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 removeRedundancyMenuItem = new JMenuItem();
  40   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  41   protected JMenuItem PCAMenuItem = new JMenuItem();
  42   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  43   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  44   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  45   BorderLayout borderLayout1 = new BorderLayout();
  46   public JLabel statusBar = new JLabel();
  47   protected JMenu saveAlignmentMenu = new JMenu();
  48   protected JMenu outputTextboxMenu = new JMenu();
  49   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  50   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  54   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  55   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  58   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  59   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  60   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  61   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  62   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  63   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  64   JMenuItem htmlMenuItem = new JMenuItem();
  65   JMenuItem overviewMenuItem = new JMenuItem();
  66   protected JMenuItem undoMenuItem = new JMenuItem();
  67   protected JMenuItem redoMenuItem = new JMenuItem();
  68   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  69   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  70   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  71   JMenuItem printMenuItem = new JMenuItem();
  72   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  73   JMenuItem findMenuItem = new JMenuItem();
  74   JMenu searchMenu = new JMenu();
  75   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  76   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
  77   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  78   JMenuItem deleteGroups = new JMenuItem();
  79   JMenuItem delete = new JMenuItem();
  80   JMenuItem copy = new JMenuItem();
  81   JMenuItem cut = new JMenuItem();
  82   JMenu jMenu1 = new JMenu();
  83   JMenuItem pasteNew = new JMenuItem();
  84   JMenuItem pasteThis = new JMenuItem();
  85   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
  86   JMenuItem createPNG = new JMenuItem();
  87   protected JMenuItem font = new JMenuItem();
  88   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
  89   JMenuItem epsFile = new JMenuItem();
  90   JMenuItem LoadtreeMenuItem = new JMenuItem();
  91   JMenuItem jpred = new JMenuItem();
  92   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
  93   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
  94   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
  95   JMenuItem modifyPID = new JMenuItem();
  96   JMenuItem modifyConservation = new JMenuItem();
  97   protected JMenu sortByTreeMenu = new JMenu();
  98   public GAlignFrame()
  99   {
 100
 101
 102     try
 103     {
 104       jbInit();
 105       setJMenuBar(alignFrameMenuBar);
 106
 107       JMenuItem item;
 108       // dynamically fill save as menu with available formats
 109       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
 110         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 111         saveAlignmentMenu.add( item );
 112         item.addActionListener(new java.awt.event.ActionListener()
 113         {
 114           public void actionPerformed(ActionEvent e)
 115           {
 116             saveAs_actionPerformed(e);
 117           }
 118         });
 119
 120         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 121         item.addActionListener(new java.awt.event.ActionListener()
 122         {
 123           public void actionPerformed(ActionEvent e)
 124           {
 125             outputText_actionPerformed(e);
 126           }
 127         });
 128
 129         outputTextboxMenu.add( item );
 130       }
 131
 132     }
 133     catch(Exception e)
 134     {
 135       e.printStackTrace();
 136     }
 137
 138     ButtonGroup colours = new ButtonGroup();
 139     colours.add(noColourmenuItem);
 140     colours.add(clustalColour);
 141     colours.add(zappoColour);
 142     colours.add(taylorColour);
