src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.UrlLink;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class PopupMenu extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44
  45   JMenuItem groupName = new JMenuItem();
  46
  47   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  48
  49   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  62
  63   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  64
  65   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  66
  67   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  70
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  72
  73   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  74
  75   AlignmentPanel ap;
  76
  77   JMenu sequenceMenu = new JMenu();
  78
  79   JMenuItem sequenceName = new JMenuItem();
  80
  81   Sequence sequence;
  82
  83   JMenuItem unGroupMenuItem = new JMenuItem();
  84
  85   JMenuItem outline = new JMenuItem();
  86
  87   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  88
  89   JMenu colourMenu = new JMenu();
  90
  91   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  92
  93   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  94
  95   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  96
  97   JMenu editMenu = new JMenu();
  98
  99   JMenuItem cut = new JMenuItem();
 100
 101   JMenuItem copy = new JMenuItem();
 102
 103   JMenuItem upperCase = new JMenuItem();
 104
 105   JMenuItem lowerCase = new JMenuItem();
 106
 107   JMenuItem toggle = new JMenuItem();
 108
 109   JMenu pdbMenu = new JMenu();
 110
 111   JMenuItem pdbFromFile = new JMenuItem();
 112
 113   JMenuItem enterPDB = new JMenuItem();
 114
 115   JMenuItem discoverPDB = new JMenuItem();
 116
 117   JMenu outputMenu = new JMenu();
 118
 119   JMenuItem sequenceFeature = new JMenuItem();
 120
 121   JMenuItem textColour = new JMenuItem();
 122
 123   JMenu jMenu1 = new JMenu();
 124
 125   JMenu structureMenu = new JMenu();
 126
 127   JMenu viewStructureMenu = new JMenu();
 128
 129   // JMenu colStructureMenu = new JMenu();
 130   JMenuItem editSequence = new JMenuItem();
 131
 132   // JMenuItem annotationMenuItem = new JMenuItem();
 133
 134   /**
 135    * Creates a new PopupMenu object.
 136    *
 137    * @param ap
 138    *                DOCUMENT ME!
 139    * @param seq
 140    *                DOCUMENT ME!
 141    */
 142   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 143   {
 144     // /////////////////////////////////////////////////////////
 145     // If this is activated from the sequence panel, the user may want to
 146     // edit or annotate a particular residue. Therefore display the residue menu
 147     //
 148     // If from the IDPanel, we must display the sequence menu
 149     // ////////////////////////////////////////////////////////
 150     this.ap = ap;
 151     sequence = seq;
 152
 153     ButtonGroup colours = new ButtonGroup();
 154     colours.add(noColourmenuItem);
 155     colours.add(clustalColour);
 156     colours.add(zappoColour);
 157     colours.add(taylorColour);
 158     colours.add(hydrophobicityColour);
 159     colours.add(helixColour);
 160     colours.add(strandColour);
 161     colours.add(turnColour);
 162     colours.add(buriedColour);
 163     colours.add(abovePIDColour);
 164     colours.add(userDefinedColour);
 165     colours.add(PIDColour);
 166     colours.add(BLOSUM62Colour);
 167
 168     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 169     {
 170       JMenuItem item = new JMenuItem(
 171               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 172
 173       item.addActionListener(new java.awt.event.ActionListener()
 174       {
 175         public void actionPerformed(ActionEvent e)
 176         {
 177           outputText_actionPerformed(e);
 178         }
 179       });
 180
 181       outputMenu.add(item);
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception e)
 188     {
 189       e.printStackTrace();
 190     }
 191
 192     if (seq != null)
 193     {
 194       sequenceMenu.setText(sequence.getName());
 195
 196       JMenuItem menuItem;
 197       if (seq.getDatasetSequence().getPDBId() != null
 198               && seq.getDatasetSequence().getPDBId().size() > 0)
 199       {
 200         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 201                 .elements();
 202
 203         while (e.hasMoreElements())
 204         {
 205           final PDBEntry pdb = (PDBEntry) e.nextElement();
 206
 207           menuItem = new JMenuItem();
 208           menuItem.setText(pdb.getId());
 209           menuItem.addActionListener(new java.awt.event.ActionListener()
 210           {
 211             public void actionPerformed(ActionEvent e)
 212             {
 213               Vector seqs = new Vector();
