src/jalview/jbgui/GAlignFrame.java

   1 /********************
   2  * 2004 Jalview Reengineered
   3  * Barton Group
   4  * Dundee University
   5  *
   6  * AM Waterhouse
   7  *******************/
   8
   9 package jalview.jbgui;
  10
  11 import javax.swing.*;
  12 import java.awt.event.*;
  13 import java.awt.*;
  14
  15 public class GAlignFrame extends JInternalFrame
  16 {
  17   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  18   protected JMenu fileMenu = new JMenu();
  19   protected JMenuItem closeMenuItem = new JMenuItem();
  20   protected JMenu editMenu = new JMenu();
  21   protected JMenu viewMenu = new JMenu();
  22   protected JMenu colourMenu = new JMenu();
  23   protected JMenu calculateMenu = new JMenu();
  24   protected JMenu webService = new JMenu();
  25   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  26   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  27   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  28   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  29   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  30   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  31   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  32   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  33   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  34   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  35   protected JMenuItem sortIDMenuItem = new JMenuItem();
  36   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  37   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  38   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  39   protected JMenuItem PCAMenuItem = new JMenuItem();
  40   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  41   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  42   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  43   BorderLayout borderLayout1 = new BorderLayout();
  44   public JLabel statusBar = new JLabel();
  45   protected JMenu saveAlignmentMenu = new JMenu();
  46   protected JMenu outputTextboxMenu = new JMenu();
  47   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  48   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  49   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  50   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  54   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  55   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  58   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  59   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  60   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  61   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  62   JMenuItem htmlMenuItem = new JMenuItem();
  63   JMenuItem overviewMenuItem = new JMenuItem();
  64   protected JMenuItem undoMenuItem = new JMenuItem();
  65   protected JMenuItem redoMenuItem = new JMenuItem();
  66   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  67   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  68   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  69   JMenuItem printMenuItem = new JMenuItem();
  70   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  71   JMenuItem findMenuItem = new JMenuItem();
  72   JMenu searchMenu = new JMenu();
  73   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  74   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
  75   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  76   JMenuItem deleteGroups = new JMenuItem();
  77   JMenuItem delete = new JMenuItem();
  78   JMenuItem copy = new JMenuItem();
  79   JMenuItem cut = new JMenuItem();
  80   JMenu jMenu1 = new JMenu();
  81   JMenuItem pasteNew = new JMenuItem();
  82   JMenuItem pasteThis = new JMenuItem();
  83   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
  84   JMenuItem createPNG = new JMenuItem();
  85   protected JMenuItem font = new JMenuItem();
  86   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
  87   JMenuItem epsFile = new JMenuItem();
  88   JMenuItem LoadtreeMenuItem = new JMenuItem();
  89   JMenuItem jpred = new JMenuItem();
  90   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
  91   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
  92   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
  93   JMenuItem modifyPID = new JMenuItem();
  94   JMenuItem modifyConservation = new JMenuItem();
  95   protected JMenu sortByTreeMenu = new JMenu();
  96   JMenu jMenu2 = new JMenu();
  97   JMenu sort = new JMenu();
  98   JMenu calculate = new JMenu();
