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