 214               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 215               {
 216                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 217                         .getDatasetSequence().getPDBId();
 218                 if (pdbs == null)
 219                   continue;
 220
 221                 for (int p = 0; p < pdbs.size(); p++)
 222                 {
 223                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 224                   if (p1.getId().equals(pdb.getId()))
 225                   {
 226                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 227                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 228
 229                     continue;
 230                   }
 231                 }
 232               }
 233
 234               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 235               seqs.toArray(seqs2);
 236
 237               new AppJmol(pdb, seqs2, null, ap);
 238               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 239             }
 240           });
 241           viewStructureMenu.add(menuItem);
 242
 243           /*
 244            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 245            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 246            * public void actionPerformed(ActionEvent e) {
 247            * colourByStructure(pdb.getId()); } });
 248            * colStructureMenu.add(menuItem);
 249            */
 250         }
 251       }
 252       else
 253       {
 254         structureMenu.remove(viewStructureMenu);
 255         // structureMenu.remove(colStructureMenu);
 256       }
 257
 258       menuItem = new JMenuItem("Hide Sequences");
 259       menuItem.addActionListener(new java.awt.event.ActionListener()
 260       {
 261         public void actionPerformed(ActionEvent e)
 262         {
 263           hideSequences(false);
 264         }
 265       });
 266       add(menuItem);
 267
 268       if (ap.av.getSelectionGroup() != null
 269               && ap.av.getSelectionGroup().getSize() > 1)
 270       {
 271         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 272         menuItem.addActionListener(new java.awt.event.ActionListener()
 273         {
 274           public void actionPerformed(ActionEvent e)
 275           {
 276             hideSequences(true);
 277           }
 278         });
 279         sequenceMenu.add(menuItem);
 280       }
 281
 282       if (ap.av.hasHiddenRows)
 283       {
 284         final int index = ap.av.alignment.findIndex(seq);
 285
 286         if (ap.av.adjustForHiddenSeqs(index)
 287                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 288         {
 289           menuItem = new JMenuItem("Reveal Sequences");
 290           menuItem.addActionListener(new ActionListener()
 291           {
 292             public void actionPerformed(ActionEvent e)
 293             {
 294               ap.av.showSequence(index);
 295               if (ap.overviewPanel != null)
 296               {
 297                 ap.overviewPanel.updateOverviewImage();
 298               }
 299             }
 300           });
 301           add(menuItem);
 302         }
 303
 304         menuItem = new JMenuItem("Reveal All");
 305         menuItem.addActionListener(new ActionListener()
 306         {
 307           public void actionPerformed(ActionEvent e)
 308           {
 309             ap.av.showAllHiddenSeqs();
 310             if (ap.overviewPanel != null)
 311             {
 312               ap.overviewPanel.updateOverviewImage();
 313             }
 314           }
 315         });
 316
 317         add(menuItem);
 318       }
 319
 320     }
 321
 322     SequenceGroup sg = ap.av.getSelectionGroup();
 323
 324     if (sg != null)
 325     {
 326       groupName.setText(sg.getName());
 327
 328       if (sg.cs instanceof ZappoColourScheme)
 329       {
 330         zappoColour.setSelected(true);
 331       }
 332       else if (sg.cs instanceof TaylorColourScheme)
 333       {
 334         taylorColour.setSelected(true);
 335       }
 336       else if (sg.cs instanceof PIDColourScheme)
 337       {
 338         PIDColour.setSelected(true);
 339       }
 340       else if (sg.cs instanceof Blosum62ColourScheme)
 341       {
 342         BLOSUM62Colour.setSelected(true);
 343       }
 344       else if (sg.cs instanceof UserColourScheme)
 345       {
 346         userDefinedColour.setSelected(true);
 347       }
 348       else if (sg.cs instanceof HydrophobicColourScheme)
 349       {
 350         hydrophobicityColour.setSelected(true);
 351       }
 352       else if (sg.cs instanceof HelixColourScheme)
 353       {
 354         helixColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof StrandColourScheme)
 357       {
 358         strandColour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof TurnColourScheme)