 143     colours.add(hydrophobicityColour);
 144     colours.add(helixColour);
 145     colours.add(strandColour);
 146     colours.add(turnColour);
 147     colours.add(buriedColour);
 148     colours.add(userDefinedColour);
 149     colours.add(PIDColour);
 150     colours.add(BLOSUM62Colour);
 151     colours.add(nucleotideColour);
 152   }
 153   private void jbInit() throws Exception
 154   {
 155     fileMenu.setMnemonic('F');
 156     fileMenu.setText("File");
 157     saveAlignmentMenu.setMnemonic('L');
 158     saveAlignmentMenu.setText("Save alignment to local file");
 159     closeMenuItem.setMnemonic('C');
 160     closeMenuItem.setText("Close");
 161     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 162     {
 163       public void actionPerformed(ActionEvent e)
 164       {
 165         closeMenuItem_actionPerformed(e);
 166       }
 167     });
 168     editMenu.setText("Edit");
 169     viewMenu.setText("View");
 170     colourMenu.setText("Colour");
 171     calculateMenu.setText("Calculate");
 172     alignMenu.setText("Web Service");
 173     selectAllSequenceMenuItem.setText("Select all");
 174     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 175     {
 176       public void actionPerformed(ActionEvent e)
 177       {
 178         selectAllSequenceMenuItem_actionPerformed(e);
 179       }
 180     });
 181     deselectAllSequenceMenuItem.setText("Clear selection");
 182     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 183     {
 184       public void actionPerformed(ActionEvent e)
 185       {
 186         deselectAllSequenceMenuItem_actionPerformed(e);
 187       }
 188     });
 189     invertSequenceMenuItem.setText("Invert sequence selection");
 190     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 191     {
 192       public void actionPerformed(ActionEvent e)
 193       {
 194         invertSequenceMenuItem_actionPerformed(e);
 195       }
 196     });
 197     deselectAllColumnsMenuItem.setText("Deselect all columns");
 198     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
 199     {
 200       public void actionPerformed(ActionEvent e)
 201       {
 202         deselectAllColumnsMenuItem_actionPerformed(e);
 203       }
 204     });
 205     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
 206     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 207     {
 208       public void actionPerformed(ActionEvent e)
 209       {
 210         remove2LeftMenuItem_actionPerformed(e);
 211       }
 212     });
 213     remove2RightMenuItem.setText("Remove sequence -> right of selected column");
 214     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 215     {
 216       public void actionPerformed(ActionEvent e)
 217       {
 218         remove2RightMenuItem_actionPerformed(e);
 219       }
 220     });
 221     removeGappedColumnMenuItem.setText("Remove gapped columns");
 222     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
 223     {
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         removeGappedColumnMenuItem_actionPerformed(e);
 227       }
 228     });
 229     removeAllGapsMenuItem.setText("Remove all gaps");
 230     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 231     {
 232       public void actionPerformed(ActionEvent e)
 233       {
 234         removeAllGapsMenuItem_actionPerformed(e);
 235       }
 236     });
 237     setGapCharMenuItem.setText("Set gap character to \".\"");
 238     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
 239     {
 240       public void actionPerformed(ActionEvent e)
 241       {
 242         setGapCharMenuItem_actionPerformed(e);
 243       }
 244     });
 245     viewBoxesMenuItem.setText("Boxes");
 246     viewBoxesMenuItem.setState(true);
 247     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 248     {
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         viewBoxesMenuItem_actionPerformed(e);
 252       }
 253     });
 254     viewTextMenuItem.setText("Text");
 255     viewTextMenuItem.setState(true);
 256     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         viewTextMenuItem_actionPerformed(e);
 261       }
 262     });
 263     sortPairwiseMenuItem.setText("Sort by pairwise identity");
 264     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent e)
 267       {
