMenu.setText("File");\r
 249     saveAlignmentMenu.setMnemonic('L');\r
 250     saveAlignmentMenu.setText("Save As");\r
 251     saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
 252         awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
 253     saveAlignmentMenu.addActionListener(new ActionListener()\r
 254     {\r
 255       public void actionPerformed(ActionEvent e)\r
 256       {\r
 257         saveAlignmentMenu_actionPerformed(e);\r
 258       }\r
 259     });\r
 260     closeMenuItem.setMnemonic('C');\r
 261     closeMenuItem.setText("Close");\r
 262     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 263     {\r
 264       public void actionPerformed(ActionEvent e)\r
 265       {\r
 266         closeMenuItem_actionPerformed(e);\r
 267       }\r
 268     });\r
 269     editMenu.setText("Edit");\r
 270     viewMenu.setText("View");\r
 271     colourMenu.setText("Colour");\r
 272     calculateMenu.setText("Calculate");\r
 273     webService.setText("Web Service");\r
 274     selectAllSequenceMenuItem.setText("Select all");\r
 275     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 276         java.awt.event.KeyEvent.VK_A,\r
 277         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 278     selectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 279                                                 ActionListener()\r
 280     {\r
 281       public void actionPerformed(ActionEvent e)\r
 282       {\r
 283         selectAllSequenceMenuItem_actionPerformed(e);\r
 284       }\r
 285     });\r
 286     deselectAllSequenceMenuItem.setText("Deselect All");\r
 287     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.\r
 288                                                getKeyStroke(\r
 289         java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
 290     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.\r
 291                                                   ActionListener()\r
 292     {\r
 293       public void actionPerformed(ActionEvent e)\r
 294       {\r
 295         deselectAllSequenceMenuItem_actionPerformed(e);\r
 296       }\r
 297     });\r
 298     invertSequenceMenuItem.setText("Invert Selection");\r
 299     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 300     {\r
 301       public void actionPerformed(ActionEvent e)\r
 302       {\r
 303         invertSequenceMenuItem_actionPerformed(e);\r
 304       }\r
 305     });\r
 306     remove2LeftMenuItem.setText("Remove Left");\r
 307     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 308     {\r
 309       public void actionPerformed(ActionEvent e)\r
 310       {\r
 311         remove2LeftMenuItem_actionPerformed(e);\r
 312       }\r
 313     });\r
 314     remove2RightMenuItem.setText("Remove Right");\r
 315     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 316     {\r
 317       public void actionPerformed(ActionEvent e)\r
 318       {\r
 319         remove2RightMenuItem_actionPerformed(e);\r
 320       }\r
 321     });\r
 322     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
 323     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
 324                                                  ActionListener()\r
 325     {\r
 326       public void actionPerformed(ActionEvent e)\r
 327       {\r
 328         removeGappedColumnMenuItem_actionPerformed(e);\r
 329       }\r
 330     });\r
 331     removeAllGapsMenuItem.setText("Remove All Gaps");\r
 332     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 333     {\r
 334       public void actionPerformed(ActionEvent e)\r
 335       {\r
 336         removeAllGapsMenuItem_actionPerformed(e);\r
 337       }\r
 338     });\r
 339     viewBoxesMenuItem.setText("Boxes");\r
 340     viewBoxesMenuItem.setState(true);\r
 341     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 342     {\r
 343       public void actionPerformed(ActionEvent e)\r
 344       {\r
 345         viewBoxesMenuItem_actionPerformed(e);\r
 346       }\r
 347     });\r
 348     viewTextMenuItem.setText("Text");\r
 349     viewTextMenuItem.setState(true);\r
 350     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 351     {\r
 352       public void actionPerformed(ActionEvent e)\r
 353       {\r
 354         viewTextMenuItem_actionPerformed(e);\r