 361       {
 362         turnColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof BuriedColourScheme)
 365       {
 366         buriedColour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof ClustalxColourScheme)
 369       {
 370         clustalColour.setSelected(true);
 371       }
 372       else
 373       {
 374         noColourmenuItem.setSelected(true);
 375       }
 376
 377       if (sg.cs != null && sg.cs.conservationApplied())
 378       {
 379         conservationMenuItem.setSelected(true);
 380       }
 381
 382       showText.setSelected(sg.getDisplayText());
 383       showColourText.setSelected(sg.getColourText());
 384       showBoxes.setSelected(sg.getDisplayBoxes());
 385     }
 386     else
 387     {
 388       groupMenu.setVisible(false);
 389       editMenu.setVisible(false);
 390     }
 391
 392     if (!ap.av.alignment.getGroups().contains(sg))
 393     {
 394       unGroupMenuItem.setVisible(false);
 395     }
 396
 397     if (seq == null)
 398     {
 399       sequenceMenu.setVisible(false);
 400       structureMenu.setVisible(false);
 401     }
 402
 403     if (links != null && links.size() > 0)
 404     {
 405       JMenu linkMenu = new JMenu("Link");
 406
 407       for (int i = 0; i < links.size(); i++)
 408       {
 409         String link = links.elementAt(i).toString();
 410         UrlLink urlLink = null;
 411         try
 412         {
 413           urlLink = new UrlLink(link);
 414         } catch (Exception foo)
 415         {
 416           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 417                   + "'", foo);
 418           continue;
 419         }
 420         ;
 421         if (!urlLink.isValid())
 422         {
 423           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 424           continue;
 425         }
 426         final String label = urlLink.getLabel();
 427         if (urlLink.isDynamic())
 428         {
 429
 430           // collect matching db-refs
 431           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 432                   .getDBRef(), new String[]
 433           { urlLink.getTarget() });
 434           // collect id string too
 435           String id = seq.getName();
 436           if (dbr != null)
 437           {
 438             for (int r = 0; r < dbr.length; r++)
 439             {
 440               if (id != null && dbr[r].getAccessionId().equals(id))
 441               {
 442                 // suppress duplicate link creation for the bare sequence ID
 443                 // string with this link
 444                 id = null;
 445               }
 446               // create Bare ID link for this RUL
 447               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 448                       true);
 449               if (urls != null)
 450               {
 451                 for (int u = 0; u < urls.length; u += 2)
 452                 {
 453                   addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 454                 }
 455               }
 456             }
 457           }
 458           if (id != null)
 459           {
 460             // create Bare ID link for this RUL
 461             String[] urls = urlLink.makeUrls(id, true);
 462             if (urls != null)
 463             {
 464               for (int u = 0; u < urls.length; u += 2)
 465               {
 466                 addshowLink(linkMenu, label, urls[u + 1]);
 467               }
 468             }
 469           }
 470         }
 471         else
 472         {
 473           // Add a non-dynamic link
 474           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 475         }
 476       }
 477       if (sequence != null)
 478       {
 479         sequenceMenu.add(linkMenu);
 480       }
 481       else
 482       {
 483         add(linkMenu);
 484       }
 485     }
 486   }
 487
 488   /**
 489    * add a show URL menu item to the given linkMenu
 490    *
 491    * @param linkMenu
 492    * @param label -
 493    *                menu label string
 494    * @param url -
 495    *                url to open
 496    */
 497   private void addshowLink(JMenu linkMenu, String label, final String url)
 498   {
 499     JMenuItem item = new JMenuItem(label);
 500     item.setToolTipText("open URL: " + url);
 501     item.addActionListener(new java.awt.event.ActionListener()
 502     {
 503       public void actionPerformed(ActionEvent e)
 504       {
 505         new Thread(new Runnable()
 506         {
 507
 508           public void run()
 509           {
 510             showLink(url);
 511           }
 512
 513         }).start();
 514       }
 515     });
 516
 517     linkMenu.add(item);
 518   }
 519
 520   /**
 521    * DOCUMENT ME!
 522    *
 523    * @throws Exception
 524    *                 DOCUMENT ME!
