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 selectAllSequenceMenuItem = new JMenuItem();
  26   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  27   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  28   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
  29   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  30   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  31   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  32   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  33   protected JMenuItem setGapCharMenuItem = new JMenuItem();
  34   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  35   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  36   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  37   protected JMenuItem sortIDMenuItem = new JMenuItem();
  38   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  39   protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
  40   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  41   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  42   protected JMenuItem PCAMenuItem = new JMenuItem();
  43   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  44   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  45   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  46   BorderLayout borderLayout1 = new BorderLayout();
  47   public JLabel statusBar = new JLabel();
  48   protected JMenu saveAlignmentMenu = new JMenu();
  49   protected JMenu outputTextboxMenu = new JMenu();
  50   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  55   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  58   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  59   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  60   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  61   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  62   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  63   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  64   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  65   JMenuItem htmlMenuItem = new JMenuItem();
  66   JMenuItem overviewMenuItem = new JMenuItem();
  67   protected JMenuItem undoMenuItem = new JMenuItem();
  68   protected JMenuItem redoMenuItem = new JMenuItem();
  69   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  70   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  71   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  72   JMenuItem printMenuItem = new JMenuItem();
  73   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  74   JMenuItem findMenuItem = new JMenuItem();
  75   JMenu searchMenu = new JMenu();
  76   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  77   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
  78   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  79   JMenuItem deleteGroups = new JMenuItem();
  80   JMenuItem delete = new JMenuItem();
  81   JMenuItem copy = new JMenuItem();
  82   JMenuItem cut = new JMenuItem();
  83   JMenu jMenu1 = new JMenu();
  84   JMenuItem pasteNew = new JMenuItem();
  85   JMenuItem pasteThis = new JMenuItem();
  86   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
  87   JMenuItem createPNG = new JMenuItem();
  88   protected JMenuItem font = new JMenuItem();
  89   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
  90   JMenuItem epsFile = new JMenuItem();
  91   JMenuItem LoadtreeMenuItem = new JMenuItem();
  92   JMenuItem jpred = 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     selectAllSequenceMenuItem.setText("Select all");
 169     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 170     {
 171       public void actionPerformed(ActionEvent e)
 172       {
 173         selectAllSequenceMenuItem_actionPerformed(e);
 174       }
 175     });
 176     deselectAllSequenceMenuItem.setText("Clear selection");
 177     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 178     {
 179       public void actionPerformed(ActionEvent e)
 180       {
 181         deselectAllSequenceMenuItem_actionPerformed(e);
 182       }
 183     });
 184     invertSequenceMenuItem.setText("Invert sequence selection");
 185     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 186     {
 187       public void actionPerformed(ActionEvent e)
 188       {
 189         invertSequenceMenuItem_actionPerformed(e);
 190       }
 191     });
