src/jalview/jbappletgui/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.jbappletgui;\r
  20 \r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 \r
  24 \r
  25 public class GAlignFrame extends Frame {\r
  26     protected MenuBar alignFrameMenuBar = new MenuBar();\r
  27     protected Menu fileMenu = new Menu();\r
  28     protected MenuItem closeMenuItem = new MenuItem();\r
  29     protected Menu editMenu = new Menu();\r
  30     protected Menu viewMenu = new Menu();\r
  31     protected Menu colourMenu = new Menu();\r
  32     protected Menu calculateMenu = new Menu();\r
  33     protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
  34     protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
  35     protected MenuItem invertSequenceMenuItem = new MenuItem();\r
  36     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
  37     protected MenuItem remove2RightMenuItem = new MenuItem();\r
  38     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
  39     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
  40     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
  41     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
  42     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
  43     protected MenuItem sortIDMenuItem = new MenuItem();\r
  44     protected MenuItem sortGroupMenuItem = new MenuItem();\r
  45     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
  46     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
  47     protected MenuItem PCAMenuItem = new MenuItem();\r
  48     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
  49     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
  50     BorderLayout borderLayout1 = new BorderLayout();\r
  51     public Label statusBar = new Label();\r
  52     protected Menu outputTextboxMenu = new Menu();\r
  53     protected MenuItem clustalColour = new MenuItem();\r
  54     protected MenuItem zappoColour = new MenuItem();\r
  55     protected MenuItem taylorColour = new MenuItem();\r
  56     protected MenuItem hydrophobicityColour = new MenuItem();\r
  57     protected MenuItem helixColour = new MenuItem();\r
  58     protected MenuItem strandColour = new MenuItem();\r
  59     protected MenuItem turnColour = new MenuItem();\r
  60     protected MenuItem buriedColour = new MenuItem();\r
  61     protected MenuItem userDefinedColour = new MenuItem();\r
  62     protected MenuItem PIDColour = new MenuItem();\r
  63     protected MenuItem BLOSUM62Colour = new MenuItem();\r
  64     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
  65     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
  66     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
  67     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
  68     MenuItem overviewMenuItem = new MenuItem();\r
  69     protected MenuItem undoMenuItem = new MenuItem();\r
  70     protected MenuItem redoMenuItem = new MenuItem();\r
  71     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
  72     MenuItem noColourmenuItem = new MenuItem();\r
  73     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
  74     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
  75     MenuItem findMenuItem = new MenuItem();\r
  76     Menu searchMenu = new Menu();\r
  77     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
  78     protected MenuItem nucleotideColour = new MenuItem();\r
  79     MenuItem deleteGroups = new MenuItem();\r
  80     MenuItem delete = new MenuItem();\r
  81     MenuItem copy = new MenuItem();\r
  82     MenuItem cut = new MenuItem();\r
  83     Menu Menu1 = new Menu();\r
  84     MenuItem pasteNew = new MenuItem();\r
  85     MenuItem pasteThis = new MenuItem();\r
  86     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
  87     protected MenuItem font = new MenuItem();\r
  88     protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
  89     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
  90     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
  91     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
  92     MenuItem modifyPID = new MenuItem();\r
  93     MenuItem modifyConservation = new MenuItem();\r
  94     protected Menu sortByTreeMenu = new Menu();\r
  95     Menu sort = new Menu();\r
  96     Menu calculate = new Menu();\r
  97     MenuItem inputText = new MenuItem();\r
  98     Menu helpMenu = new Menu();\r
  99     MenuItem documentation = new MenuItem();\r
 100     MenuItem about = new MenuItem();\r