 268         sortPairwiseMenuItem_actionPerformed(e);
 269       }
 270     });
 271     sortIDMenuItem.setText("Sort by ID");
 272     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 273     {
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         sortIDMenuItem_actionPerformed(e);
 277       }
 278     });
 279     sortGroupMenuItem.setText("Sort by group");
 280     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 281     {
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         sortGroupMenuItem_actionPerformed(e);
 285       }
 286     });
 287     removeRedundancyMenuItem.setText("Remove redundancy");
 288     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
 289     {
 290       public void actionPerformed(ActionEvent e)
 291       {
 292         removeRedundancyMenuItem_actionPerformed(e);
 293       }
 294     });
 295     pairwiseAlignmentMenuItem.setText("Pairwise alignments");
 296     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
 297     {
 298       public void actionPerformed(ActionEvent e)
 299       {
 300         pairwiseAlignmentMenuItem_actionPerformed(e);
 301       }
 302     });
 303     PCAMenuItem.setText("Principal component analysis");
 304     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 305     {
 306       public void actionPerformed(ActionEvent e)
 307       {
 308         PCAMenuItem_actionPerformed(e);
 309       }
 310     });
 311     averageDistanceTreeMenuItem.setText("Average distance tree using PID");
 312     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 313     {
 314       public void actionPerformed(ActionEvent e)
 315       {
 316         averageDistanceTreeMenuItem_actionPerformed(e);
 317       }
 318     });
 319     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
 320     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 321     {
 322       public void actionPerformed(ActionEvent e)
 323       {
 324         neighbourTreeMenuItem_actionPerformed(e);
 325       }
 326     });
 327     clustalAlignMenuItem.setText("Clustal alignment");
 328     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
 329     {
 330       public void actionPerformed(ActionEvent e)
 331       {
 332         clustalAlignMenuItem_actionPerformed(e);
 333       }
 334     });
 335     this.getContentPane().setLayout(borderLayout1);
 336     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 337     statusBar.setBackground(Color.white);
 338     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 339     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 340     statusBar.setText("Status bar");
 341     outputTextboxMenu.setMnemonic('T');
 342     outputTextboxMenu.setText("Output alignment via textbox");
 343     clustalColour.setSelected(false);
 344     clustalColour.setText("Clustalx colours");
 345     clustalColour.addActionListener(new java.awt.event.ActionListener()
 346     {
 347       public void actionPerformed(ActionEvent e)
 348       {
 349         clustalColour_actionPerformed(e);
 350       }
 351     });
 352     zappoColour.setText("Zappo colour scheme");
 353     zappoColour.addActionListener(new java.awt.event.ActionListener()
 354     {
 355       public void actionPerformed(ActionEvent e)
 356       {
 357         zappoColour_actionPerformed(e);
 358       }
 359     });
 360     taylorColour.setText("Taylor colour scheme");
 361     taylorColour.addActionListener(new java.awt.event.ActionListener()
 362     {
 363       public void actionPerformed(ActionEvent e)
 364       {
 365         taylorColour_actionPerformed(e);
 366       }
 367     });
 368     hydrophobicityColour.setText("By hydrophobicity");
 369     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 370     {
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         hydrophobicityColour_actionPerformed(e);
 374       }
 375     });
 376     helixColour.setText("Helix propensity");
 377     helixColour.addActionListener(new java.awt.event.ActionListener()
 378     {
 379       public void actionPerformed(ActionEvent e)
 380       {
 381         helixColour_actionPerformed(e);
 382       }
 383     });
 384     strandColour.setText("Strand propensity");
 385     strandColour.addActionListener(new java.awt.event.ActionListener()
 386     {
 387       public void actionPerformed(ActionEvent e)