 192     deselectAllColumnsMenuItem.setText("Deselect all columns");
 193     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
 194     {
 195       public void actionPerformed(ActionEvent e)
 196       {
 197         deselectAllColumnsMenuItem_actionPerformed(e);
 198       }
 199     });
 200     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
 201     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 202     {
 203       public void actionPerformed(ActionEvent e)
 204       {
 205         remove2LeftMenuItem_actionPerformed(e);
 206       }
 207     });
 208     remove2RightMenuItem.setText("Remove sequence -> right of selected column");
 209     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 210     {
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         remove2RightMenuItem_actionPerformed(e);
 214       }
 215     });
 216     removeGappedColumnMenuItem.setText("Remove gapped columns");
 217     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
 218     {
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         removeGappedColumnMenuItem_actionPerformed(e);
 222       }
 223     });
 224     removeAllGapsMenuItem.setText("Remove all gaps");
 225     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 226     {
 227       public void actionPerformed(ActionEvent e)
 228       {
 229         removeAllGapsMenuItem_actionPerformed(e);
 230       }
 231     });
 232     setGapCharMenuItem.setText("Set gap character to \".\"");
 233     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
 234     {
 235       public void actionPerformed(ActionEvent e)
 236       {
 237         setGapCharMenuItem_actionPerformed(e);
 238       }
 239     });
 240     viewBoxesMenuItem.setText("Boxes");
 241     viewBoxesMenuItem.setState(true);
 242     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         viewBoxesMenuItem_actionPerformed(e);
 247       }
 248     });
 249     viewTextMenuItem.setText("Text");
 250     viewTextMenuItem.setState(true);
 251     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 252     {
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         viewTextMenuItem_actionPerformed(e);
 256       }
 257     });
 258     sortPairwiseMenuItem.setText("Sort by pairwise identity");
 259     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 260     {
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         sortPairwiseMenuItem_actionPerformed(e);
 264       }
 265     });
 266     sortIDMenuItem.setText("Sort by ID");
 267     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 268     {
 269       public void actionPerformed(ActionEvent e)
 270       {
 271         sortIDMenuItem_actionPerformed(e);
 272       }
 273     });
 274     sortGroupMenuItem.setText("Sort by group");
 275     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 276     {
 277       public void actionPerformed(ActionEvent e)
 278       {
 279         sortGroupMenuItem_actionPerformed(e);
 280       }
 281     });
 282     sortTreeOrderMenuItem.setText("Sort by tree order");
 283     sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
 284     {
 285       public void actionPerformed(ActionEvent e)
 286       {
 287         sortTreeOrderMenuItem_actionPerformed(e);
 288       }
 289     });
 290     removeRedundancyMenuItem.setText("Remove redundancy");
 291     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
 292     {
 293       public void actionPerformed(ActionEvent e)
 294       {
 295         removeRedundancyMenuItem_actionPerformed(e);
 296       }
 297     });
 298     pairwiseAlignmentMenuItem.setText("Pairwise alignments");
 299     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
 300     {
 301       public void actionPerformed(ActionEvent e)
 302       {
 303         pairwiseAlignmentMenuItem_actionPerformed(e);
 304       }
 305     });
 306     PCAMenuItem.setText("Principal component analysis");
 307     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 308     {
 309       public void actionPerformed(ActionEvent e)
 310       {
 311         PCAMenuItem_actionPerformed(e);
 312       }
 313     });
 314     averageDistanceTreeMenuItem.setText("Average distance tree using PID");
 315     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 316     {
 317       public void actionPerformed(ActionEvent e)
 318       {
 319         averageDistanceTreeMenuItem_actionPerformed(e);