 101 \r
 102     public GAlignFrame() {\r
 103         try {\r
 104             jbInit();\r
 105             setMenuBar(alignFrameMenuBar);\r
 106 \r
 107             MenuItem item;\r
 108 \r
 109             // dynamically fill save as menu with available formats\r
 110             for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
 111                 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
 112                             i));\r
 113                 item.addActionListener(new java.awt.event.ActionListener() {\r
 114                         public void actionPerformed(ActionEvent e) {\r
 115                             saveAs_actionPerformed(e);\r
 116                         }\r
 117                     });\r
 118 \r
 119                 item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
 120                             i));\r
 121                 item.addActionListener(new java.awt.event.ActionListener() {\r
 122                         public void actionPerformed(ActionEvent e) {\r
 123                             outputText_actionPerformed(e);\r
 124                         }\r
 125                     });\r
 126 \r
 127                 outputTextboxMenu.add(item);\r
 128             }\r
 129         } catch (Exception e) {\r
 130             e.printStackTrace();\r
 131         }\r
 132     }\r
 133 \r
 134     private void jbInit() throws Exception {\r
 135         fileMenu.setLabel("File");\r
 136         closeMenuItem.setLabel("Close");\r
 137         closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 138                 public void actionPerformed(ActionEvent e) {\r
 139                     closeMenuItem_actionPerformed(e);\r
 140                 }\r
 141             });\r
 142         editMenu.setLabel("Edit");\r
 143         viewMenu.setLabel("View");\r
 144         colourMenu.setLabel("Colour");\r
 145         calculateMenu.setLabel("Calculate");\r
 146         selectAllSequenceMenuItem.setLabel("Select all");\r
 147         selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 148                 public void actionPerformed(ActionEvent e) {\r
 149                     selectAllSequenceMenuItem_actionPerformed(e);\r
 150                 }\r
 151             });\r
 152         deselectAllSequenceMenuItem.setLabel("Deselect All");\r
 153         deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 154                 public void actionPerformed(ActionEvent e) {\r
 155                     deselectAllSequenceMenuItem_actionPerformed(e);\r
 156                 }\r
 157             });\r
 158         invertSequenceMenuItem.setLabel("Invert Selection");\r
 159         invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 160                 public void actionPerformed(ActionEvent e) {\r
 161                     invertSequenceMenuItem_actionPerformed(e);\r
 162                 }\r
 163             });\r
 164         remove2LeftMenuItem.setLabel("Remove Left");\r
 165         remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 166                 public void actionPerformed(ActionEvent e) {\r
 167                     remove2LeftMenuItem_actionPerformed(e);\r
 168                 }\r
 169             });\r
 170         remove2RightMenuItem.setLabel("Remove Right");\r
 171         remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 172                 public void actionPerformed(ActionEvent e) {\r
 173                     remove2RightMenuItem_actionPerformed(e);\r
 174                 }\r
 175             });\r
 176         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
 177         removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 178                 public void actionPerformed(ActionEvent e) {\r
 179                     removeGappedColumnMenuItem_actionPerformed(e);\r
 180                 }\r
 181             });\r
 182         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
 183         removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 184                 public void actionPerformed(ActionEvent e) {\r
 185                     removeAllGapsMenuItem_actionPerformed(e);\r
 186                 }\r
 187             });\r
 188         viewBoxesMenuItem.setLabel("Boxes");\r
 189         viewBoxesMenuItem.setState(true);\r
 190         viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 191                 public void itemStateChanged(ItemEvent e) {\r
 192                     viewBoxesMenuItem_actionPerformed(null);\r
 193                 }\r