  99   JMenuItem preferences = new JMenuItem();
 100   JMenuItem msaAlignMenuItem = new JMenuItem();
 101   public GAlignFrame()
 102   {
 103
 104
 105     try
 106     {
 107       jbInit();
 108       setJMenuBar(alignFrameMenuBar);
 109
 110       JMenuItem item;
 111       // dynamically fill save as menu with available formats
 112       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
 113         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 114         saveAlignmentMenu.add( item );
 115         item.addActionListener(new java.awt.event.ActionListener()
 116         {
 117           public void actionPerformed(ActionEvent e)
 118           {
 119             saveAs_actionPerformed(e);
 120           }
 121         });
 122
 123         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 124         item.addActionListener(new java.awt.event.ActionListener()
 125         {
 126           public void actionPerformed(ActionEvent e)
 127           {
 128             outputText_actionPerformed(e);
 129           }
 130         });
 131
 132         outputTextboxMenu.add( item );
 133       }
 134
 135     }
 136     catch(Exception e)
 137     {
 138       e.printStackTrace();
 139     }
 140
 141     ButtonGroup colours = new ButtonGroup();
 142     colours.add(noColourmenuItem);
 143     colours.add(clustalColour);
 144     colours.add(zappoColour);
 145     colours.add(taylorColour);
 146     colours.add(hydrophobicityColour);
 147     colours.add(helixColour);
 148     colours.add(strandColour);
 149     colours.add(turnColour);
 150     colours.add(buriedColour);
 151     colours.add(userDefinedColour);
 152     colours.add(PIDColour);
 153     colours.add(BLOSUM62Colour);
 154     colours.add(nucleotideColour);
 155   }
 156   private void jbInit() throws Exception
 157   {
 158     fileMenu.setMnemonic('F');
 159     fileMenu.setText("File");
 160     saveAlignmentMenu.setMnemonic('L');
 161     saveAlignmentMenu.setText("Save");
 162     closeMenuItem.setMnemonic('C');
 163     closeMenuItem.setText("Close");
 164     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 165     {
 166       public void actionPerformed(ActionEvent e)
 167       {
 168         closeMenuItem_actionPerformed(e);
 169       }
 170     });
 171     editMenu.setText("Edit");
 172     viewMenu.setText("View");
 173     colourMenu.setText("Colour");
 174     calculateMenu.setText("Calculate");
 175     webService.setText("Web Service");
 176     selectAllSequenceMenuItem.setText("Select all");
 177     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
 178         java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
 179     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 180     {
 181       public void actionPerformed(ActionEvent e)
 182       {
 183         selectAllSequenceMenuItem_actionPerformed(e);
 184       }
 185     });
 186     deselectAllSequenceMenuItem.setText("Deselect All");
 187     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
 188                                                getKeyStroke(java.awt.event.
 189         KeyEvent.VK_ESCAPE, 0, false));
 190     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         deselectAllSequenceMenuItem_actionPerformed(e);
 195       }
 196     });
 197     invertSequenceMenuItem.setText("Invert Selection");
 198     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 199     {
 200       public void actionPerformed(ActionEvent e)
 201       {
 202         invertSequenceMenuItem_actionPerformed(e);
 203       }
 204     });
 205     remove2LeftMenuItem.setText("Remove Left");
 206     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 207     {
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         remove2LeftMenuItem_actionPerformed(e);
 211       }
 212     });
 213     remove2RightMenuItem.setText("Remove Right");
 214     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 215     {
 216       public void actionPerformed(ActionEvent e)
 217       {
 218         remove2RightMenuItem_actionPerformed(e);
 219       }
 220     });
 221     removeGappedColumnMenuItem.setText("Remove Empty Columns");
 222     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         removeGappedColumnMenuItem_actionPerformed(e);
 227       }
 228     });
 229     removeAllGapsMenuItem.setText("Remove All Gaps");
 230     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 231     {
 232       public void actionPerformed(ActionEvent e)
 233       {
 234         removeAllGapsMenuItem_actionPerformed(e);
 235       }