 320       }
 321     });
 322     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
 323     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 324     {
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         neighbourTreeMenuItem_actionPerformed(e);
 328       }
 329     });
 330     clustalAlignMenuItem.setText("Clustal alignment");
 331     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
 332     {
 333       public void actionPerformed(ActionEvent e)
 334       {
 335         clustalAlignMenuItem_actionPerformed(e);
 336       }
 337     });
 338     this.getContentPane().setLayout(borderLayout1);
 339     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 340     statusBar.setBackground(Color.white);
 341     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 342     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 343     statusBar.setText("Status bar");
 344     outputTextboxMenu.setMnemonic('T');
 345     outputTextboxMenu.setText("Output alignment via textbox");
 346     clustalColour.setSelected(false);
 347     clustalColour.setText("Clustalx colours");
 348     clustalColour.addActionListener(new java.awt.event.ActionListener()
 349     {
 350       public void actionPerformed(ActionEvent e)
 351       {
 352         clustalColour_actionPerformed(e);
 353       }
 354     });
 355     zappoColour.setText("Zappo colour scheme");
 356     zappoColour.addActionListener(new java.awt.event.ActionListener()
 357     {
 358       public void actionPerformed(ActionEvent e)
 359       {
 360         zappoColour_actionPerformed(e);
 361       }
 362     });
 363     taylorColour.setText("Taylor colour scheme");
 364     taylorColour.addActionListener(new java.awt.event.ActionListener()
 365     {
 366       public void actionPerformed(ActionEvent e)
 367       {
 368         taylorColour_actionPerformed(e);
 369       }
 370     });
 371     hydrophobicityColour.setText("By hydrophobicity");
 372     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 373     {
 374       public void actionPerformed(ActionEvent e)
 375       {
 376         hydrophobicityColour_actionPerformed(e);
 377       }
 378     });
 379     helixColour.setText("Helix propensity");
 380     helixColour.addActionListener(new java.awt.event.ActionListener()
 381     {
 382       public void actionPerformed(ActionEvent e)
 383       {
 384         helixColour_actionPerformed(e);
 385       }
 386     });
 387     strandColour.setText("Strand propensity");
 388     strandColour.addActionListener(new java.awt.event.ActionListener()
 389     {
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         strandColour_actionPerformed(e);
 393       }
 394     });
 395     turnColour.setText("Turn propensity");
 396     turnColour.addActionListener(new java.awt.event.ActionListener()
 397     {
 398       public void actionPerformed(ActionEvent e)
 399       {
 400         turnColour_actionPerformed(e);
 401       }
 402     });
 403     buriedColour.setText("Buried index");
 404     buriedColour.addActionListener(new java.awt.event.ActionListener()
 405     {
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         buriedColour_actionPerformed(e);
 409       }
 410     });
 411     userDefinedColour.setText("User defined colours");
 412     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 413     {
 414       public void actionPerformed(ActionEvent e)
 415       {
 416         userDefinedColour_actionPerformed(e);
 417       }
 418     });
 419     PIDColour.setText("Percentage Identity");
 420     PIDColour.addActionListener(new java.awt.event.ActionListener()
 421     {
 422       public void actionPerformed(ActionEvent e)
 423       {
 424         PIDColour_actionPerformed(e);
 425       }
 426     });
 427     BLOSUM62Colour.setText("BLOSUM62 score");
 428     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 429     {
 430       public void actionPerformed(ActionEvent e)
 431       {
 432         BLOSUM62Colour_actionPerformed(e);
 433       }
 434     });
 435     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
 436     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 437     {
 438       public void actionPerformed(ActionEvent e)
 439       {
 440         avTreeBlosumMenuItem_actionPerformed(e);
 441       }
 442     });
 443     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
