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