 194             });\r
 195         viewTextMenuItem.setLabel("Text");\r
 196         viewTextMenuItem.setState(true);\r
 197         viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 198                 public void itemStateChanged(ItemEvent e) {\r
 199                     viewTextMenuItem_actionPerformed(null);\r
 200                 }\r
 201             });\r
 202         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
 203         sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 204                 public void actionPerformed(ActionEvent e) {\r
 205                     sortPairwiseMenuItem_actionPerformed(e);\r
 206                 }\r
 207             });\r
 208         sortIDMenuItem.setLabel("by ID");\r
 209         sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 210                 public void actionPerformed(ActionEvent e) {\r
 211                     sortIDMenuItem_actionPerformed(e);\r
 212                 }\r
 213             });\r
 214         sortGroupMenuItem.setLabel("by Group");\r
 215         sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 216                 public void actionPerformed(ActionEvent e) {\r
 217                     sortGroupMenuItem_actionPerformed(e);\r
 218                 }\r
 219             });\r
 220         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
 221         removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 222                 public void actionPerformed(ActionEvent e) {\r
 223                     removeRedundancyMenuItem_actionPerformed(e);\r
 224                 }\r
 225             });\r
 226         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
 227         pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 228                 public void actionPerformed(ActionEvent e) {\r
 229                     pairwiseAlignmentMenuItem_actionPerformed(e);\r
 230                 }\r
 231             });\r
 232         PCAMenuItem.setLabel("Principal Component Analysis");\r
 233         PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 234                 public void actionPerformed(ActionEvent e) {\r
 235                     PCAMenuItem_actionPerformed(e);\r
 236                 }\r
 237             });\r
 238         averageDistanceTreeMenuItem.setLabel(\r
 239             "Average Distance Using % Identity");\r
 240         averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 241                 public void actionPerformed(ActionEvent e) {\r
 242                     averageDistanceTreeMenuItem_actionPerformed(e);\r
 243                 }\r
 244             });\r
 245         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
 246         neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 247                 public void actionPerformed(ActionEvent e) {\r
 248                     neighbourTreeMenuItem_actionPerformed(e);\r
 249                 }\r
 250             });\r
 251         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 252         statusBar.setBackground(Color.white);\r
 253         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
 254         statusBar.setText("Status bar");\r
 255         outputTextboxMenu.setLabel("Output to Textbox");\r
 256         clustalColour.setLabel("Clustalx");\r
 257 \r
 258         clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
 259                 public void actionPerformed(ActionEvent e) {\r
 260                     clustalColour_actionPerformed(e);\r
 261                 }\r
 262             });\r
 263         zappoColour.setLabel("Zappo");\r
 264         zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
 265                 public void actionPerformed(ActionEvent e) {\r
 266                     zappoColour_actionPerformed(e);\r
 267                 }\r
 268             });\r
 269         taylorColour.setLabel("Taylor");\r
 270         taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
 271                 public void actionPerformed(ActionEvent e) {\r
 272                     taylorColour_actionPerformed(e);\r
 273                 }\r
 274             });\r
 275         hydrophobicityColour.setLabel("Hydrophobicity");\r
 276         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
 277                 public void actionPerformed(ActionEvent e) {\r
 278                     hydrophobicityColour_actionPerformed(e);\r
 279                 }\r
 280             });\r
 281         helixColour.setLabel("Helix Propensity");\r