 444     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 445     {
 446       public void actionPerformed(ActionEvent e)
 447       {
 448         njTreeBlosumMenuItem_actionPerformed(e);
 449       }
 450     });
 451     annotationPanelMenuItem.setActionCommand("");
 452     annotationPanelMenuItem.setText("Annotation Panel");
 453     annotationPanelMenuItem.setState(true);
 454     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 455     {
 456       public void actionPerformed(ActionEvent e)
 457       {
 458         annotationPanelMenuItem_actionPerformed(e);
 459       }
 460     });
 461     colourTextMenuItem.setText("Colour text");
 462     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 463     {
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         colourTextMenuItem_actionPerformed(e);
 467       }
 468     });
 469     htmlMenuItem.setText("Output as HTML");
 470     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 471     {
 472       public void actionPerformed(ActionEvent e)
 473       {
 474         htmlMenuItem_actionPerformed(e);
 475       }
 476     });
 477     overviewMenuItem.setText("Overview window");
 478     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 479     {
 480       public void actionPerformed(ActionEvent e)
 481       {
 482         overviewMenuItem_actionPerformed(e);
 483       }
 484     });
 485     undoMenuItem.setEnabled(false);
 486     undoMenuItem.setMnemonic('Z');
 487     undoMenuItem.setText("Undo");
 488     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 489     {
 490       public void actionPerformed(ActionEvent e)
 491       {
 492         undoMenuItem_actionPerformed(e);
 493       }
 494     });
 495     redoMenuItem.setEnabled(false);
 496     redoMenuItem.setMnemonic('0');
 497     redoMenuItem.setText("Redo");
 498     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 499     {
 500       public void actionPerformed(ActionEvent e)
 501       {
 502         redoMenuItem_actionPerformed(e);
 503       }
 504     });
 505     conservationMenuItem.setText("By conservation");
 506     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 507     {
 508       public void actionPerformed(ActionEvent e)
 509       {
 510         conservationMenuItem_actionPerformed(e);
 511       }
 512     });
 513     noColourmenuItem.setText("None");
 514     noColourmenuItem.setSelected(true);
 515     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 516     {
 517       public void actionPerformed(ActionEvent e)
 518       {
 519         noColourmenuItem_actionPerformed(e);
 520       }
 521     });
 522     wrapMenuItem.setText("Wrap alignment");
 523     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 524     {
 525       public void actionPerformed(ActionEvent e)
 526       {
 527         wrapMenuItem_actionPerformed(e);
 528       }
 529     });
 530     printMenuItem.setText("Print");
 531     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 532     {
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         printMenuItem_actionPerformed(e);
 536       }
 537     });
 538     renderGapsMenuItem.setText("Render gaps");
 539     renderGapsMenuItem.setState(true);
 540     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 541     {
 542       public void actionPerformed(ActionEvent e)
 543       {
 544         renderGapsMenuItem_actionPerformed(e);
 545       }
 546     });
 547     findMenuItem.setText("Find");
 548     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 549     {
 550       public void actionPerformed(ActionEvent e)
 551       {
 552         findMenuItem_actionPerformed(e);
 553       }
 554     });
 555     searchMenu.setText("Search");
 556
 557     abovePIDThreshold.setText("Above PID threshold");
 558     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
 559       public void actionPerformed(ActionEvent e) {
 560         abovePIDThreshold_actionPerformed(e);
 561       }
 562     });
 563     sequenceFeatures.setText("Sequence Features");
 564     sequenceFeatures.addActionListener(new ActionListener()
 565     {
 566       public void actionPerformed(ActionEvent actionEvent)
 567       {
 568         sequenceFeatures_actionPerformed(actionEvent);
 569       }
 570     });
 571     nucleotideColour.setText("Nucleotide colours");
 572     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 573     {
