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