 355       }\r
 356     });\r
 357     sortPairwiseMenuItem.setText("by Pairwise Identity");\r
 358     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 359     {\r
 360       public void actionPerformed(ActionEvent e)\r
 361       {\r
 362         sortPairwiseMenuItem_actionPerformed(e);\r
 363       }\r
 364     });\r
 365     sortIDMenuItem.setText("by ID");\r
 366     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 367     {\r
 368       public void actionPerformed(ActionEvent e)\r
 369       {\r
 370         sortIDMenuItem_actionPerformed(e);\r
 371       }\r
 372     });\r
 373     sortGroupMenuItem.setText("by Group");\r
 374     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 375     {\r
 376       public void actionPerformed(ActionEvent e)\r
 377       {\r
 378         sortGroupMenuItem_actionPerformed(e);\r
 379       }\r
 380     });\r
 381     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
 382     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
 383                                                ActionListener()\r
 384     {\r
 385       public void actionPerformed(ActionEvent e)\r
 386       {\r
 387         removeRedundancyMenuItem_actionPerformed(e);\r
 388       }\r
 389     });\r
 390     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
 391     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.\r
 392                                                 ActionListener()\r
 393     {\r
 394       public void actionPerformed(ActionEvent e)\r
 395       {\r
 396         pairwiseAlignmentMenuItem_actionPerformed(e);\r
 397       }\r
 398     });\r
 399     PCAMenuItem.setText("Principal Component Analysis");\r
 400     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 401     {\r
 402       public void actionPerformed(ActionEvent e)\r
 403       {\r
 404         PCAMenuItem_actionPerformed(e);\r
 405       }\r
 406     });\r
 407     averageDistanceTreeMenuItem.setText(\r
 408         "Average Distance Using % Identity");\r
 409     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.\r
 410                                                   ActionListener()\r
 411     {\r
 412       public void actionPerformed(ActionEvent e)\r
 413       {\r
 414         averageDistanceTreeMenuItem_actionPerformed(e);\r
 415       }\r
 416     });\r
 417     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");\r
 418     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 419     {\r
 420       public void actionPerformed(ActionEvent e)\r
 421       {\r
 422         neighbourTreeMenuItem_actionPerformed(e);\r
 423       }\r
 424     });\r
 425     clustalAlignMenuItem.setText("Clustal Alignment");\r
 426     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 427     {\r
 428       public void actionPerformed(ActionEvent e)\r
 429       {\r
 430         clustalAlignMenuItem_actionPerformed(e);\r
 431       }\r
 432     });\r
 433     this.getContentPane().setLayout(borderLayout1);\r
 434     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 435     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
 436     {\r
 437       public void ancestorAdded(AncestorEvent event)\r
 438       {\r
 439         alignFrameMenuBar_ancestorAdded(event);\r
 440       }\r
 441 \r
 442       public void ancestorRemoved(AncestorEvent event)\r
 443       {\r
 444       }\r
 445 \r
 446       public void ancestorMoved(AncestorEvent event)\r
 447       {\r
 448       }\r
 449     });\r
 450     statusBar.setBackground(Color.white);\r
 451     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 452     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
 453     statusBar.setText("Status bar");\r
 454     outputTextboxMenu.setMnemonic('T');\r
 455     outputTextboxMenu.setText("Output to Textbox");\r
 456     clustalColour.setText("Clustalx");\r
 457 \r
 458     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 459     {\r
 460       public void actionPerformed(ActionEvent e)\r
 461       {\r
 462         clustalColour_actionPerformed(e);\r
 463       }\r
 464     });\r
 465     zappoColour.setText("Zappo");\r
 466     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         zappoColour_actionPerformed(e);\r
 471       }\r
 472     });\r