 574       public void actionPerformed(ActionEvent e)
 575       {
 576         nucleotideColour_actionPerformed(e);
 577       }
 578     });
 579     deleteGroups.setSelected(false);
 580     deleteGroups.setText("Delete all groups");
 581     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 582     {
 583       public void actionPerformed(ActionEvent e)
 584       {
 585         deleteGroups_actionPerformed(e);
 586       }
 587     });
 588     copy.setText("Copy");
 589     copy.setMnemonic(KeyEvent.VK_C);
 590
 591     copy.addActionListener(new java.awt.event.ActionListener()
 592     {
 593       public void actionPerformed(ActionEvent e)
 594       {
 595         copy_actionPerformed(e);
 596       }
 597     });
 598     cut.setText("Cut");
 599     cut.setMnemonic(KeyEvent.VK_X);
 600     cut.addActionListener(new java.awt.event.ActionListener()
 601     {
 602       public void actionPerformed(ActionEvent e)
 603       {
 604         cut_actionPerformed(e);
 605       }
 606     });
 607     delete.setText("Delete");
 608     delete.addActionListener(new java.awt.event.ActionListener()
 609     {
 610       public void actionPerformed(ActionEvent e)
 611       {
 612         delete_actionPerformed(e);
 613       }
 614     });
 615     jMenu1.setMnemonic('V');
 616     jMenu1.setText("Paste");
 617     pasteNew.setText("to new alignment");
 618     pasteNew.addActionListener(new java.awt.event.ActionListener()
 619     {
 620       public void actionPerformed(ActionEvent e)
 621       {
 622         pasteNew_actionPerformed(e);
 623       }
 624     });
 625     pasteThis.setText("add to this alignment");
 626     pasteThis.addActionListener(new java.awt.event.ActionListener()
 627     {
 628       public void actionPerformed(ActionEvent e)
 629       {
 630         pasteThis_actionPerformed(e);
 631       }
 632     });
 633     applyToAllGroups.setText("Apply colour to all groups");
 634     applyToAllGroups.setState(true);
 635     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 636     {
 637       public void actionPerformed(ActionEvent e)
 638       {
 639         applyToAllGroups_actionPerformed(e);
 640       }
 641     });
 642     createPNG.addActionListener(new java.awt.event.ActionListener()
 643     {
 644       public void actionPerformed(ActionEvent e)
 645       {
 646         createPNG_actionPerformed(e);
 647       }
 648     });
 649     createPNG.setActionCommand("Save as PNG Image");
 650     createPNG.setText("Save as PNG Image");
 651     font.setText("Change Font");
 652     font.addActionListener(new java.awt.event.ActionListener()
 653     {
 654       public void actionPerformed(ActionEvent e)
 655       {
 656         font_actionPerformed(e);
 657       }
 658     });
 659     fullSeqId.setText("Show full sequence id");
 660     fullSeqId.addActionListener(new java.awt.event.ActionListener()
 661     {
 662       public void actionPerformed(ActionEvent e)
 663       {
 664         fullSeqId_actionPerformed(e);
 665       }
 666     });
 667     epsFile.setText("Save as EPS file");
 668     epsFile.addActionListener(new java.awt.event.ActionListener()
 669     {
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         epsFile_actionPerformed(e);
 673       }
 674     });
 675     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 676     LoadtreeMenuItem.setText("Load assocated tree");
 677     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         LoadtreeMenuItem_actionPerformed(e);
 681       }
 682     });
 683     jpred.setText("JPred");
 684     jpred.addActionListener(new java.awt.event.ActionListener()
 685     {
 686       public void actionPerformed(ActionEvent e)
 687       {
 688         jpred_actionPerformed(e);
 689       }
 690     });
 691     alignFrameMenuBar.add(fileMenu);
 692     alignFrameMenuBar.add(editMenu);
 693     alignFrameMenuBar.add(searchMenu);
 694     alignFrameMenuBar.add(viewMenu);
 695     alignFrameMenuBar.add(colourMenu);
 696     alignFrameMenuBar.add(calculateMenu);
 697     alignFrameMenuBar.add(alignMenu);
 698     fileMenu.add(saveAlignmentMenu);
 699     fileMenu.add(outputTextboxMenu);
 700     fileMenu.add(htmlMenuItem);
 701     fileMenu.add(epsFile);
 702     fileMenu.add(createPNG);
 703     fileMenu.add(printMenuItem);
 704     fileMenu.addSeparator();
 705     fileMenu.add(LoadtreeMenuItem);
 706     fileMenu.addSeparator();