 236     });
 237     viewBoxesMenuItem.setText("Boxes");
 238     viewBoxesMenuItem.setState(true);
 239     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         viewBoxesMenuItem_actionPerformed(e);
 244       }
 245     });
 246     viewTextMenuItem.setText("Text");
 247     viewTextMenuItem.setState(true);
 248     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         viewTextMenuItem_actionPerformed(e);
 253       }
 254     });
 255     sortPairwiseMenuItem.setText("Pairwise Identity");
 256     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         sortPairwiseMenuItem_actionPerformed(e);
 261       }
 262     });
 263     sortIDMenuItem.setText("ID");
 264     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent e)
 267       {
 268         sortIDMenuItem_actionPerformed(e);
 269       }
 270     });
 271     sortGroupMenuItem.setText("Group");
 272     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 273     {
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         sortGroupMenuItem_actionPerformed(e);
 277       }
 278     });
 279     removeRedundancyMenuItem.setText("Remove Redundancy...");
 280     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
 281     {
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         removeRedundancyMenuItem_actionPerformed(e);
 285       }
 286     });
 287     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
 288     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
 289     {
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         pairwiseAlignmentMenuItem_actionPerformed(e);
 293       }
 294     });
 295     PCAMenuItem.setText("Principal Component Analysis...");
 296     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 297     {
 298       public void actionPerformed(ActionEvent e)
 299       {
 300         PCAMenuItem_actionPerformed(e);
 301       }
 302     });
 303     averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
 304     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 305     {
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         averageDistanceTreeMenuItem_actionPerformed(e);
 309       }
 310     });
 311     neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
 312     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 313     {
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         neighbourTreeMenuItem_actionPerformed(e);
 317       }
 318     });
 319     clustalAlignMenuItem.setText("Clustal Alignment...");
 320     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
 321     {
 322       public void actionPerformed(ActionEvent e)
 323       {
 324         clustalAlignMenuItem_actionPerformed(e);
 325       }
 326     });
 327     this.getContentPane().setLayout(borderLayout1);
 328     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 329     statusBar.setBackground(Color.white);
 330     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 331     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 332     statusBar.setText("Status bar");
 333     outputTextboxMenu.setMnemonic('T');
 334     outputTextboxMenu.setText("Output to Textbox");
 335     clustalColour.setSelected(false);
 336     clustalColour.setText("Clustalx");
 337     clustalColour.addActionListener(new java.awt.event.ActionListener()
 338     {
 339       public void actionPerformed(ActionEvent e)
 340       {
 341         clustalColour_actionPerformed(e);
 342       }
 343     });
 344     zappoColour.setText("Zappo");
 345     zappoColour.addActionListener(new java.awt.event.ActionListener()
 346     {
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         zappoColour_actionPerformed(e);
 350       }
 351     });
 352     taylorColour.setText("Taylor");
 353     taylorColour.addActionListener(new java.awt.event.ActionListener()
 354     {
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         taylorColour_actionPerformed(e);
 358       }
 359     });
 360     hydrophobicityColour.setText("Hydrophobicity");
 361     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 362     {
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         hydrophobicityColour_actionPerformed(e);
 366       }
 367     });
 368     helixColour.setText("Helix Propensity");
 369     helixColour.addActionListener(new java.awt.event.ActionListener()
 370     {
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         helixColour_actionPerformed(e);
 374       }
 375     });
 376     strandColour.setText("Strand Propensity");