 282         helixColour.addActionListener(new java.awt.event.ActionListener() {\r
 283                 public void actionPerformed(ActionEvent e) {\r
 284                     helixColour_actionPerformed(e);\r
 285                 }\r
 286             });\r
 287         strandColour.setLabel("Strand Propensity");\r
 288         strandColour.addActionListener(new java.awt.event.ActionListener() {\r
 289                 public void actionPerformed(ActionEvent e) {\r
 290                     strandColour_actionPerformed(e);\r
 291                 }\r
 292             });\r
 293         turnColour.setLabel("Turn Propensity");\r
 294         turnColour.addActionListener(new java.awt.event.ActionListener() {\r
 295                 public void actionPerformed(ActionEvent e) {\r
 296                     turnColour_actionPerformed(e);\r
 297                 }\r
 298             });\r
 299         buriedColour.setLabel("Buried Index");\r
 300         buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
 301                 public void actionPerformed(ActionEvent e) {\r
 302                     buriedColour_actionPerformed(e);\r
 303                 }\r
 304             });\r
 305         userDefinedColour.setLabel("User Defined...");\r
 306         userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
 307                 public void actionPerformed(ActionEvent e) {\r
 308                     userDefinedColour_actionPerformed(e);\r
 309                 }\r
 310             });\r
 311         PIDColour.setLabel("Percentage Identity");\r
 312         PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
 313                 public void actionPerformed(ActionEvent e) {\r
 314                     PIDColour_actionPerformed(e);\r
 315                 }\r
 316             });\r
 317         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
 318         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
 319                 public void actionPerformed(ActionEvent e) {\r
 320                     BLOSUM62Colour_actionPerformed(e);\r
 321                 }\r
 322             });\r
 323         avDistanceTreeBlosumMenuItem.setLabel(\r
 324             "Average Distance Using BLOSUM62");\r
 325         avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 326                 public void actionPerformed(ActionEvent e) {\r
 327                     avTreeBlosumMenuItem_actionPerformed(e);\r
 328                 }\r
 329             });\r
 330         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
 331         njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 332                 public void actionPerformed(ActionEvent e) {\r
 333                     njTreeBlosumMenuItem_actionPerformed(e);\r
 334                 }\r
 335             });\r
 336         annotationPanelMenuItem.setActionCommand("");\r
 337         annotationPanelMenuItem.setState(true);\r
 338         annotationPanelMenuItem.setLabel("Show Annotations");\r
 339         annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 340                 public void itemStateChanged(ItemEvent e) {\r
 341                     annotationPanelMenuItem_actionPerformed(null);\r
 342                 }\r
 343             });\r
 344         colourTextMenuItem.setLabel("Colour Text");\r
 345         colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 346                 public void itemStateChanged(ItemEvent e) {\r
 347                     colourTextMenuItem_actionPerformed(null);\r
 348                 }\r
 349             });\r
 350         overviewMenuItem.setLabel("Overview Window");\r
 351         overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 352                 public void actionPerformed(ActionEvent e) {\r
 353                     overviewMenuItem_actionPerformed(e);\r
 354                 }\r
 355             });\r
 356         undoMenuItem.setEnabled(false);\r
 357         undoMenuItem.setLabel("Undo");\r
 358         undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 359                 public void actionPerformed(ActionEvent e) {\r
 360                     undoMenuItem_actionPerformed(e);\r
 361                 }\r
 362             });\r
 363         redoMenuItem.setEnabled(false);\r
 364         redoMenuItem.setLabel("Redo");\r
 365         redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 366                 public void actionPerformed(ActionEvent e) {\r
 367                     redoMenuItem_actionPerformed(e);\r
 368                 }\r
 369             });\r