 707     fileMenu.add(closeMenuItem);
 708     editMenu.add(copy);
 709     editMenu.add(jMenu1);
 710     editMenu.add(cut);
 711     editMenu.add(delete);
 712     editMenu.addSeparator();
 713     editMenu.add(undoMenuItem);
 714     editMenu.add(redoMenuItem);
 715     editMenu.addSeparator();
 716     editMenu.add(deselectAllSequenceMenuItem);
 717     editMenu.add(selectAllSequenceMenuItem);
 718     editMenu.add(invertSequenceMenuItem);
 719     editMenu.add(deleteGroups);
 720     editMenu.addSeparator();
 721     editMenu.add(deselectAllColumnsMenuItem);
 722     editMenu.add(remove2LeftMenuItem);
 723     editMenu.add(remove2RightMenuItem);
 724     editMenu.addSeparator();
 725     editMenu.add(removeGappedColumnMenuItem);
 726     editMenu.add(removeAllGapsMenuItem);
 727     editMenu.add(setGapCharMenuItem);
 728     searchMenu.add(findMenuItem);
 729     viewMenu.add(font);
 730     viewMenu.add(fullSeqId);
 731     viewMenu.add(wrapMenuItem);
 732     viewMenu.add(viewBoxesMenuItem);
 733     viewMenu.add(viewTextMenuItem);
 734     viewMenu.add(colourTextMenuItem);
 735     viewMenu.add(renderGapsMenuItem);
 736     viewMenu.add(annotationPanelMenuItem);
 737     viewMenu.add(overviewMenuItem);
 738     viewMenu.add(sequenceFeatures);
 739     colourMenu.add(applyToAllGroups);
 740     colourMenu.add(noColourmenuItem);
 741     colourMenu.add(clustalColour);
 742     colourMenu.add(zappoColour);
 743     colourMenu.add(taylorColour);
 744     colourMenu.add(hydrophobicityColour);
 745     colourMenu.add(helixColour);
 746     colourMenu.add(strandColour);
 747     colourMenu.add(turnColour);
 748     colourMenu.add(buriedColour);
 749     colourMenu.add(nucleotideColour);
 750     colourMenu.add(userDefinedColour);
 751     colourMenu.add(PIDColour);
 752     colourMenu.add(BLOSUM62Colour);
 753     colourMenu.addSeparator();
 754     colourMenu.add(abovePIDThreshold);
 755     colourMenu.add(conservationMenuItem);
 756     calculateMenu.add(sortPairwiseMenuItem);
 757     calculateMenu.add(sortIDMenuItem);
 758     calculateMenu.add(sortGroupMenuItem);
 759     calculateMenu.add(sortTreeOrderMenuItem);
 760     calculateMenu.add(removeRedundancyMenuItem);
 761     calculateMenu.addSeparator();
 762     calculateMenu.add(pairwiseAlignmentMenuItem);
 763     calculateMenu.add(PCAMenuItem);
 764     calculateMenu.addSeparator();
 765     calculateMenu.add(averageDistanceTreeMenuItem);
 766     calculateMenu.add(neighbourTreeMenuItem);
 767     calculateMenu.add(avDistanceTreeBlosumMenuItem);
 768     calculateMenu.add(njTreeBlosumMenuItem);
 769     alignMenu.add(clustalAlignMenuItem);
 770     alignMenu.add(jpred);
 771     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
 772     jMenu1.add(pasteNew);
 773     jMenu1.add(pasteThis);
 774   }
 775
 776   protected void saveAs_actionPerformed(ActionEvent e)
 777   {
 778
 779   }
 780
 781   protected void outputText_actionPerformed(ActionEvent e)
 782   {
 783
 784   }
 785
 786   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 787   {
 788
 789   }
 790
 791
 792
 793
 794
 795   protected void closeMenuItem_actionPerformed(ActionEvent e)
 796   {
 797
 798   }
 799
 800   protected void redoMenuItem_actionPerformed(ActionEvent e)
 801   {
 802
 803   }
 804
 805   protected void undoMenuItem_actionPerformed(ActionEvent e)
 806   {
 807
 808   }
 809
 810
 811
 812
 813   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 814   {
 815
 816   }
 817
 818   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 819   {
 820
 821   }
 822
 823   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 824   {
 825
 826   }
 827
 828
 829   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
 830   {
 831
 832   }
 833
 834   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 835   {
 836
 837   }
 838
 839   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
 840   {
 841
 842   }
 843
 844   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 845   {
 846
 847   }
 848
 849   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 850   {
 851
 852   }
 853
 854   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
 855   {
 856
 857   }
 858
 859
 860
 861
 862
 863   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 864   {
 865
 866   }
 867
 868
 869   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 870   {
 871
 872   }