 388       {
 389         strandColour_actionPerformed(e);
 390       }
 391     });
 392     turnColour.setText("Turn propensity");
 393     turnColour.addActionListener(new java.awt.event.ActionListener()
 394     {
 395       public void actionPerformed(ActionEvent e)
 396       {
 397         turnColour_actionPerformed(e);
 398       }
 399     });
 400     buriedColour.setText("Buried index");
 401     buriedColour.addActionListener(new java.awt.event.ActionListener()
 402     {
 403       public void actionPerformed(ActionEvent e)
 404       {
 405         buriedColour_actionPerformed(e);
 406       }
 407     });
 408     userDefinedColour.setText("User defined colours");
 409     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 410     {
 411       public void actionPerformed(ActionEvent e)
 412       {
 413         userDefinedColour_actionPerformed(e);
 414       }
 415     });
 416     PIDColour.setText("Percentage Identity");
 417     PIDColour.addActionListener(new java.awt.event.ActionListener()
 418     {
 419       public void actionPerformed(ActionEvent e)
 420       {
 421         PIDColour_actionPerformed(e);
 422       }
 423     });
 424     BLOSUM62Colour.setText("BLOSUM62 score");
 425     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 426     {
 427       public void actionPerformed(ActionEvent e)
 428       {
 429         BLOSUM62Colour_actionPerformed(e);
 430       }
 431     });
 432     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
 433     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 434     {
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         avTreeBlosumMenuItem_actionPerformed(e);
 438       }
 439     });
 440     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
 441     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 442     {
 443       public void actionPerformed(ActionEvent e)
 444       {
 445         njTreeBlosumMenuItem_actionPerformed(e);
 446       }
 447     });
 448     annotationPanelMenuItem.setActionCommand("");
 449     annotationPanelMenuItem.setText("Annotation Panel");
 450     annotationPanelMenuItem.setState(true);
 451     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 452     {
 453       public void actionPerformed(ActionEvent e)
 454       {
 455         annotationPanelMenuItem_actionPerformed(e);
 456       }
 457     });
 458     colourTextMenuItem.setText("Colour text");
 459     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 460     {
 461       public void actionPerformed(ActionEvent e)
 462       {
 463         colourTextMenuItem_actionPerformed(e);
 464       }
 465     });
 466     htmlMenuItem.setText("Output as HTML");
 467     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 468     {
 469       public void actionPerformed(ActionEvent e)
 470       {
 471         htmlMenuItem_actionPerformed(e);
 472       }
 473     });
 474     overviewMenuItem.setText("Overview window");
 475     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 476     {
 477       public void actionPerformed(ActionEvent e)
 478       {
 479         overviewMenuItem_actionPerformed(e);
 480       }
 481     });
 482     undoMenuItem.setEnabled(false);
 483     undoMenuItem.setMnemonic('Z');
 484     undoMenuItem.setText("Undo");
 485     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 486     {
 487       public void actionPerformed(ActionEvent e)
 488       {
 489         undoMenuItem_actionPerformed(e);
 490       }
 491     });
 492     redoMenuItem.setEnabled(false);
 493     redoMenuItem.setMnemonic('0');
 494     redoMenuItem.setText("Redo");
 495     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 496     {
 497       public void actionPerformed(ActionEvent e)
 498       {
 499         redoMenuItem_actionPerformed(e);
 500       }
 501     });
 502     conservationMenuItem.setText("By conservation");
 503     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 504     {
 505       public void actionPerformed(ActionEvent e)
 506       {
 507         conservationMenuItem_actionPerformed(e);
 508       }
 509     });
 510     noColourmenuItem.setText("None");
 511     noColourmenuItem.setSelected(true);
 512     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 513     {