 473     taylorColour.setText("Taylor");\r
 474     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 475     {\r
 476       public void actionPerformed(ActionEvent e)\r
 477       {\r
 478         taylorColour_actionPerformed(e);\r
 479       }\r
 480     });\r
 481     hydrophobicityColour.setText("Hydrophobicity");\r
 482     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 483     {\r
 484       public void actionPerformed(ActionEvent e)\r
 485       {\r
 486         hydrophobicityColour_actionPerformed(e);\r
 487       }\r
 488     });\r
 489     helixColour.setText("Helix Propensity");\r
 490     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 491     {\r
 492       public void actionPerformed(ActionEvent e)\r
 493       {\r
 494         helixColour_actionPerformed(e);\r
 495       }\r
 496     });\r
 497     strandColour.setText("Strand Propensity");\r
 498     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 499     {\r
 500       public void actionPerformed(ActionEvent e)\r
 501       {\r
 502         strandColour_actionPerformed(e);\r
 503       }\r
 504     });\r
 505     turnColour.setText("Turn Propensity");\r
 506     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 507     {\r
 508       public void actionPerformed(ActionEvent e)\r
 509       {\r
 510         turnColour_actionPerformed(e);\r
 511       }\r
 512     });\r
 513     buriedColour.setText("Buried Index");\r
 514     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 515     {\r
 516       public void actionPerformed(ActionEvent e)\r
 517       {\r
 518         buriedColour_actionPerformed(e);\r
 519       }\r
 520     });\r
 521     userDefinedColour.setText("User Defined...");\r
 522     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 523     {\r
 524       public void actionPerformed(ActionEvent e)\r
 525       {\r
 526         userDefinedColour_actionPerformed(e);\r
 527       }\r
 528     });\r
 529     PIDColour.setText("Percentage Identity");\r
 530     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 531     {\r
 532       public void actionPerformed(ActionEvent e)\r
 533       {\r
 534         PIDColour_actionPerformed(e);\r
 535       }\r
 536     });\r
 537     BLOSUM62Colour.setText("BLOSUM62 Score");\r
 538     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 539     {\r
 540       public void actionPerformed(ActionEvent e)\r
 541       {\r
 542         BLOSUM62Colour_actionPerformed(e);\r
 543       }\r
 544     });\r
 545     avDistanceTreeBlosumMenuItem.setText(\r
 546         "Average Distance Using BLOSUM62");\r
 547     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
 548         ActionListener()\r
 549     {\r
 550       public void actionPerformed(ActionEvent e)\r
 551       {\r
 552         avTreeBlosumMenuItem_actionPerformed(e);\r
 553       }\r
 554     });\r
 555     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
 556     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 557     {\r
 558       public void actionPerformed(ActionEvent e)\r
 559       {\r
 560         njTreeBlosumMenuItem_actionPerformed(e);\r
 561       }\r
 562     });\r
 563     annotationPanelMenuItem.setActionCommand("");\r
 564     annotationPanelMenuItem.setText("Show Annotations");\r
 565     annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
 566     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 567     {\r
 568       public void actionPerformed(ActionEvent e)\r
 569       {\r
 570         annotationPanelMenuItem_actionPerformed(e);\r
 571       }\r
 572     });\r
 573     colourTextMenuItem.setText("Colour Text");\r
 574     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 575     {\r
 576       public void actionPerformed(ActionEvent e)\r
 577       {\r
 578         colourTextMenuItem_actionPerformed(e);\r
 579       }\r
 580     });\r
 581     htmlMenuItem.setText("HTML");\r
 582     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 583     {\r
 584       public void actionPerformed(ActionEvent e)\r
 585       {\r
 586         htmlMenuItem_actionPerformed(e);\r
 587       }\r
 588     });\r
 589     overviewMenuItem.setText("Overview Window");\r
 590     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 591     {\r
 592       public void actionPerformed(ActionEvent e)\r