 370         conservationMenuItem.setLabel("by Conservation");\r
 371         conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 372                 public void itemStateChanged(ItemEvent e) {\r
 373                     conservationMenuItem_actionPerformed(null);\r
 374                 }\r
 375             });\r
 376         noColourmenuItem.setLabel("None");\r
 377         noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 378                 public void actionPerformed(ActionEvent e) {\r
 379                     noColourmenuItem_actionPerformed(e);\r
 380                 }\r
 381             });\r
 382         wrapMenuItem.setLabel("Wrap");\r
 383         wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 384                 public void itemStateChanged(ItemEvent e) {\r
 385                     wrapMenuItem_actionPerformed(null);\r
 386                 }\r
 387             });\r
 388         renderGapsMenuItem.setLabel("Show Gaps");\r
 389         renderGapsMenuItem.setState(true);\r
 390         renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
 391                 public void itemStateChanged(ItemEvent e) {\r
 392                     renderGapsMenuItem_actionPerformed(null);\r
 393                 }\r
 394             });\r
 395         findMenuItem.setLabel("Find...");\r
 396         findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
 397                 public void actionPerformed(ActionEvent e) {\r
 398                     findMenuItem_actionPerformed(e);\r
 399                 }\r
 400             });\r
 401         searchMenu.setLabel("Search");\r
 402 \r
 403         abovePIDThreshold.setLabel("Above Identity Threshold");\r
 404         abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
 405                 public void itemStateChanged(ItemEvent e) {\r
 406                     abovePIDThreshold_actionPerformed(null);\r
 407                 }\r
 408             });\r
 409         nucleotideColour.setLabel("Nucleotide");\r
 410         nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
 411                 public void actionPerformed(ActionEvent e) {\r
 412                     nucleotideColour_actionPerformed(e);\r
 413                 }\r
 414             });\r
 415         deleteGroups.setLabel("Undefine Groups");\r
 416         deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
 417                 public void actionPerformed(ActionEvent e) {\r
 418                     deleteGroups_actionPerformed(e);\r
 419                 }\r
 420             });\r
 421         copy.setLabel("Copy");\r
 422         copy.addActionListener(new java.awt.event.ActionListener() {\r
 423                 public void actionPerformed(ActionEvent e) {\r
 424                     copy_actionPerformed(e);\r
 425                 }\r
 426             });\r
 427         cut.setLabel("Cut");\r
 428         cut.addActionListener(new java.awt.event.ActionListener() {\r
 429                 public void actionPerformed(ActionEvent e) {\r
 430                     cut_actionPerformed(e);\r
 431                 }\r
 432             });\r
 433         delete.setLabel("Delete");\r
 434         delete.addActionListener(new java.awt.event.ActionListener() {\r
 435                 public void actionPerformed(ActionEvent e) {\r
 436                     delete_actionPerformed(e);\r
 437                 }\r
 438             });\r
 439         Menu1.setLabel("Paste");\r
 440         pasteNew.setLabel("To New Alignment");\r
 441         pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
 442                 public void actionPerformed(ActionEvent e) {\r
 443                     pasteNew_actionPerformed(e);\r
 444                 }\r
 445             });\r
 446         pasteThis.setLabel("Add To This Alignment");\r
 447         pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
 448                 public void actionPerformed(ActionEvent e) {\r
 449                     pasteThis_actionPerformed(e);\r
 450                 }\r
 451             });\r
 452         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
 453         applyToAllGroups.setState(true);\r
 454         applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
 455                 public void itemStateChanged(ItemEvent e) {\r
 456                     applyToAllGroups_actionPerformed(null);\r
 457                 }\r
 458             });\r
 459         font.setLabel("Font...");\r
 460         font.addActionListener(new java.awt.event.ActionListener() {\r