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         noColourmenuItem_actionPerformed(e);
 517       }
 518     });
 519     wrapMenuItem.setText("Wrap alignment");
 520     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 521     {
 522       public void actionPerformed(ActionEvent e)
 523       {
 524         wrapMenuItem_actionPerformed(e);
 525       }
 526     });
 527     printMenuItem.setText("Print");
 528     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 529     {
 530       public void actionPerformed(ActionEvent e)
 531       {
 532         printMenuItem_actionPerformed(e);
 533       }
 534     });
 535     renderGapsMenuItem.setText("Render gaps");
 536     renderGapsMenuItem.setState(true);
 537     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 538     {
 539       public void actionPerformed(ActionEvent e)
 540       {
 541         renderGapsMenuItem_actionPerformed(e);
 542       }
 543     });
 544     findMenuItem.setText("Find");
 545     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 546     {
 547       public void actionPerformed(ActionEvent e)
 548       {
 549         findMenuItem_actionPerformed(e);
 550       }
 551     });
 552     searchMenu.setText("Search");
 553
 554     abovePIDThreshold.setText("Above PID threshold");
 555     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
 556       public void actionPerformed(ActionEvent e) {
 557         abovePIDThreshold_actionPerformed(e);
 558       }
 559     });
 560     sequenceFeatures.setText("Sequence Features");
 561     sequenceFeatures.addActionListener(new ActionListener()
 562     {
 563       public void actionPerformed(ActionEvent actionEvent)
 564       {
 565         sequenceFeatures_actionPerformed(actionEvent);
 566       }
 567     });
 568     nucleotideColour.setText("Nucleotide colours");
 569     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         nucleotideColour_actionPerformed(e);
 574       }
 575     });
 576     deleteGroups.setSelected(false);
 577     deleteGroups.setText("Delete all groups");
 578     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 579     {
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         deleteGroups_actionPerformed(e);
 583       }
 584     });
 585     copy.setText("Copy");
 586     copy.setMnemonic(KeyEvent.VK_C);
 587
 588     copy.addActionListener(new java.awt.event.ActionListener()
 589     {
 590       public void actionPerformed(ActionEvent e)
 591       {
 592         copy_actionPerformed(e);
 593       }
 594     });
 595     cut.setText("Cut");
 596     cut.setMnemonic(KeyEvent.VK_X);
 597     cut.addActionListener(new java.awt.event.ActionListener()
 598     {
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         cut_actionPerformed(e);
 602       }
 603     });
 604     delete.setText("Delete");
 605     delete.addActionListener(new java.awt.event.ActionListener()
 606     {
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         delete_actionPerformed(e);
 610       }
 611     });
 612     jMenu1.setMnemonic('V');
 613     jMenu1.setText("Paste");
 614     pasteNew.setText("to new alignment");
 615     pasteNew.addActionListener(new java.awt.event.ActionListener()
 616     {
 617       public void actionPerformed(ActionEvent e)
 618       {
 619         pasteNew_actionPerformed(e);
 620       }
 621     });
 622     pasteThis.setText("add to this alignment");
 623     pasteThis.addActionListener(new java.awt.event.ActionListener()
 624     {
 625       public void actionPerformed(ActionEvent e)
 626       {
 627         pasteThis_actionPerformed(e);
 628       }
 629     });
 630     applyToAllGroups.setText("Apply colour to all groups");
 631     applyToAllGroups.setState(true);
 632     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 633     {
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         applyToAllGroups_actionPerformed(e);
 637       }
 638     });
 639     createPNG.addActionListener(new java.awt.event.ActionListener()
 640     {
 641       public void actionPerformed(ActionEvent e)
 642       {
 643         createPNG_actionPerformed(e);
 644       }
 645     });
 646     createPNG.setActionCommand("Save as PNG Image");
 647     createPNG.setText("Save as PNG Image");
 648     font.setText("Change Font");