 593       {\r
 594         overviewMenuItem_actionPerformed(e);\r
 595       }\r
 596     });\r
 597     undoMenuItem.setEnabled(false);\r
 598     undoMenuItem.setMnemonic('Z');\r
 599     undoMenuItem.setText("Undo");\r
 600     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 601         java.awt.event.KeyEvent.VK_Z,\r
 602         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 603     undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 604     {\r
 605       public void actionPerformed(ActionEvent e)\r
 606       {\r
 607         undoMenuItem_actionPerformed(e);\r
 608       }\r
 609     });\r
 610     redoMenuItem.setEnabled(false);\r
 611     redoMenuItem.setMnemonic('0');\r
 612     redoMenuItem.setText("Redo");\r
 613     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 614     {\r
 615       public void actionPerformed(ActionEvent e)\r
 616       {\r
 617         redoMenuItem_actionPerformed(e);\r
 618       }\r
 619     });\r
 620     conservationMenuItem.setText("By Conservation");\r
 621     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 622     {\r
 623       public void actionPerformed(ActionEvent e)\r
 624       {\r
 625         conservationMenuItem_actionPerformed(e);\r
 626       }\r
 627     });\r
 628     noColourmenuItem.setText("None");\r
 629     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 630     {\r
 631       public void actionPerformed(ActionEvent e)\r
 632       {\r
 633         noColourmenuItem_actionPerformed(e);\r
 634       }\r
 635     });\r
 636     wrapMenuItem.setText("Wrap");\r
 637     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 638     {\r
 639       public void actionPerformed(ActionEvent e)\r
 640       {\r
 641         wrapMenuItem_actionPerformed(e);\r
 642       }\r
 643     });\r
 644     printMenuItem.setText("Print");\r
 645     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 646     {\r
 647       public void actionPerformed(ActionEvent e)\r
 648       {\r
 649         printMenuItem_actionPerformed(e);\r
 650       }\r
 651     });\r
 652     renderGapsMenuItem.setText("Show Gaps");\r
 653     renderGapsMenuItem.setState(true);\r
 654     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 655     {\r
 656       public void actionPerformed(ActionEvent e)\r
 657       {\r
 658         renderGapsMenuItem_actionPerformed(e);\r
 659       }\r
 660     });\r
 661     findMenuItem.setText("Find...");\r
 662     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 663         java.awt.event.KeyEvent.VK_F,\r
 664         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 665     findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 666     {\r
 667       public void actionPerformed(ActionEvent e)\r
 668       {\r
 669         findMenuItem_actionPerformed(e);\r
 670       }\r
 671     });\r
 672     searchMenu.setText("Search");\r
 673 \r
 674     abovePIDThreshold.setText("Above Identity Threshold");\r
 675     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
 676     {\r
 677       public void actionPerformed(ActionEvent e)\r
 678       {\r
 679         abovePIDThreshold_actionPerformed(e);\r
 680       }\r
 681     });\r
 682     sequenceFeatures.setText("Sequence Features");\r
 683     sequenceFeatures.addActionListener(new ActionListener()\r
 684     {\r
 685       public void actionPerformed(ActionEvent actionEvent)\r
 686       {\r
 687         sequenceFeatures_actionPerformed(actionEvent);\r
 688       }\r
 689     });\r
 690     nucleotideColour.setText("Nucleotide");\r
 691     nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
 692     {\r
 693       public void actionPerformed(ActionEvent e)\r
 694       {\r
 695         nucleotideColour_actionPerformed(e);\r
 696       }\r
 697     });\r
 698     deleteGroups.setText("Undefine groups");\r
 699     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
 700     {\r
 701       public void actionPerformed(ActionEvent e)\r
 702       {\r
 703         deleteGroups_actionPerformed(e);\r
 704       }\r
 705     });\r
 706     copy.setText("Copy");\r
 707     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 708         java.awt.event.KeyEvent.VK_C,\r
 709         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 710     copy.setMnemonic(KeyEvent.VK_C);\r