 377     strandColour.addActionListener(new java.awt.event.ActionListener()
 378     {
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         strandColour_actionPerformed(e);
 382       }
 383     });
 384     turnColour.setText("Turn Propensity");
 385     turnColour.addActionListener(new java.awt.event.ActionListener()
 386     {
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         turnColour_actionPerformed(e);
 390       }
 391     });
 392     buriedColour.setText("Buried Index");
 393     buriedColour.addActionListener(new java.awt.event.ActionListener()
 394     {
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         buriedColour_actionPerformed(e);
 398       }
 399     });
 400     userDefinedColour.setText("User Defined...");
 401     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 402     {
 403       public void actionPerformed(ActionEvent e)
 404       {
 405         userDefinedColour_actionPerformed(e);
 406       }
 407     });
 408     PIDColour.setText("Percentage Identity");
 409     PIDColour.addActionListener(new java.awt.event.ActionListener()
 410     {
 411       public void actionPerformed(ActionEvent e)
 412       {
 413         PIDColour_actionPerformed(e);
 414       }
 415     });
 416     BLOSUM62Colour.setText("BLOSUM62 Score");
 417     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 418     {
 419       public void actionPerformed(ActionEvent e)
 420       {
 421         BLOSUM62Colour_actionPerformed(e);
 422       }
 423     });
 424     avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
 425     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 426     {
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         avTreeBlosumMenuItem_actionPerformed(e);
 430       }
 431     });
 432     njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
 433     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 434     {
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         njTreeBlosumMenuItem_actionPerformed(e);
 438       }
 439     });
 440     annotationPanelMenuItem.setActionCommand("");
 441     annotationPanelMenuItem.setText("Show Annotations");
 442     annotationPanelMenuItem.setState(true);
 443     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 444     {
 445       public void actionPerformed(ActionEvent e)
 446       {
 447         annotationPanelMenuItem_actionPerformed(e);
 448       }
 449     });
 450     colourTextMenuItem.setText("Colour Text");
 451     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 452     {
 453       public void actionPerformed(ActionEvent e)
 454       {
 455         colourTextMenuItem_actionPerformed(e);
 456       }
 457     });
 458     htmlMenuItem.setText("HTML");
 459     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 460     {
 461       public void actionPerformed(ActionEvent e)
 462       {
 463         htmlMenuItem_actionPerformed(e);
 464       }
 465     });
 466     overviewMenuItem.setText("Overview Window...");
 467     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 468     {
 469       public void actionPerformed(ActionEvent e)
 470       {
 471         overviewMenuItem_actionPerformed(e);
 472       }
 473     });
 474     undoMenuItem.setEnabled(false);
 475     undoMenuItem.setMnemonic('Z');
 476     undoMenuItem.setText("Undo");
 477     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 478         event.KeyEvent.VK_Z, java.awt.event.KeyEvent.CTRL_MASK, false));
 479     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 480     {
 481       public void actionPerformed(ActionEvent e)
 482       {
 483         undoMenuItem_actionPerformed(e);
 484       }
 485     });
 486     redoMenuItem.setEnabled(false);
 487     redoMenuItem.setMnemonic('0');
 488     redoMenuItem.setText("Redo");
 489     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 490     {
 491       public void actionPerformed(ActionEvent e)
 492       {
 493         redoMenuItem_actionPerformed(e);
 494       }
 495     });
 496     conservationMenuItem.setText("By Conservation");
 497     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 498     {
 499       public void actionPerformed(ActionEvent e)
 500       {
 501         conservationMenuItem_actionPerformed(e);
 502       }
 503     });
 504     noColourmenuItem.setText("None");
 505     noColourmenuItem.setSelected(true);
 506     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 507     {
 508       public void actionPerformed(ActionEvent e)
 509       {
 510         noColourmenuItem_actionPerformed(e);