 649     font.addActionListener(new java.awt.event.ActionListener()
 650     {
 651       public void actionPerformed(ActionEvent e)
 652       {
 653         font_actionPerformed(e);
 654       }
 655     });
 656     fullSeqId.setText("Show full sequence id");
 657     fullSeqId.addActionListener(new java.awt.event.ActionListener()
 658     {
 659       public void actionPerformed(ActionEvent e)
 660       {
 661         fullSeqId_actionPerformed(e);
 662       }
 663     });
 664     epsFile.setText("Save as EPS file");
 665     epsFile.addActionListener(new java.awt.event.ActionListener()
 666     {
 667       public void actionPerformed(ActionEvent e)
 668       {
 669         epsFile_actionPerformed(e);
 670       }
 671     });
 672     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 673     LoadtreeMenuItem.setText("Load assocated tree");
 674     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         LoadtreeMenuItem_actionPerformed(e);
 678       }
 679     });
 680     jpred.setText("JPred");
 681     jpred.addActionListener(new java.awt.event.ActionListener()
 682     {
 683       public void actionPerformed(ActionEvent e)
 684       {
 685         jpred_actionPerformed(e);
 686       }
 687     });
 688     scaleAbove.setVisible(false);
 689     scaleAbove.setText("Scale above alignment");
 690     scaleAbove.addActionListener(new java.awt.event.ActionListener()
 691     {
 692       public void actionPerformed(ActionEvent e)
 693       {
 694         scaleAbove_actionPerformed(e);
 695       }
 696     });
 697     scaleLeft.setVisible(false);
 698     scaleLeft.setSelected(true);
 699     scaleLeft.setText("Scale left of sequence");
 700     scaleLeft.addActionListener(new java.awt.event.ActionListener()
 701     {
 702       public void actionPerformed(ActionEvent e)
 703       {
 704         scaleLeft_actionPerformed(e);
 705       }
 706     });
 707     scaleRight.setVisible(false);
 708     scaleRight.setSelected(true);
 709     scaleRight.setText("Scale right of sequence");
 710     scaleRight.addActionListener(new java.awt.event.ActionListener()
 711     {
 712       public void actionPerformed(ActionEvent e)
 713       {
 714         scaleRight_actionPerformed(e);
 715       }
 716     });
 717     modifyPID.setText("Modify PID Threshold");
 718     modifyPID.addActionListener(new java.awt.event.ActionListener()
 719     {
 720       public void actionPerformed(ActionEvent e)
 721       {
 722         modifyPID_actionPerformed(e);
 723       }
 724     });
 725     modifyConservation.setText("Modify Conservation Threshold");
 726     modifyConservation.addActionListener(new java.awt.event.ActionListener()
 727     {
 728       public void actionPerformed(ActionEvent e)
 729       {
 730         modifyConservation_actionPerformed(e);
 731       }
 732     });
 733     sortByTreeMenu.setText("Sort by tree order");
 734     alignFrameMenuBar.add(fileMenu);
 735     alignFrameMenuBar.add(editMenu);
 736     alignFrameMenuBar.add(searchMenu);
 737     alignFrameMenuBar.add(viewMenu);
 738     alignFrameMenuBar.add(colourMenu);
 739     alignFrameMenuBar.add(calculateMenu);
 740     alignFrameMenuBar.add(alignMenu);
 741     fileMenu.add(saveAlignmentMenu);
 742     fileMenu.add(outputTextboxMenu);
 743     fileMenu.add(htmlMenuItem);
 744     fileMenu.add(epsFile);
 745     fileMenu.add(createPNG);
 746     fileMenu.add(printMenuItem);
 747     fileMenu.addSeparator();
 748     fileMenu.add(LoadtreeMenuItem);
 749     fileMenu.addSeparator();
 750     fileMenu.add(closeMenuItem);
 751     editMenu.add(copy);
 752     editMenu.add(jMenu1);
 753     editMenu.add(cut);
 754     editMenu.add(delete);
 755     editMenu.addSeparator();
 756     editMenu.add(undoMenuItem);
 757     editMenu.add(redoMenuItem);
 758     editMenu.addSeparator();
 759     editMenu.add(deselectAllSequenceMenuItem);
 760     editMenu.add(selectAllSequenceMenuItem);
 761     editMenu.add(invertSequenceMenuItem);
 762     editMenu.add(deleteGroups);
 763     editMenu.addSeparator();
 764     editMenu.add(deselectAllColumnsMenuItem);
 765     editMenu.add(remove2LeftMenuItem);
 766     editMenu.add(remove2RightMenuItem);
 767     editMenu.addSeparator();
 768     editMenu.add(removeGappedColumnMenuItem);
 769     editMenu.add(removeAllGapsMenuItem);
