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