 511       }
 512     });
 513     wrapMenuItem.setText("Wrap");
 514     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 515     {
 516       public void actionPerformed(ActionEvent e)
 517       {
 518         wrapMenuItem_actionPerformed(e);
 519       }
 520     });
 521     printMenuItem.setText("Print");
 522     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 523     {
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         printMenuItem_actionPerformed(e);
 527       }
 528     });
 529     renderGapsMenuItem.setText("Show Gaps");
 530     renderGapsMenuItem.setState(true);
 531     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 532     {
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         renderGapsMenuItem_actionPerformed(e);
 536       }
 537     });
 538     findMenuItem.setText("Find...");
 539     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
 540         event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
 541     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 542     {
 543       public void actionPerformed(ActionEvent e)
 544       {
 545         findMenuItem_actionPerformed(e);
 546       }
 547     });
 548     searchMenu.setText("Search");
 549
 550     abovePIDThreshold.setText("Above Identity threshold");
 551     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
 552       public void actionPerformed(ActionEvent e) {
 553         abovePIDThreshold_actionPerformed(e);
 554       }
 555     });
 556     sequenceFeatures.setText("Sequence Features");
 557     sequenceFeatures.addActionListener(new ActionListener()
 558     {
 559       public void actionPerformed(ActionEvent actionEvent)
 560       {
 561         sequenceFeatures_actionPerformed(actionEvent);
 562       }
 563     });
 564     nucleotideColour.setText("Nucleotide");
 565     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 566     {
 567       public void actionPerformed(ActionEvent e)
 568       {
 569         nucleotideColour_actionPerformed(e);
 570       }
 571     });
 572     deleteGroups.setSelected(false);
 573     deleteGroups.setText("Undefine groups");
 574     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 575     {
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         deleteGroups_actionPerformed(e);
 579       }
 580     });
 581     copy.setText("Copy");
 582     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
 583         KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
 584     copy.setMnemonic(KeyEvent.VK_C);
 585
 586     copy.addActionListener(new java.awt.event.ActionListener()
 587     {
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         copy_actionPerformed(e);
 591       }
 592     });
 593     cut.setText("Cut");
 594     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
 595         KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
 596     cut.setMnemonic(KeyEvent.VK_X);
 597     cut.addActionListener(new java.awt.event.ActionListener()
 598     {
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         cut_actionPerformed(e);
 602       }
 603     });
 604     delete.setText("Delete");
 605     delete.addActionListener(new java.awt.event.ActionListener()
 606     {
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         delete_actionPerformed(e);
 610       }
 611     });
 612     jMenu1.setMnemonic('V');
 613     jMenu1.setText("Paste");
 614     pasteNew.setText("to new alignment");
 615     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
 616         KeyEvent.VK_V, java.awt.event.KeyEvent.CTRL_MASK, false));
 617     pasteNew.addActionListener(new java.awt.event.ActionListener()
 618     {
 619       public void actionPerformed(ActionEvent e)
 620       {
 621         pasteNew_actionPerformed(e);
 622       }
 623     });
 624     pasteThis.setText("add to this alignment");
 625     pasteThis.addActionListener(new java.awt.event.ActionListener()
 626     {
 627       public void actionPerformed(ActionEvent e)
 628       {
 629         pasteThis_actionPerformed(e);
 630       }
 631     });
 632     applyToAllGroups.setText("Apply Colour To All Groups");
 633     applyToAllGroups.setState(true);
 634     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 635     {
 636       public void actionPerformed(ActionEvent e)
 637       {
 638         applyToAllGroups_actionPerformed(e);
 639       }
 640     });
 641     createPNG.addActionListener(new java.awt.event.ActionListener()
 642     {
 643       public void actionPerformed(ActionEvent e)