 711 \r
 712     copy.addActionListener(new java.awt.event.ActionListener()\r
 713     {\r
 714       public void actionPerformed(ActionEvent e)\r
 715       {\r
 716         copy_actionPerformed(e);\r
 717       }\r
 718     });\r
 719     cut.setText("Cut");\r
 720     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 721         java.awt.event.KeyEvent.VK_X,\r
 722         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 723     cut.setMnemonic(KeyEvent.VK_X);\r
 724     cut.addActionListener(new java.awt.event.ActionListener()\r
 725     {\r
 726       public void actionPerformed(ActionEvent e)\r
 727       {\r
 728         cut_actionPerformed(e);\r
 729       }\r
 730     });\r
 731     delete.setText("Delete");\r
 732     delete.addActionListener(new java.awt.event.ActionListener()\r
 733     {\r
 734       public void actionPerformed(ActionEvent e)\r
 735       {\r
 736         delete_actionPerformed(e);\r
 737       }\r
 738     });\r
 739     jMenu1.setMnemonic('V');\r
 740     jMenu1.setText("Paste");\r
 741     pasteNew.setText("To New Alignment");\r
 742     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
 743         java.awt.event.KeyEvent.VK_V,\r
 744         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
 745     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
 746     {\r
 747       public void actionPerformed(ActionEvent e)\r
 748       {\r
 749         pasteNew_actionPerformed(e);\r
 750       }\r
 751     });\r
 752     pasteThis.setText("Add To This Alignment");\r
 753     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
 754     {\r
 755       public void actionPerformed(ActionEvent e)\r
 756       {\r
 757         pasteThis_actionPerformed(e);\r
 758       }\r
 759     });\r
 760     applyToAllGroups.setText("Apply Colour To All Groups");\r
 761     applyToAllGroups.setState(true);\r
 762     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
 763     {\r
 764       public void actionPerformed(ActionEvent e)\r
 765       {\r
 766         applyToAllGroups_actionPerformed(e);\r
 767       }\r
 768     });\r
 769     createPNG.addActionListener(new java.awt.event.ActionListener()\r
 770     {\r
 771       public void actionPerformed(ActionEvent e)\r
 772       {\r
 773         createPNG(null);\r
 774       }\r
 775     });\r
 776     createPNG.setActionCommand("Save As PNG Image");\r
 777     createPNG.setText("PNG");\r
 778     font.setText("Font...");\r
 779     font.addActionListener(new java.awt.event.ActionListener()\r
 780     {\r
 781       public void actionPerformed(ActionEvent e)\r
 782       {\r
 783         font_actionPerformed(e);\r
 784       }\r
 785     });\r
 786     fullSeqId.setText("Show Full Sequence ID");\r
 787     fullSeqId.setState(true);\r
 788     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
 789     {\r
 790       public void actionPerformed(ActionEvent e)\r
 791       {\r
 792         fullSeqId_actionPerformed(e);\r
 793       }\r
 794     });\r
 795     epsFile.setText("EPS");\r
 796     epsFile.addActionListener(new java.awt.event.ActionListener()\r
 797     {\r
 798       public void actionPerformed(ActionEvent e)\r
 799       {\r
 800         createEPS(null);\r
 801       }\r
 802     });\r
 803     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
 804     LoadtreeMenuItem.setText("Load Assocated Tree");\r
 805     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 806     {\r
 807       public void actionPerformed(ActionEvent e)\r
 808       {\r
 809         LoadtreeMenuItem_actionPerformed(e);\r
 810       }\r
 811     });\r
 812     jnet.setText("JNet");\r
 813     jnet.addActionListener(new java.awt.event.ActionListener()\r
 814     {\r
 815       public void actionPerformed(ActionEvent e)\r
 816       {\r
 817         jpred_actionPerformed(e);\r
 818       }\r
 819     });\r
 820     scaleAbove.setVisible(false);\r
 821     scaleAbove.setText("Scale Above");\r
 822     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
 823     {\r
 824       public void actionPerformed(ActionEvent e)\r
 825       {\r
 826         scaleAbove_actionPerformed(e);\r
 827       }\r
 828     });\r
 829     scaleLeft.setVisible(false);\r
 830     scaleLeft.setSelected(true);\r