 770     editMenu.add(setGapCharMenuItem);
 771     searchMenu.add(findMenuItem);
 772     viewMenu.add(font);
 773     viewMenu.add(fullSeqId);
 774     viewMenu.addSeparator();
 775     viewMenu.add(wrapMenuItem);
 776     viewMenu.add(scaleAbove);
 777     viewMenu.add(scaleLeft);
 778     viewMenu.add(scaleRight);
 779     viewMenu.addSeparator();
 780     viewMenu.add(viewBoxesMenuItem);
 781     viewMenu.add(viewTextMenuItem);
 782     viewMenu.add(colourTextMenuItem);
 783     viewMenu.add(renderGapsMenuItem);
 784     viewMenu.add(annotationPanelMenuItem);
 785     viewMenu.add(overviewMenuItem);
 786     viewMenu.add(sequenceFeatures);
 787     colourMenu.add(applyToAllGroups);
 788     colourMenu.add(noColourmenuItem);
 789     colourMenu.add(clustalColour);
 790     colourMenu.add(zappoColour);
 791     colourMenu.add(taylorColour);
 792     colourMenu.add(hydrophobicityColour);
 793     colourMenu.add(helixColour);
 794     colourMenu.add(strandColour);
 795     colourMenu.add(turnColour);
 796     colourMenu.add(buriedColour);
 797     colourMenu.add(nucleotideColour);
 798     colourMenu.add(userDefinedColour);
 799     colourMenu.add(PIDColour);
 800     colourMenu.add(BLOSUM62Colour);
 801     colourMenu.addSeparator();
 802     colourMenu.add(conservationMenuItem);
 803     colourMenu.add(modifyConservation);
 804     colourMenu.add(abovePIDThreshold);
 805     colourMenu.add(modifyPID);
 806     calculateMenu.add(sortPairwiseMenuItem);
 807     calculateMenu.add(sortIDMenuItem);
 808     calculateMenu.add(sortGroupMenuItem);
 809     calculateMenu.add(sortByTreeMenu);
 810     calculateMenu.add(removeRedundancyMenuItem);
 811     calculateMenu.addSeparator();
 812     calculateMenu.add(pairwiseAlignmentMenuItem);
 813     calculateMenu.add(PCAMenuItem);
 814     calculateMenu.addSeparator();
 815     calculateMenu.add(averageDistanceTreeMenuItem);
 816     calculateMenu.add(neighbourTreeMenuItem);
 817     calculateMenu.add(avDistanceTreeBlosumMenuItem);
 818     calculateMenu.add(njTreeBlosumMenuItem);
 819     alignMenu.add(clustalAlignMenuItem);
 820     alignMenu.add(jpred);
 821     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
 822     jMenu1.add(pasteNew);
 823     jMenu1.add(pasteThis);
 824   }
 825
 826   protected void saveAs_actionPerformed(ActionEvent e)
 827   {
 828
 829   }
 830
 831   protected void outputText_actionPerformed(ActionEvent e)
 832   {
 833
 834   }
 835
 836   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 837   {
 838
 839   }
 840
 841
 842
 843
 844
 845   protected void closeMenuItem_actionPerformed(ActionEvent e)
 846   {
 847
 848   }
 849
 850   protected void redoMenuItem_actionPerformed(ActionEvent e)
 851   {
 852
 853   }
 854
 855   protected void undoMenuItem_actionPerformed(ActionEvent e)
 856   {
 857
 858   }
 859
 860
 861
 862
 863   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 864   {
 865
 866   }
 867
 868   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 869   {
 870
 871   }
 872
 873   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 874   {
 875
 876   }
 877
 878
 879   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
 880   {
 881
 882   }
 883
 884   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 885   {
 886
 887   }
 888
 889   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
 890   {
 891
 892   }
 893
 894   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 895   {
 896
 897   }
 898
 899   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 900   {
 901
 902   }
 903
 904   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
 905   {
 906
 907   }
 908
 909
 910
 911
 912
 913   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 914   {
 915
 916   }
 917
 918
 919   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 920   {
 921
 922   }
 923
 924   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
 925   {
 926
 927   }
 928
 929
 930   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 931   {
 932
 933   }
 934
 935
 936
 937   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 938   {
 939
 940   }
 941
 942   protected void overviewMenuItem_actionPerformed(ActionEvent e)
 943   {
 944
 945   }
 946
 947   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 948   {
 949
 950   }
 951