 644       {
 645         createPNG_actionPerformed(e);
 646       }
 647     });
 648     createPNG.setActionCommand("Save as PNG Image");
 649     createPNG.setText("PNG");
 650     font.setText("Font...");
 651     font.addActionListener(new java.awt.event.ActionListener()
 652     {
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         font_actionPerformed(e);
 656       }
 657     });
 658     fullSeqId.setText("Show Full Sequence ID");
 659     fullSeqId.addActionListener(new java.awt.event.ActionListener()
 660     {
 661       public void actionPerformed(ActionEvent e)
 662       {
 663         fullSeqId_actionPerformed(e);
 664       }
 665     });
 666     epsFile.setText("EPS");
 667     epsFile.addActionListener(new java.awt.event.ActionListener()
 668     {
 669       public void actionPerformed(ActionEvent e)
 670       {
 671         epsFile_actionPerformed(e);
 672       }
 673     });
 674     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 675     LoadtreeMenuItem.setText("Load Assocated Tree");
 676     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
 677       public void actionPerformed(ActionEvent e)
 678       {
 679         LoadtreeMenuItem_actionPerformed(e);
 680       }
 681     });
 682     jpred.setText("JPred...");
 683     jpred.addActionListener(new java.awt.event.ActionListener()
 684     {
 685       public void actionPerformed(ActionEvent e)
 686       {
 687         jpred_actionPerformed(e);
 688       }
 689     });
 690     scaleAbove.setVisible(false);
 691     scaleAbove.setText("Scale Above");
 692     scaleAbove.addActionListener(new java.awt.event.ActionListener()
 693     {
 694       public void actionPerformed(ActionEvent e)
 695       {
 696         scaleAbove_actionPerformed(e);
 697       }
 698     });
 699     scaleLeft.setVisible(false);
 700     scaleLeft.setSelected(true);
 701     scaleLeft.setText("Scale Left");
 702     scaleLeft.addActionListener(new java.awt.event.ActionListener()
 703     {
 704       public void actionPerformed(ActionEvent e)
 705       {
 706         scaleLeft_actionPerformed(e);
 707       }
 708     });
 709     scaleRight.setVisible(false);
 710     scaleRight.setSelected(true);
 711     scaleRight.setText("Scale Right");
 712     scaleRight.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         scaleRight_actionPerformed(e);
 717       }
 718     });
 719     modifyPID.setText("Modify Identity Threshold...");
 720     modifyPID.addActionListener(new java.awt.event.ActionListener()
 721     {
 722       public void actionPerformed(ActionEvent e)
 723       {
 724         modifyPID_actionPerformed(e);
 725       }
 726     });
 727     modifyConservation.setText("Modify Conservation Threshold...");
 728     modifyConservation.addActionListener(new java.awt.event.ActionListener()
 729     {
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         modifyConservation_actionPerformed(e);
 733       }
 734     });
 735     sortByTreeMenu.setText("Tree Order");
 736     jMenu2.setText("Save as");
 737     sort.setText("Sort");
 738     calculate.setText("Calculate Tree");
 739     preferences.setText("Preferences...");
 740     preferences.addActionListener(new ActionListener()
 741     {
 742       public void actionPerformed(ActionEvent e)
 743       {
 744         preferences_actionPerformed(e);
 745       }
 746     });
 747     msaAlignMenuItem.setText("Muscle Alignment...");
 748     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
 749       public void actionPerformed(ActionEvent e) {
 750         msaAlignMenuItem_actionPerformed(e);
 751       }
 752     });
 753     alignFrameMenuBar.add(fileMenu);
 754     alignFrameMenuBar.add(editMenu);
 755     alignFrameMenuBar.add(searchMenu);
 756     alignFrameMenuBar.add(viewMenu);
 757     alignFrameMenuBar.add(colourMenu);
 758     alignFrameMenuBar.add(calculateMenu);
 759     fileMenu.add(saveAlignmentMenu);
 760     fileMenu.add(jMenu2);
 761     fileMenu.add(outputTextboxMenu);
 762     fileMenu.add(printMenuItem);
 763     fileMenu.addSeparator();
 764     fileMenu.add(LoadtreeMenuItem);
 765     fileMenu.addSeparator();
 766     fileMenu.add(closeMenuItem);
 767     editMenu.add(undoMenuItem);
 768     editMenu.add(redoMenuItem);
 769     editMenu.add(cut);
 770     editMenu.add(copy);
 771     editMenu.add(jMenu1);
 772     editMenu.add(delete);
 773     editMenu.addSeparator();
 774     editMenu.add(selectAllSequenceMenuItem);
 775     editMenu.add(deselectAllSequenceMenuItem);
 776     editMenu.add(invertSequenceMenuItem);