 831     scaleLeft.setText("Scale Left");\r
 832     scaleLeft.addActionListener(new java.awt.event.ActionListener()\r
 833     {\r
 834       public void actionPerformed(ActionEvent e)\r
 835       {\r
 836         scaleLeft_actionPerformed(e);\r
 837       }\r
 838     });\r
 839     scaleRight.setVisible(false);\r
 840     scaleRight.setSelected(true);\r
 841     scaleRight.setText("Scale Right");\r
 842     scaleRight.addActionListener(new java.awt.event.ActionListener()\r
 843     {\r
 844       public void actionPerformed(ActionEvent e)\r
 845       {\r
 846         scaleRight_actionPerformed(e);\r
 847       }\r
 848     });\r
 849     modifyPID.setText("Modify Identity Threshold...");\r
 850     modifyPID.addActionListener(new java.awt.event.ActionListener()\r
 851     {\r
 852       public void actionPerformed(ActionEvent e)\r
 853       {\r
 854         modifyPID_actionPerformed(e);\r
 855       }\r
 856     });\r
 857     modifyConservation.setText("Modify Conservation Threshold...");\r
 858     modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
 859     {\r
 860       public void actionPerformed(ActionEvent e)\r
 861       {\r
 862         modifyConservation_actionPerformed(e);\r
 863       }\r
 864     });\r
 865     sortByTreeMenu.setText("By Tree Order");\r
 866     sort.setText("Sort");\r
 867     calculate.setText("Calculate Tree");\r
 868     msaAlignMenuItem.setText("Muscle Alignment");\r
 869     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 870     {\r
 871       public void actionPerformed(ActionEvent e)\r
 872       {\r
 873         msaAlignMenuItem_actionPerformed(e);\r
 874       }\r
 875     });\r
 876     jMenu2.setText("Export");\r
 877     padGapsMenuitem.setText("Pad Gaps");\r
 878     padGapsMenuitem.addActionListener(new ActionListener()\r
 879     {\r
 880       public void actionPerformed(ActionEvent e)\r
 881       {\r
 882         padGapsMenuitem_actionPerformed(e);\r
 883       }\r
 884     });\r
 885     ClustalRealign.setText("Clustal Realign");\r
 886     ClustalRealign.addActionListener(new ActionListener()\r
 887     {\r
 888       public void actionPerformed(ActionEvent e)\r
 889       {\r
 890         ClustalRealign_actionPerformed(e);\r
 891       }\r
 892     });\r
 893     alignFrameMenuBar.add(fileMenu);\r
 894     alignFrameMenuBar.add(editMenu);\r
 895     alignFrameMenuBar.add(searchMenu);\r
 896     alignFrameMenuBar.add(viewMenu);\r
 897     alignFrameMenuBar.add(colourMenu);\r
 898     alignFrameMenuBar.add(calculateMenu);\r
 899     fileMenu.add(saveAlignmentMenu);\r
 900     fileMenu.add(jMenu2);\r
 901     fileMenu.add(outputTextboxMenu);\r
 902     fileMenu.add(printMenuItem);\r
 903     fileMenu.addSeparator();\r
 904     fileMenu.add(LoadtreeMenuItem);\r
 905     fileMenu.addSeparator();\r
 906     fileMenu.add(closeMenuItem);\r
 907     editMenu.add(undoMenuItem);\r
 908     editMenu.add(redoMenuItem);\r
 909     editMenu.add(cut);\r
 910     editMenu.add(copy);\r
 911     editMenu.add(jMenu1);\r
 912     editMenu.add(delete);\r
 913     editMenu.addSeparator();\r
 914     editMenu.add(selectAllSequenceMenuItem);\r
 915     editMenu.add(deselectAllSequenceMenuItem);\r
 916     editMenu.add(invertSequenceMenuItem);\r
 917     editMenu.add(deleteGroups);\r
 918     editMenu.addSeparator();\r
 919     editMenu.add(remove2LeftMenuItem);\r
 920     editMenu.add(remove2RightMenuItem);\r
 921     editMenu.add(removeGappedColumnMenuItem);\r
 922     editMenu.add(removeAllGapsMenuItem);\r
 923     editMenu.add(removeRedundancyMenuItem);\r
 924     editMenu.addSeparator();\r
 925     editMenu.add(padGapsMenuitem);\r
 926     searchMenu.add(findMenuItem);\r
 927     viewMenu.add(font);\r
 928     viewMenu.addSeparator();\r
 929     viewMenu.add(wrapMenuItem);\r
 930     viewMenu.add(fullSeqId);\r
 931     viewMenu.add(scaleAbove);\r
 932     viewMenu.add(scaleLeft);\r
 933     viewMenu.add(scaleRight);\r
 934     viewMenu.add(viewBoxesMenuItem);\r
 935     viewMenu.add(viewTextMenuItem);\r
 936     viewMenu.add(colourTextMenuItem);\r
 937     viewMenu.add(renderGapsMenuItem);\r
 938     viewMenu.add(annotationPanelMenuItem);\r
 939     viewMenu.add(sequenceFeatures);\r
 940     viewMenu.addSeparator();\r