 525    */
 526   private void jbInit() throws Exception
 527   {
 528     groupMenu.setText("Group");
 529     groupMenu.setText("Selection");
 530     groupName.setText("Name");
 531     groupName.addActionListener(new java.awt.event.ActionListener()
 532     {
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         groupName_actionPerformed();
 536       }
 537     });
 538     sequenceMenu.setText("Sequence");
 539     sequenceName.setText("Edit Name/Description");
 540     sequenceName.addActionListener(new java.awt.event.ActionListener()
 541     {
 542       public void actionPerformed(ActionEvent e)
 543       {
 544         sequenceName_actionPerformed();
 545       }
 546     });
 547     PIDColour.setFocusPainted(false);
 548     unGroupMenuItem.setText("Remove Group");
 549     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 550     {
 551       public void actionPerformed(ActionEvent e)
 552       {
 553         unGroupMenuItem_actionPerformed();
 554       }
 555     });
 556
 557     outline.setText("Border colour");
 558     outline.addActionListener(new java.awt.event.ActionListener()
 559     {
 560       public void actionPerformed(ActionEvent e)
 561       {
 562         outline_actionPerformed();
 563       }
 564     });
 565     nucleotideMenuItem.setText("Nucleotide");
 566     nucleotideMenuItem.addActionListener(new ActionListener()
 567     {
 568       public void actionPerformed(ActionEvent e)
 569       {
 570         nucleotideMenuItem_actionPerformed();
 571       }
 572     });
 573     colourMenu.setText("Group Colour");
 574     showBoxes.setText("Boxes");
 575     showBoxes.setState(true);
 576     showBoxes.addActionListener(new ActionListener()
 577     {
 578       public void actionPerformed(ActionEvent e)
 579       {
 580         showBoxes_actionPerformed();
 581       }
 582     });
 583     showText.setText("Text");
 584     showText.setState(true);
 585     showText.addActionListener(new ActionListener()
 586     {
 587       public void actionPerformed(ActionEvent e)
 588       {
 589         showText_actionPerformed();
 590       }
 591     });
 592     showColourText.setText("Colour Text");
 593     showColourText.addActionListener(new ActionListener()
 594     {
 595       public void actionPerformed(ActionEvent e)
 596       {
 597         showColourText_actionPerformed();
 598       }
 599     });
 600     editMenu.setText("Edit");
 601     cut.setText("Cut");
 602     cut.addActionListener(new ActionListener()
 603     {
 604       public void actionPerformed(ActionEvent e)
 605       {
 606         cut_actionPerformed();
 607       }
 608     });
 609     upperCase.setText("To Upper Case");
 610     upperCase.addActionListener(new ActionListener()
 611     {
 612       public void actionPerformed(ActionEvent e)
 613       {
 614         changeCase(e);
 615       }
 616     });
 617     copy.setText("Copy");
 618     copy.addActionListener(new ActionListener()
 619     {
 620       public void actionPerformed(ActionEvent e)
 621       {
 622         copy_actionPerformed();
 623       }
 624     });
 625     lowerCase.setText("To Lower Case");
 626     lowerCase.addActionListener(new ActionListener()
 627     {
 628       public void actionPerformed(ActionEvent e)
 629       {
 630         changeCase(e);
 631       }
 632     });
 633     toggle.setText("Toggle Case");
 634     toggle.addActionListener(new ActionListener()
 635     {
 636       public void actionPerformed(ActionEvent e)
 637       {
 638         changeCase(e);
 639       }
 640     });
 641     pdbMenu.setText("Associate Structure with Sequence");
 642     pdbFromFile.setText("From File");
 643     pdbFromFile.addActionListener(new ActionListener()
 644     {
 645       public void actionPerformed(ActionEvent e)
 646       {
 647         pdbFromFile_actionPerformed();
 648       }
 649     });
 650     enterPDB.setText("Enter PDB Id");
 651     enterPDB.addActionListener(new ActionListener()
 652     {
 653       public void actionPerformed(ActionEvent e)
 654       {
 655         enterPDB_actionPerformed();
 656       }
 657     });
 658     discoverPDB.setText("Discover PDB ids");
 659     discoverPDB.addActionListener(new ActionListener()
 660     {
 661       public void actionPerformed(ActionEvent e)
 662       {
 663         discoverPDB_actionPerformed();
 664       }
 665     });