 873
 874   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
 875   {
 876
 877   }
 878
 879
 880   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 881   {
 882
 883   }
 884
 885
 886
 887   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 888   {
 889
 890   }
 891
 892   protected void overviewMenuItem_actionPerformed(ActionEvent e)
 893   {
 894
 895   }
 896
 897   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 898   {
 899
 900   }
 901
 902   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
 903   {
 904
 905   }
 906
 907   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
 908   {
 909
 910   }
 911
 912   protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
 913   {
 914
 915   }
 916
 917   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 918   {
 919
 920   }
 921
 922   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
 923   {
 924
 925   }
 926
 927   protected void PCAMenuItem_actionPerformed(ActionEvent e)
 928   {
 929
 930   }
 931
 932   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
 933   {
 934
 935   }
 936
 937   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
 938   {
 939
 940   }
 941
 942
 943   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 944   {
 945
 946   }
 947
 948   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 949   {
 950
 951   }
 952
 953
 954
 955   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
 956   {
 957
 958   }
 959
 960
 961
 962
 963   protected void clustalColour_actionPerformed(ActionEvent e)
 964   {
 965
 966   }
 967
 968   protected void zappoColour_actionPerformed(ActionEvent e)
 969   {
 970
 971   }
 972
 973   protected void taylorColour_actionPerformed(ActionEvent e)
 974   {
 975
 976   }
 977
 978
 979   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
 980   {
 981
 982   }
 983
 984   protected void helixColour_actionPerformed(ActionEvent e)
 985   {
 986
 987   }
 988
 989   protected void strandColour_actionPerformed(ActionEvent e)
 990   {
 991
 992   }
 993
 994   protected void turnColour_actionPerformed(ActionEvent e)
 995   {
 996
 997   }
 998
 999   protected void buriedColour_actionPerformed(ActionEvent e)
1000   {
1001
1002   }
1003
1004
1005
1006   protected void userDefinedColour_actionPerformed(ActionEvent e)
1007   {
1008
1009   }
1010
1011   protected void PIDColour_actionPerformed(ActionEvent e)
1012   {
1013
1014   }
1015
1016   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1017   {
1018
1019   }
1020
1021
1022   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1023   {
1024
1025   }
1026
1027   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
1028   {
1029
1030   }
1031
1032
1033   protected void printMenuItem_actionPerformed(ActionEvent e)
1034   {
1035
1036   }
1037
1038   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1039   {
1040
1041   }
1042
1043   protected void findMenuItem_actionPerformed(ActionEvent e)
1044   {
1045
1046   }
1047
1048
1049   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1050
1051   }
1052
1053   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1054   {
1055
1056   }
1057
1058   protected void nucleotideColour_actionPerformed(ActionEvent e)
1059   {
1060
1061   }
1062
1063   protected void deleteGroups_actionPerformed(ActionEvent e)
1064   {
1065
1066   }
1067
1068  protected void copy_actionPerformed(ActionEvent e)
1069   {
1070
1071   }
1072
1073
1074   protected void cut_actionPerformed(ActionEvent e)
1075   {
1076
1077   }
1078
1079   protected void delete_actionPerformed(ActionEvent e)
1080   {
1081
1082   }
1083
1084   protected void pasteNew_actionPerformed(ActionEvent e)
1085   {
1086
1087   }
1088
1089   protected void pasteThis_actionPerformed(ActionEvent e)
1090   {
1091
1092   }
1093
1094   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1095   {
1096
1097   }
1098
1099   protected void createPNG_actionPerformed(ActionEvent e)
1100   {
1101
1102   }
1103
1104   protected void font_actionPerformed(ActionEvent e)
1105   {
1106
1107   }
1108
1109   protected void fullSeqId_actionPerformed(ActionEvent e)
1110   {
1111
1112   }
1113
1114   protected void epsFile_actionPerformed(ActionEvent e)
1115   {
1116
1117   }
1118
1119   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1120
1121   }
1122
1123   protected void jpred_actionPerformed(ActionEvent e)
1124   {
1125
1126   }
1127
1128 }