 461                 public void actionPerformed(ActionEvent e) {\r
 462                     font_actionPerformed(e);\r
 463                 }\r
 464             });\r
 465         fullSeqId.setLabel("Show Full Sequence ID");\r
 466         fullSeqId.setState(true);\r
 467         fullSeqId.addItemListener(new java.awt.event.ItemListener() {\r
 468                 public void itemStateChanged(ItemEvent e) {\r
 469                     fullSeqId_actionPerformed(null);\r
 470                 }\r
 471             });\r
 472         scaleAbove.setLabel("Scale Above");\r
 473         scaleAbove.setState(true);\r
 474         scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
 475                 public void itemStateChanged(ItemEvent e) {\r
 476                     scaleAbove_actionPerformed(null);\r
 477                 }\r
 478             });\r
 479         scaleLeft.setEnabled(false);\r
 480         scaleLeft.setState(true);\r
 481         scaleLeft.setLabel("Scale Left");\r
 482         scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
 483                 public void itemStateChanged(ItemEvent e) {\r
 484                     scaleLeft_actionPerformed(null);\r
 485                 }\r
 486             });\r
 487         scaleRight.setEnabled(false);\r
 488         scaleRight.setState(true);\r
 489         scaleRight.setLabel("Scale Right");\r
 490         scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
 491                 public void itemStateChanged(ItemEvent e) {\r
 492                     scaleRight_actionPerformed(null);\r
 493                 }\r
 494             });\r
 495         modifyPID.setLabel("Modify Identity Threshold...");\r
 496         modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
 497                 public void actionPerformed(ActionEvent e) {\r
 498                     modifyPID_actionPerformed(e);\r
 499                 }\r
 500             });\r
 501         modifyConservation.setLabel("Modify Conservation Threshold...");\r
 502         modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
 503                 public void actionPerformed(ActionEvent e) {\r
 504                     modifyConservation_actionPerformed(e);\r
 505                 }\r
 506             });\r
 507         sortByTreeMenu.setLabel("By Tree Order");\r
 508         sort.setLabel("Sort");\r
 509         calculate.setLabel("Calculate Tree");\r
 510         inputText.setLabel("Input from textbox");\r
 511         inputText.addActionListener(new java.awt.event.ActionListener() {\r
 512                 public void actionPerformed(ActionEvent e) {\r
 513                     inputText_actionPerformed(e);\r
 514                 }\r
 515             });\r
 516 \r
 517         helpMenu.setLabel("Help");\r
 518         documentation.setLabel("Documentation");\r
 519         documentation.addActionListener(new java.awt.event.ActionListener() {\r
 520                 public void actionPerformed(ActionEvent e) {\r
 521                     documentation_actionPerformed(e);\r
 522                 }\r
 523             });\r
 524 \r
 525         about.setLabel("About...");\r
 526         about.addActionListener(new java.awt.event.ActionListener() {\r
 527                 public void actionPerformed(ActionEvent e) {\r
 528                     about_actionPerformed(e);\r
 529                 }\r
 530             });\r
 531 \r
 532         alignFrameMenuBar.add(fileMenu);\r
 533         alignFrameMenuBar.add(editMenu);\r
 534         alignFrameMenuBar.add(searchMenu);\r
 535         alignFrameMenuBar.add(viewMenu);\r
 536         alignFrameMenuBar.add(colourMenu);\r
 537         alignFrameMenuBar.add(calculateMenu);\r
 538         alignFrameMenuBar.add(helpMenu);\r
 539         fileMenu.add(inputText);\r
 540         fileMenu.add(outputTextboxMenu);\r
 541         fileMenu.addSeparator();\r
 542         fileMenu.add(closeMenuItem);\r
 543         editMenu.add(undoMenuItem);\r
 544         editMenu.add(redoMenuItem);\r
 545         editMenu.add(cut);\r
 546         editMenu.add(copy);\r
 547         editMenu.add(Menu1);\r
 548         editMenu.add(delete);\r
 549         editMenu.addSeparator();\r
 550         editMenu.add(selectAllSequenceMenuItem);\r
 551         editMenu.add(deselectAllSequenceMenuItem);\r
 552         editMenu.add(invertSequenceMenuItem);\r
 553         editMenu.add(deleteGroups);\r
 554         editMenu.addSeparator();\r
 555         editMenu.add(remove2LeftMenuItem);\r
 556         editMenu.add(remove2RightMenuItem);\r