 777     editMenu.add(deleteGroups);
 778     editMenu.addSeparator();
 779     editMenu.add(remove2LeftMenuItem);
 780     editMenu.add(remove2RightMenuItem);
 781     editMenu.add(removeGappedColumnMenuItem);
 782     editMenu.add(removeAllGapsMenuItem);
 783     editMenu.add(removeRedundancyMenuItem);
 784     editMenu.addSeparator();
 785     editMenu.add(preferences);
 786
 787     searchMenu.add(findMenuItem);
 788     viewMenu.add(font);
 789     viewMenu.add(fullSeqId);
 790     viewMenu.addSeparator();
 791     viewMenu.add(wrapMenuItem);
 792     viewMenu.add(scaleAbove);
 793     viewMenu.add(scaleLeft);
 794     viewMenu.add(scaleRight);
 795     viewMenu.addSeparator();
 796     viewMenu.add(viewBoxesMenuItem);
 797     viewMenu.add(viewTextMenuItem);
 798     viewMenu.add(colourTextMenuItem);
 799     viewMenu.add(renderGapsMenuItem);
 800     viewMenu.add(annotationPanelMenuItem);
 801     viewMenu.add(sequenceFeatures);
 802     viewMenu.addSeparator();
 803     viewMenu.add(overviewMenuItem);
 804     colourMenu.add(applyToAllGroups);
 805     colourMenu.add(noColourmenuItem);
 806     colourMenu.addSeparator();
 807     colourMenu.add(clustalColour);
 808     colourMenu.add(BLOSUM62Colour);
 809     colourMenu.add(PIDColour);
 810     colourMenu.add(zappoColour);
 811     colourMenu.add(taylorColour);
 812     colourMenu.add(hydrophobicityColour);
 813     colourMenu.add(helixColour);
 814     colourMenu.add(strandColour);
 815     colourMenu.add(turnColour);
 816     colourMenu.add(buriedColour);
 817     colourMenu.add(nucleotideColour);
 818     colourMenu.add(userDefinedColour);
 819     colourMenu.addSeparator();
 820     colourMenu.add(conservationMenuItem);
 821     colourMenu.add(modifyConservation);
 822     colourMenu.add(abovePIDThreshold);
 823     colourMenu.add(modifyPID);
 824     calculateMenu.add(sort);
 825     calculateMenu.add(calculate);
 826     calculateMenu.addSeparator();
 827     calculateMenu.add(pairwiseAlignmentMenuItem);
 828     calculateMenu.add(PCAMenuItem);
 829     calculateMenu.addSeparator();
 830     calculateMenu.add(webService);
 831     webService.add(clustalAlignMenuItem);
 832     webService.add(jpred);
 833     webService.add(msaAlignMenuItem);
 834     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
 835     jMenu1.add(pasteNew);
 836     jMenu1.add(pasteThis);
 837     jMenu2.add(htmlMenuItem);
 838     jMenu2.add(epsFile);
 839     jMenu2.add(createPNG);
 840     sort.add(sortIDMenuItem);
 841     sort.add(sortGroupMenuItem);
 842     sort.add(sortByTreeMenu);
 843     sort.add(sortPairwiseMenuItem);
 844     calculate.add(averageDistanceTreeMenuItem);
 845     calculate.add(neighbourTreeMenuItem);
 846     calculate.add(avDistanceTreeBlosumMenuItem);
 847     calculate.add(njTreeBlosumMenuItem);
 848   }
 849
 850   protected void saveAs_actionPerformed(ActionEvent e)
 851   {
 852
 853   }
 854
 855   protected void outputText_actionPerformed(ActionEvent e)
 856   {
 857
 858   }
 859
 860   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 861   {
 862
 863   }
 864
 865
 866   protected void closeMenuItem_actionPerformed(ActionEvent e)
 867   {
 868
 869   }
 870
 871   protected void redoMenuItem_actionPerformed(ActionEvent e)
 872   {
 873
 874   }
 875
 876   protected void undoMenuItem_actionPerformed(ActionEvent e)
 877   {
 878
 879   }
 880
 881
 882   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 883   {
 884
 885   }
 886
 887   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 888   {
 889
 890   }
 891
 892   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 893   {
 894
 895   }
 896
 897   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 898   {
 899
 900   }
 901
 902   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
 903   {
 904
 905   }
 906
 907   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 908   {
 909
 910   }
 911
 912   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 913   {
 914
 915   }
 916
 917
 918   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 919   {
 920
 921   }
 922
 923
 924   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 925   {
 926
 927   }
 928
 929   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
 930   {
 931
 932   }
 933
 934
 935   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 936   {
 937
 938   }
 939
 940   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 941   {
 942
 943   }
 944
 945   protected void overviewMenuItem_actionPerformed(ActionEvent e)
 946   {
 947
 948   }
 949