 666     outputMenu.setText("Output to Textbox...");
 667     sequenceFeature.setText("Create Sequence Feature");
 668     sequenceFeature.addActionListener(new ActionListener()
 669     {
 670       public void actionPerformed(ActionEvent e)
 671       {
 672         sequenceFeature_actionPerformed();
 673       }
 674     });
 675     textColour.setText("Text Colour");
 676     textColour.addActionListener(new ActionListener()
 677     {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         textColour_actionPerformed();
 681       }
 682     });
 683     jMenu1.setText("Group");
 684     structureMenu.setText("Structure");
 685     viewStructureMenu.setText("View Structure");
 686     // colStructureMenu.setText("Colour By Structure");
 687     editSequence.setText("Edit Sequence...");
 688     editSequence.addActionListener(new ActionListener()
 689     {
 690       public void actionPerformed(ActionEvent actionEvent)
 691       {
 692         editSequence_actionPerformed(actionEvent);
 693       }
 694     });
 695     /*
 696      * annotationMenuItem.setText("By Annotation");
 697      * annotationMenuItem.addActionListener(new ActionListener() { public void
 698      * actionPerformed(ActionEvent actionEvent) {
 699      * annotationMenuItem_actionPerformed(actionEvent); } });
 700      */
 701
 702     add(groupMenu);
 703
 704     add(sequenceMenu);
 705     this.add(structureMenu);
 706     groupMenu.add(editMenu);
 707     groupMenu.add(outputMenu);
 708     groupMenu.add(sequenceFeature);
 709     groupMenu.add(jMenu1);
 710     sequenceMenu.add(sequenceName);
 711     colourMenu.add(textColour);
 712     colourMenu.add(noColourmenuItem);
 713     colourMenu.add(clustalColour);
 714     colourMenu.add(BLOSUM62Colour);
 715     colourMenu.add(PIDColour);
 716     colourMenu.add(zappoColour);
 717     colourMenu.add(taylorColour);
 718     colourMenu.add(hydrophobicityColour);
 719     colourMenu.add(helixColour);
 720     colourMenu.add(strandColour);
 721     colourMenu.add(turnColour);
 722     colourMenu.add(buriedColour);
 723     colourMenu.add(nucleotideMenuItem);
 724     colourMenu.add(userDefinedColour);
 725
 726     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 727     {
 728       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 729               .getUserColourSchemes().keys();
 730
 731       while (userColours.hasMoreElements())
 732       {
 733         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 734         item.addActionListener(new ActionListener()
 735         {
 736           public void actionPerformed(ActionEvent evt)
 737           {
 738             userDefinedColour_actionPerformed(evt);
 739           }
 740         });
 741         colourMenu.add(item);
 742       }
 743     }
 744
 745     colourMenu.addSeparator();
 746     colourMenu.add(abovePIDColour);
 747     colourMenu.add(conservationMenuItem);
 748     // colourMenu.add(annotationMenuItem);
 749     editMenu.add(copy);
 750     editMenu.add(cut);
 751     editMenu.add(editSequence);
 752     editMenu.add(upperCase);
 753     editMenu.add(lowerCase);
 754     editMenu.add(toggle);
 755     pdbMenu.add(pdbFromFile);
 756     pdbMenu.add(enterPDB);
 757     pdbMenu.add(discoverPDB);
 758     jMenu1.add(groupName);
 759     jMenu1.add(unGroupMenuItem);
 760     jMenu1.add(colourMenu);
 761     jMenu1.add(showBoxes);
 762     jMenu1.add(showText);
 763     jMenu1.add(showColourText);
 764     jMenu1.add(outline);
 765     structureMenu.add(pdbMenu);
 766     structureMenu.add(viewStructureMenu);
 767     // structureMenu.add(colStructureMenu);
 768     noColourmenuItem.setText("None");
 769     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 770     {
 771       public void actionPerformed(ActionEvent e)
 772       {
 773         noColourmenuItem_actionPerformed();
 774       }
 775     });
 776
 777     clustalColour.setText("Clustalx colours");
 778     clustalColour.addActionListener(new java.awt.event.ActionListener()
 779     {
 780       public void actionPerformed(ActionEvent e)
 781       {
 782         clustalColour_actionPerformed();
 783       }
 784     });
 785     zappoColour.setText("Zappo");
 786     zappoColour.addActionListener(new java.awt.event.ActionListener()
 787     {
 788       public void actionPerformed(ActionEvent e)
 789       {
 790         zappoColour_actionPerformed();