 557         editMenu.add(removeGappedColumnMenuItem);\r
 558         editMenu.add(removeAllGapsMenuItem);\r
 559         editMenu.add(removeRedundancyMenuItem);\r
 560         searchMenu.add(findMenuItem);\r
 561         viewMenu.add(font);\r
 562         viewMenu.addSeparator();\r
 563         viewMenu.add(wrapMenuItem);\r
 564         viewMenu.add(scaleAbove);\r
 565         viewMenu.add(scaleLeft);\r
 566         viewMenu.add(scaleRight);\r
 567         viewMenu.addSeparator();\r
 568         viewMenu.add(fullSeqId);\r
 569         viewMenu.add(viewBoxesMenuItem);\r
 570         viewMenu.add(viewTextMenuItem);\r
 571         viewMenu.add(colourTextMenuItem);\r
 572         viewMenu.add(renderGapsMenuItem);\r
 573         viewMenu.add(annotationPanelMenuItem);\r
 574         viewMenu.addSeparator();\r
 575         viewMenu.add(overviewMenuItem);\r
 576         colourMenu.add(applyToAllGroups);\r
 577         colourMenu.addSeparator();\r
 578         colourMenu.add(noColourmenuItem);\r
 579         colourMenu.add(clustalColour);\r
 580         colourMenu.add(BLOSUM62Colour);\r
 581         colourMenu.add(PIDColour);\r
 582         colourMenu.add(zappoColour);\r
 583         colourMenu.add(taylorColour);\r
 584         colourMenu.add(hydrophobicityColour);\r
 585         colourMenu.add(helixColour);\r
 586         colourMenu.add(strandColour);\r
 587         colourMenu.add(turnColour);\r
 588         colourMenu.add(buriedColour);\r
 589         colourMenu.add(nucleotideColour);\r
 590         colourMenu.add(userDefinedColour);\r
 591         colourMenu.addSeparator();\r
 592         colourMenu.add(conservationMenuItem);\r
 593         colourMenu.add(modifyConservation);\r
 594         colourMenu.add(abovePIDThreshold);\r
 595         colourMenu.add(modifyPID);\r
 596         calculateMenu.add(sort);\r
 597         calculateMenu.add(calculate);\r
 598         calculateMenu.addSeparator();\r
 599         calculateMenu.add(pairwiseAlignmentMenuItem);\r
 600         calculateMenu.add(PCAMenuItem);\r
 601         this.add(statusBar, BorderLayout.SOUTH);\r
 602         Menu1.add(pasteNew);\r
 603         Menu1.add(pasteThis);\r
 604         sort.add(sortIDMenuItem);\r
 605         sort.add(sortByTreeMenu);\r
 606         sort.add(sortGroupMenuItem);\r
 607         sort.add(sortPairwiseMenuItem);\r
 608         calculate.add(averageDistanceTreeMenuItem);\r
 609         calculate.add(neighbourTreeMenuItem);\r
 610         calculate.add(avDistanceTreeBlosumMenuItem);\r
 611         calculate.add(njTreeBlosumMenuItem);\r
 612         helpMenu.add(documentation);\r
 613         helpMenu.add(about);\r
 614     }\r
 615 \r
 616     protected void saveAs_actionPerformed(ActionEvent e) {\r
 617     }\r
 618 \r
 619     protected void outputText_actionPerformed(ActionEvent e) {\r
 620     }\r
 621 \r
 622     protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
 623     }\r
 624 \r
 625     protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
 626     }\r
 627 \r
 628     protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
 629     }\r
 630 \r
 631     protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
 632     }\r
 633 \r
 634     protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 635     }\r
 636 \r
 637     protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 638     }\r
 639 \r
 640     protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
 641     }\r
 642 \r
 643     protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
 644     }\r
 645 \r
 646     protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
 647     }\r
 648 \r
 649     protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
 650     }\r
 651 \r
 652     protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
 653     }\r
 654 \r
 655     protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
 656     }\r
 657 \r
 658     protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
 659     }\r
 660 \r
 661     protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
 662     }\r
 663 \r
 664     protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
 665     }\r
 666 \r
 667     protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
 668     }\r
 669 \r
 670     protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
 671     }\r
 672 \r
 673     protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
 674     }\r
 675 \r
 676     protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
 677     }\r
 678 \r
 679     protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