 941     viewMenu.add(overviewMenuItem);\r
 942     colourMenu.add(applyToAllGroups);\r
 943     colourMenu.addSeparator();\r
 944     colourMenu.add(noColourmenuItem);\r
 945     colourMenu.add(clustalColour);\r
 946     colourMenu.add(BLOSUM62Colour);\r
 947     colourMenu.add(PIDColour);\r
 948     colourMenu.add(zappoColour);\r
 949     colourMenu.add(taylorColour);\r
 950     colourMenu.add(hydrophobicityColour);\r
 951     colourMenu.add(helixColour);\r
 952     colourMenu.add(strandColour);\r
 953     colourMenu.add(turnColour);\r
 954     colourMenu.add(buriedColour);\r
 955     colourMenu.add(nucleotideColour);\r
 956     colourMenu.add(userDefinedColour);\r
 957     colourMenu.addSeparator();\r
 958     colourMenu.add(conservationMenuItem);\r
 959     colourMenu.add(modifyConservation);\r
 960     colourMenu.add(abovePIDThreshold);\r
 961     colourMenu.add(modifyPID);\r
 962     calculateMenu.add(sort);\r
 963     calculateMenu.add(calculate);\r
 964     calculateMenu.addSeparator();\r
 965     calculateMenu.add(pairwiseAlignmentMenuItem);\r
 966     calculateMenu.add(PCAMenuItem);\r
 967     calculateMenu.addSeparator();\r
 968     calculateMenu.add(webService);\r
 969     webService.add(clustalAlignMenuItem);\r
 970     webService.add(msaAlignMenuItem);\r
 971     webService.add(jnet);\r
 972     webService.add(ClustalRealign);\r
 973     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
 974     jMenu1.add(pasteNew);\r
 975     jMenu1.add(pasteThis);\r
 976     sort.add(sortIDMenuItem);\r
 977     sort.add(sortGroupMenuItem);\r
 978     sort.add(sortPairwiseMenuItem);\r
 979     calculate.add(averageDistanceTreeMenuItem);\r
 980     calculate.add(neighbourTreeMenuItem);\r
 981     calculate.add(avDistanceTreeBlosumMenuItem);\r
 982     calculate.add(njTreeBlosumMenuItem);\r
 983     jMenu2.add(htmlMenuItem);\r
 984     jMenu2.add(epsFile);\r
 985     jMenu2.add(createPNG);\r
 986   }\r
 987 \r
 988   protected void outputText_actionPerformed(ActionEvent e)\r
 989   {\r
 990   }\r
 991 \r
 992   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 993   {\r
 994   }\r
 995 \r
 996   protected void closeMenuItem_actionPerformed(ActionEvent e)\r
 997   {\r
 998   }\r
 999 \r
1000   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
1001   {\r
1002   }\r
1003 \r
1004   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
1005   {\r
1006   }\r
1007 \r
1008   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1009   {\r
1010   }\r
1011 \r
1012   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
1013   {\r
1014   }\r
1015 \r
1016   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
1017   {\r
1018   }\r
1019 \r
1020   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
1021   {\r
1022   }\r
1023 \r
1024   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
1025   {\r
1026   }\r
1027 \r
1028   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
1029   {\r
1030   }\r
1031 \r
1032   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
1033   {\r
1034   }\r
1035 \r
1036   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038   }\r
1039 \r
1040   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1041   {\r
1042   }\r
1043 \r
1044   protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046   }\r
1047 \r
1048   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1049   {\r
1050   }\r
1051 \r
1052   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1053   {\r
1054   }\r
1055 \r
1056   protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
1057   {\r
1058   }\r
1059 \r
1060   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1061   {\r
1062   }\r
1063 \r
1064   protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1065   {\r
1066   }\r
1067 \r
1068   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1069   {\r
1070   }\r
1071 \r
1072   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1073   {\r
1074   }\r
1075 \r
1076   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1077   {\r
1078   }\r
1079 \r
1080   protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
1081   {\r
1082   }\r
1083 \r
1084   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1085   {\r
1086   }\r
1087 \r
1088   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1089   {\r
1090   }\r