 791       }
 792     });
 793     taylorColour.setText("Taylor");
 794     taylorColour.addActionListener(new java.awt.event.ActionListener()
 795     {
 796       public void actionPerformed(ActionEvent e)
 797       {
 798         taylorColour_actionPerformed();
 799       }
 800     });
 801     hydrophobicityColour.setText("Hydrophobicity");
 802     hydrophobicityColour
 803             .addActionListener(new java.awt.event.ActionListener()
 804             {
 805               public void actionPerformed(ActionEvent e)
 806               {
 807                 hydrophobicityColour_actionPerformed();
 808               }
 809             });
 810     helixColour.setText("Helix propensity");
 811     helixColour.addActionListener(new java.awt.event.ActionListener()
 812     {
 813       public void actionPerformed(ActionEvent e)
 814       {
 815         helixColour_actionPerformed();
 816       }
 817     });
 818     strandColour.setText("Strand propensity");
 819     strandColour.addActionListener(new java.awt.event.ActionListener()
 820     {
 821       public void actionPerformed(ActionEvent e)
 822       {
 823         strandColour_actionPerformed();
 824       }
 825     });
 826     turnColour.setText("Turn propensity");
 827     turnColour.addActionListener(new java.awt.event.ActionListener()
 828     {
 829       public void actionPerformed(ActionEvent e)
 830       {
 831         turnColour_actionPerformed();
 832       }
 833     });
 834     buriedColour.setText("Buried Index");
 835     buriedColour.addActionListener(new java.awt.event.ActionListener()
 836     {
 837       public void actionPerformed(ActionEvent e)
 838       {
 839         buriedColour_actionPerformed();
 840       }
 841     });
 842     abovePIDColour.setText("Above % Identity");
 843     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 844     {
 845       public void actionPerformed(ActionEvent e)
 846       {
 847         abovePIDColour_actionPerformed();
 848       }
 849     });
 850     userDefinedColour.setText("User Defined...");
 851     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 852     {
 853       public void actionPerformed(ActionEvent e)
 854       {
 855         userDefinedColour_actionPerformed(e);
 856       }
 857     });
 858     PIDColour.setText("Percentage Identity");
 859     PIDColour.addActionListener(new java.awt.event.ActionListener()
 860     {
 861       public void actionPerformed(ActionEvent e)
 862       {
 863         PIDColour_actionPerformed();
 864       }
 865     });
 866     BLOSUM62Colour.setText("BLOSUM62");
 867     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 868     {
 869       public void actionPerformed(ActionEvent e)
 870       {
 871         BLOSUM62Colour_actionPerformed();
 872       }
 873     });
 874     conservationMenuItem.setText("Conservation");
 875     conservationMenuItem
 876             .addActionListener(new java.awt.event.ActionListener()
 877             {
 878               public void actionPerformed(ActionEvent e)
 879               {
 880                 conservationMenuItem_actionPerformed();
 881               }
 882             });
 883   }
 884
 885   /**
 886    * DOCUMENT ME!
 887    */
 888   void refresh()
 889   {
 890     ap.paintAlignment(true);
 891
 892     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 893   }
 894
 895   /**
 896    * DOCUMENT ME!
 897    *
 898    * @param e
 899    *                DOCUMENT ME!
 900    */
 901   protected void clustalColour_actionPerformed()
 902   {
 903     SequenceGroup sg = getGroup();
 904     sg.cs = new ClustalxColourScheme(sg
 905             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 906             .getWidth());
 907     refresh();
 908   }
 909
 910   /**
 911    * DOCUMENT ME!
 912    *
 913    * @param e
 914    *                DOCUMENT ME!
 915    */
 916   protected void zappoColour_actionPerformed()
 917   {
 918     getGroup().cs = new ZappoColourScheme();
 919     refresh();
 920   }
 921
 922   /**
 923    * DOCUMENT ME!
 924    *
 925    * @param e
 926    *                DOCUMENT ME!
 927    */
 928   protected void taylorColour_actionPerformed()
 929   {
 930     getGroup().cs = new TaylorColourScheme();
 931     refresh();
 932   }
 933
 934   /**
 935    * DOCUMENT ME!
 936    *
 937    * @param e
 938    *                DOCUMENT ME!
