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