 952   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
 953   {
 954
 955   }
 956
 957   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
 958   {
 959
 960   }
 961
 962
 963   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 964   {
 965
 966   }
 967
 968   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
 969   {
 970
 971   }
 972
 973   protected void PCAMenuItem_actionPerformed(ActionEvent e)
 974   {
 975
 976   }
 977
 978   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
 979   {
 980
 981   }
 982
 983   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
 984   {
 985
 986   }
 987
 988
 989   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 990   {
 991
 992   }
 993
 994   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
 995   {
 996
 997   }
 998
 999
1000
1001   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1002   {
1003
1004   }
1005
1006
1007
1008
1009   protected void clustalColour_actionPerformed(ActionEvent e)
1010   {
1011
1012   }
1013
1014   protected void zappoColour_actionPerformed(ActionEvent e)
1015   {
1016
1017   }
1018
1019   protected void taylorColour_actionPerformed(ActionEvent e)
1020   {
1021
1022   }
1023
1024
1025   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1026   {
1027
1028   }
1029
1030   protected void helixColour_actionPerformed(ActionEvent e)
1031   {
1032
1033   }
1034
1035   protected void strandColour_actionPerformed(ActionEvent e)
1036   {
1037
1038   }
1039
1040   protected void turnColour_actionPerformed(ActionEvent e)
1041   {
1042
1043   }
1044
1045   protected void buriedColour_actionPerformed(ActionEvent e)
1046   {
1047
1048   }
1049
1050
1051
1052   protected void userDefinedColour_actionPerformed(ActionEvent e)
1053   {
1054
1055   }
1056
1057   protected void PIDColour_actionPerformed(ActionEvent e)
1058   {
1059
1060   }
1061
1062   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1063   {
1064
1065   }
1066
1067
1068   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1069   {
1070
1071   }
1072
1073   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
1074   {
1075
1076   }
1077
1078
1079   protected void printMenuItem_actionPerformed(ActionEvent e)
1080   {
1081
1082   }
1083
1084   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1085   {
1086
1087   }
1088
1089   protected void findMenuItem_actionPerformed(ActionEvent e)
1090   {
1091
1092   }
1093
1094
1095   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1096
1097   }
1098
1099   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1100   {
1101
1102   }
1103
1104   protected void nucleotideColour_actionPerformed(ActionEvent e)
1105   {
1106
1107   }
1108
1109   protected void deleteGroups_actionPerformed(ActionEvent e)
1110   {
1111
1112   }
1113
1114  protected void copy_actionPerformed(ActionEvent e)
1115   {
1116
1117   }
1118
1119
1120   protected void cut_actionPerformed(ActionEvent e)
1121   {
1122
1123   }
1124
1125   protected void delete_actionPerformed(ActionEvent e)
1126   {
1127
1128   }
1129
1130   protected void pasteNew_actionPerformed(ActionEvent e)
1131   {
1132
1133   }
1134
1135   protected void pasteThis_actionPerformed(ActionEvent e)
1136   {
1137
1138   }
1139
1140   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1141   {
1142
1143   }
1144
1145   protected void createPNG_actionPerformed(ActionEvent e)
1146   {
1147
1148   }
1149
1150   protected void font_actionPerformed(ActionEvent e)
1151   {
1152
1153   }
1154
1155   protected void fullSeqId_actionPerformed(ActionEvent e)
1156   {
1157
1158   }
1159
1160   protected void epsFile_actionPerformed(ActionEvent e)
1161   {
1162
1163   }
1164
1165   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1166
1167   }
1168
1169   protected void jpred_actionPerformed(ActionEvent e)
1170   {
1171
1172   }
1173
1174   protected void scaleAbove_actionPerformed(ActionEvent e)
1175   {
1176
1177   }
1178
1179   protected void scaleLeft_actionPerformed(ActionEvent e)
1180   {
1181
1182   }
1183
1184   protected void scaleRight_actionPerformed(ActionEvent e)
1185   {
1186
1187   }
1188
1189   protected void modifyPID_actionPerformed(ActionEvent e)
1190   {
1191
1192   }
1193
1194   protected void modifyConservation_actionPerformed(ActionEvent e)
1195   {
1196
1197   }
1198
1199
1200
1201
1202 }