 939    */
 940   protected void hydrophobicityColour_actionPerformed()
 941   {
 942     getGroup().cs = new HydrophobicColourScheme();
 943     refresh();
 944   }
 945
 946   /**
 947    * DOCUMENT ME!
 948    *
 949    * @param e
 950    *                DOCUMENT ME!
 951    */
 952   protected void helixColour_actionPerformed()
 953   {
 954     getGroup().cs = new HelixColourScheme();
 955     refresh();
 956   }
 957
 958   /**
 959    * DOCUMENT ME!
 960    *
 961    * @param e
 962    *                DOCUMENT ME!
 963    */
 964   protected void strandColour_actionPerformed()
 965   {
 966     getGroup().cs = new StrandColourScheme();
 967     refresh();
 968   }
 969
 970   /**
 971    * DOCUMENT ME!
 972    *
 973    * @param e
 974    *                DOCUMENT ME!
 975    */
 976   protected void turnColour_actionPerformed()
 977   {
 978     getGroup().cs = new TurnColourScheme();
 979     refresh();
 980   }
 981
 982   /**
 983    * DOCUMENT ME!
 984    *
 985    * @param e
 986    *                DOCUMENT ME!
 987    */
 988   protected void buriedColour_actionPerformed()
 989   {
 990     getGroup().cs = new BuriedColourScheme();
 991     refresh();
 992   }
 993
 994   /**
 995    * DOCUMENT ME!
 996    *
 997    * @param e
 998    *                DOCUMENT ME!
 999    */
1000   public void nucleotideMenuItem_actionPerformed()
1001   {
1002     getGroup().cs = new NucleotideColourScheme();
1003     refresh();
1004   }
1005
1006   /**
1007    * DOCUMENT ME!
1008    *
1009    * @param e
1010    *                DOCUMENT ME!
1011    */
1012   protected void abovePIDColour_actionPerformed()
1013   {
1014     SequenceGroup sg = getGroup();
1015     if (sg.cs == null)
1016     {
1017       return;
1018     }
1019
1020     if (abovePIDColour.isSelected())
1021     {
1022       sg.cs.setConsensus(AAFrequency.calculate(sg
1023               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1024               .getEndRes() + 1));
1025
1026       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1027               .getName());
1028
1029       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1030
1031       SliderPanel.showPIDSlider();
1032     }
1033     else
1034     // remove PIDColouring
1035     {
1036       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1037     }
1038
1039     refresh();
1040   }
1041
1042   /**
1043    * DOCUMENT ME!
1044    *
1045    * @param e
1046    *                DOCUMENT ME!
1047    */
1048   protected void userDefinedColour_actionPerformed(ActionEvent e)
1049   {
1050     SequenceGroup sg = getGroup();
1051
1052     if (e.getActionCommand().equals("User Defined..."))
1053     {
1054       new UserDefinedColours(ap, sg);
1055     }
1056     else
1057     {
1058       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1059               .getUserColourSchemes().get(e.getActionCommand());
1060
1061       sg.cs = udc;
1062     }
1063     refresh();
1064   }
1065
1066   /**
1067    * DOCUMENT ME!
1068    *
1069    * @param e
1070    *                DOCUMENT ME!
1071    */
1072   protected void PIDColour_actionPerformed()
1073   {
1074     SequenceGroup sg = getGroup();
1075     sg.cs = new PIDColourScheme();
1076     sg.cs.setConsensus(AAFrequency.calculate(sg
1077             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1078             .getEndRes() + 1));
1079     refresh();
1080   }
1081
1082   /**
1083    * DOCUMENT ME!
1084    *
1085    * @param e
1086    *                DOCUMENT ME!
1087    */
1088   protected void BLOSUM62Colour_actionPerformed()
1089   {
1090     SequenceGroup sg = getGroup();
1091
1092     sg.cs = new Blosum62ColourScheme();
1093
1094     sg.cs.setConsensus(AAFrequency.calculate(sg
1095             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1096             .getEndRes() + 1));
1097
1098     refresh();
1099   }
1100
1101   /**
1102    * DOCUMENT ME!
1103    *
1104    * @param e
1105    *                DOCUMENT ME!
1106    */
1107   protected void noColourmenuItem_actionPerformed()
1108   {
1109     getGroup().cs = null;
1110     refresh();
1111   }
1112
1113   /**
1114    * DOCUMENT ME!