 950   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 951   {
 952
 953   }
 954
 955   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
 956   {
 957
 958   }
 959
 960   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
 961   {
 962
 963   }
 964
 965
 966   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 967   {
 968
 969   }
 970
 971   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
 972   {
 973
 974   }
 975
 976   protected void PCAMenuItem_actionPerformed(ActionEvent e)
 977   {
 978
 979   }
 980
 981   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
 982   {
 983
 984   }
 985
 986   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
 987   {
 988
 989   }
 990
 991
 992   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 993   {
 994
 995   }
 996
 997   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 998   {
 999
1000   }
1001
1002
1003
1004   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1005   {
1006
1007   }
1008
1009
1010
1011
1012   protected void clustalColour_actionPerformed(ActionEvent e)
1013   {
1014
1015   }
1016
1017   protected void zappoColour_actionPerformed(ActionEvent e)
1018   {
1019
1020   }
1021
1022   protected void taylorColour_actionPerformed(ActionEvent e)
1023   {
1024
1025   }
1026
1027
1028   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1029   {
1030
1031   }
1032
1033   protected void helixColour_actionPerformed(ActionEvent e)
1034   {
1035
1036   }
1037
1038   protected void strandColour_actionPerformed(ActionEvent e)
1039   {
1040
1041   }
1042
1043   protected void turnColour_actionPerformed(ActionEvent e)
1044   {
1045
1046   }
1047
1048   protected void buriedColour_actionPerformed(ActionEvent e)
1049   {
1050
1051   }
1052
1053
1054
1055   protected void userDefinedColour_actionPerformed(ActionEvent e)
1056   {
1057
1058   }
1059
1060   protected void PIDColour_actionPerformed(ActionEvent e)
1061   {
1062
1063   }
1064
1065   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1066   {
1067
1068   }
1069
1070
1071   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1072   {
1073
1074   }
1075
1076   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
1077   {
1078
1079   }
1080
1081
1082   protected void printMenuItem_actionPerformed(ActionEvent e)
1083   {
1084
1085   }
1086
1087   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1088   {
1089
1090   }
1091
1092   protected void findMenuItem_actionPerformed(ActionEvent e)
1093   {
1094
1095   }
1096
1097
1098   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1099
1100   }
1101
1102   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1103   {
1104
1105   }
1106
1107   protected void nucleotideColour_actionPerformed(ActionEvent e)
1108   {
1109
1110   }
1111
1112   protected void deleteGroups_actionPerformed(ActionEvent e)
1113   {
1114
1115   }
1116
1117  protected void copy_actionPerformed(ActionEvent e)
1118   {
1119
1120   }
1121
1122
1123   protected void cut_actionPerformed(ActionEvent e)
1124   {
1125
1126   }
1127
1128   protected void delete_actionPerformed(ActionEvent e)
1129   {
1130
1131   }
1132
1133   protected void pasteNew_actionPerformed(ActionEvent e)
1134   {
1135
1136   }
1137
1138   protected void pasteThis_actionPerformed(ActionEvent e)
1139   {
1140
1141   }
1142
1143   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1144   {
1145
1146   }
1147
1148   protected void createPNG_actionPerformed(ActionEvent e)
1149   {
1150
1151   }
1152
1153   protected void font_actionPerformed(ActionEvent e)
1154   {
1155
1156   }
1157
1158   protected void fullSeqId_actionPerformed(ActionEvent e)
1159   {
1160
1161   }
1162
1163   protected void epsFile_actionPerformed(ActionEvent e)
1164   {
1165
1166   }
1167
1168   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1169
1170   }
1171
1172   protected void jpred_actionPerformed(ActionEvent e)
1173   {
1174
1175   }
1176
1177   protected void scaleAbove_actionPerformed(ActionEvent e)
1178   {
1179
1180   }
1181
1182   protected void scaleLeft_actionPerformed(ActionEvent e)
1183   {
1184
1185   }
1186
1187   protected void scaleRight_actionPerformed(ActionEvent e)
1188   {
1189
1190   }
1191
1192   protected void modifyPID_actionPerformed(ActionEvent e)
1193   {
1194
1195   }
1196
1197   protected void modifyConservation_actionPerformed(ActionEvent e)
1198   {
1199
1200   }
1201
1202   protected void preferences_actionPerformed(ActionEvent e)
1203   {
1204
1205   }
1206
1207   protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
1208
1209   }
1210
1211 }