1091 \r
1092   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1093   {\r
1094   }\r
1095 \r
1096   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1097   {\r
1098   }\r
1099 \r
1100   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1101   {\r
1102   }\r
1103 \r
1104   protected void clustalColour_actionPerformed(ActionEvent e)\r
1105   {\r
1106   }\r
1107 \r
1108   protected void zappoColour_actionPerformed(ActionEvent e)\r
1109   {\r
1110   }\r
1111 \r
1112   protected void taylorColour_actionPerformed(ActionEvent e)\r
1113   {\r
1114   }\r
1115 \r
1116   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1117   {\r
1118   }\r
1119 \r
1120   protected void helixColour_actionPerformed(ActionEvent e)\r
1121   {\r
1122   }\r
1123 \r
1124   protected void strandColour_actionPerformed(ActionEvent e)\r
1125   {\r
1126   }\r
1127 \r
1128   protected void turnColour_actionPerformed(ActionEvent e)\r
1129   {\r
1130   }\r
1131 \r
1132   protected void buriedColour_actionPerformed(ActionEvent e)\r
1133   {\r
1134   }\r
1135 \r
1136   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1137   {\r
1138   }\r
1139 \r
1140   protected void PIDColour_actionPerformed(ActionEvent e)\r
1141   {\r
1142   }\r
1143 \r
1144   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1145   {\r
1146   }\r
1147 \r
1148   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1149   {\r
1150   }\r
1151 \r
1152   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1153   {\r
1154   }\r
1155 \r
1156   protected void printMenuItem_actionPerformed(ActionEvent e)\r
1157   {\r
1158   }\r
1159 \r
1160   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1161   {\r
1162   }\r
1163 \r
1164   protected void findMenuItem_actionPerformed(ActionEvent e)\r
1165   {\r
1166   }\r
1167 \r
1168   protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1169   {\r
1170   }\r
1171 \r
1172   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
1173   {\r
1174   }\r
1175 \r
1176   protected void nucleotideColour_actionPerformed(ActionEvent e)\r
1177   {\r
1178   }\r
1179 \r
1180   protected void deleteGroups_actionPerformed(ActionEvent e)\r
1181   {\r
1182   }\r
1183 \r
1184   protected void copy_actionPerformed(ActionEvent e)\r
1185   {\r
1186   }\r
1187 \r
1188   protected void cut_actionPerformed(ActionEvent e)\r
1189   {\r
1190   }\r
1191 \r
1192   protected void delete_actionPerformed(ActionEvent e)\r
1193   {\r
1194   }\r
1195 \r
1196   protected void pasteNew_actionPerformed(ActionEvent e)\r
1197   {\r
1198   }\r
1199 \r
1200   protected void pasteThis_actionPerformed(ActionEvent e)\r
1201   {\r
1202   }\r
1203 \r
1204   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1205   {\r
1206   }\r
1207 \r
1208   public void createPNG(java.io.File f)\r
1209   {\r
1210   }\r
1211 \r
1212   protected void font_actionPerformed(ActionEvent e)\r
1213   {\r
1214   }\r
1215 \r
1216   protected void fullSeqId_actionPerformed(ActionEvent e)\r
1217   {\r
1218   }\r
1219 \r
1220   public void createEPS(java.io.File f)\r
1221   {\r
1222   }\r
1223 \r
1224   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1225   {\r
1226   }\r
1227 \r
1228   protected void jpred_actionPerformed(ActionEvent e)\r
1229   {\r
1230   }\r
1231 \r
1232   protected void scaleAbove_actionPerformed(ActionEvent e)\r
1233   {\r
1234   }\r
1235 \r
1236   protected void scaleLeft_actionPerformed(ActionEvent e)\r
1237   {\r
1238   }\r
1239 \r
1240   protected void scaleRight_actionPerformed(ActionEvent e)\r
1241   {\r
1242   }\r
1243 \r
1244   protected void modifyPID_actionPerformed(ActionEvent e)\r
1245   {\r
1246   }\r
1247 \r
1248   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1249   {\r
1250   }\r
1251 \r
1252   protected void preferences_actionPerformed(ActionEvent e)\r
1253   {\r
1254   }\r
1255 \r
1256   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1257   {\r
1258   }\r
1259 \r
1260   protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
1261   {\r
1262   }\r
1263 \r
1264   protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
1265   {\r
1266   }\r
1267 \r
1268   protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
1269   {\r
1270   }\r
1271 \r
1272   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
1273   {\r
1274   }\r
1275 }\r