 680     }\r
 681 \r
 682     protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
 683     }\r
 684 \r
 685     protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
 686     }\r
 687 \r
 688     protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
 689     }\r
 690 \r
 691     protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
 692     }\r
 693 \r
 694     protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
 695     }\r
 696 \r
 697     protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 698     }\r
 699 \r
 700     protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
 701     }\r
 702 \r
 703     protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
 704     }\r
 705 \r
 706     protected void clustalColour_actionPerformed(ActionEvent e) {\r
 707     }\r
 708 \r
 709     protected void zappoColour_actionPerformed(ActionEvent e) {\r
 710     }\r
 711 \r
 712     protected void taylorColour_actionPerformed(ActionEvent e) {\r
 713     }\r
 714 \r
 715     protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
 716     }\r
 717 \r
 718     protected void helixColour_actionPerformed(ActionEvent e) {\r
 719     }\r
 720 \r
 721     protected void strandColour_actionPerformed(ActionEvent e) {\r
 722     }\r
 723 \r
 724     protected void turnColour_actionPerformed(ActionEvent e) {\r
 725     }\r
 726 \r
 727     protected void buriedColour_actionPerformed(ActionEvent e) {\r
 728     }\r
 729 \r
 730     protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
 731     }\r
 732 \r
 733     protected void PIDColour_actionPerformed(ActionEvent e) {\r
 734     }\r
 735 \r
 736     protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
 737     }\r
 738 \r
 739     protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
 740     }\r
 741 \r
 742     protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
 743     }\r
 744 \r
 745     protected void printMenuItem_actionPerformed(ActionEvent e) {\r
 746     }\r
 747 \r
 748     protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
 749     }\r
 750 \r
 751     protected void findMenuItem_actionPerformed(ActionEvent e) {\r
 752     }\r
 753 \r
 754     protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
 755     }\r
 756 \r
 757     public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
 758     }\r
 759 \r
 760     protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
 761     }\r
 762 \r
 763     protected void deleteGroups_actionPerformed(ActionEvent e) {\r
 764     }\r
 765 \r
 766     protected void copy_actionPerformed(ActionEvent e) {\r
 767     }\r
 768 \r
 769     protected void cut_actionPerformed(ActionEvent e) {\r
 770     }\r
 771 \r
 772     protected void delete_actionPerformed(ActionEvent e) {\r
 773     }\r
 774 \r
 775     protected void pasteNew_actionPerformed(ActionEvent e) {\r
 776     }\r
 777 \r
 778     protected void pasteThis_actionPerformed(ActionEvent e) {\r
 779     }\r
 780 \r
 781     protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
 782     }\r
 783 \r
 784     protected void createPNG_actionPerformed(ActionEvent e) {\r
 785     }\r
 786 \r
 787     protected void font_actionPerformed(ActionEvent e) {\r
 788     }\r
 789 \r
 790     protected void fullSeqId_actionPerformed(ActionEvent e) {\r
 791     }\r
 792 \r
 793     protected void epsFile_actionPerformed(ActionEvent e) {\r
 794     }\r
 795 \r
 796     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
 797     }\r
 798 \r
 799     protected void jpred_actionPerformed(ActionEvent e) {\r
 800     }\r
 801 \r
 802     protected void scaleAbove_actionPerformed(ActionEvent e) {\r
 803     }\r
 804 \r
 805     protected void scaleLeft_actionPerformed(ActionEvent e) {\r
 806     }\r
 807 \r
 808     protected void scaleRight_actionPerformed(ActionEvent e) {\r
 809     }\r
 810 \r
 811     protected void modifyPID_actionPerformed(ActionEvent e) {\r
 812     }\r
 813 \r
 814     protected void modifyConservation_actionPerformed(ActionEvent e) {\r
 815     }\r
 816 \r
 817     protected void preferences_actionPerformed(ActionEvent e) {\r
 818     }\r
 819 \r
 820     protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
 821     }\r
 822 \r
 823     protected void inputText_actionPerformed(ActionEvent e) {\r
 824     }\r
 825 \r
 826     protected void documentation_actionPerformed(ActionEvent e) {\r
 827     }\r
 828 \r
 829     protected void about_actionPerformed(ActionEvent e) {\r
 830     }\r
 831 }\r