1115    *
1116    * @param e
1117    *                DOCUMENT ME!
1118    */
1119   protected void conservationMenuItem_actionPerformed()
1120   {
1121     SequenceGroup sg = getGroup();
1122     if (sg.cs == null)
1123     {
1124       return;
1125     }
1126
1127     if (conservationMenuItem.isSelected())
1128     {
1129       Conservation c = new Conservation("Group",
1130               ResidueProperties.propHash, 3, sg
1131                       .getSequences(ap.av.hiddenRepSequences), sg
1132                       .getStartRes(), sg.getEndRes() + 1);
1133
1134       c.calculate();
1135       c.verdict(false, ap.av.ConsPercGaps);
1136
1137       sg.cs.setConservation(c);
1138
1139       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1140       SliderPanel.showConservationSlider();
1141     }
1142     else
1143     // remove ConservationColouring
1144     {
1145       sg.cs.setConservation(null);
1146     }
1147
1148     refresh();
1149   }
1150
1151   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1152   {
1153     SequenceGroup sg = getGroup();
1154     if (sg == null)
1155     {
1156       return;
1157     }
1158
1159     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1160             .getAnnotation()[0], null,
1161             AnnotationColourGradient.NO_THRESHOLD);
1162
1163     acg.predefinedColours = true;
1164     sg.cs = acg;
1165
1166     refresh();
1167   }
1168
1169   /**
1170    * DOCUMENT ME!
1171    *
1172    * @param e
1173    *                DOCUMENT ME!
1174    */
1175   protected void groupName_actionPerformed()
1176   {
1177
1178     SequenceGroup sg = getGroup();
1179     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1180             .getDescription(), "       Group Name ", "Group Description ",
1181             "Edit Group Name/Description");
1182
1183     if (!dialog.accept)
1184     {
1185       return;
1186     }
1187
1188     sg.setName(dialog.getName());
1189     sg.setDescription(dialog.getDescription());
1190   }
1191
1192   /**
1193    * DOCUMENT ME!
1194    *
1195    * @return DOCUMENT ME!
1196    */
1197   SequenceGroup getGroup()
1198   {
1199     SequenceGroup sg = ap.av.getSelectionGroup();
1200     // this method won't add a new group if it already exists
1201     if (sg != null)
1202     {
1203       ap.av.alignment.addGroup(sg);
1204     }
1205
1206     return sg;
1207   }
1208
1209   /**
1210    * DOCUMENT ME!
1211    *
1212    * @param e
1213    *                DOCUMENT ME!
1214    */
1215   void sequenceName_actionPerformed()
1216   {
1217     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1218             .getDescription(), "       Sequence Name ",
1219             "Sequence Description ", "Edit Sequence Name/Description");
1220
1221     if (!dialog.accept)
1222     {
1223       return;
1224     }
1225
1226     if (dialog.getName() != null)
1227     {
1228       if (dialog.getName().indexOf(" ") > -1)
1229       {
1230         JOptionPane.showMessageDialog(ap,
1231                 "Spaces have been converted to \"_\"",
1232                 "No spaces allowed in Sequence Name",
1233                 JOptionPane.WARNING_MESSAGE);
1234       }
1235
1236       sequence.setName(dialog.getName().replace(' ', '_'));
1237       ap.paintAlignment(false);
1238     }
1239
1240     sequence.setDescription(dialog.getDescription());
1241
1242     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1243             .getSequences());
1244
1245   }
1246
1247   /**
1248    * DOCUMENT ME!
1249    *
1250    * @param e
1251    *                DOCUMENT ME!
1252    */
1253   void unGroupMenuItem_actionPerformed()
1254   {
1255     SequenceGroup sg = ap.av.getSelectionGroup();
1256     ap.av.alignment.deleteGroup(sg);
1257     ap.av.setSelectionGroup(null);
1258     refresh();
1259   }
1260
1261   /**
1262    * DOCUMENT ME!
1263    *
1264    * @param e
1265    *                DOCUMENT ME!
1266    */
1267   protected void outline_actionPerformed()
1268   {
1269     SequenceGroup sg = getGroup();
1270     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1271             Color.BLUE);
1272
1273     if (col != null)
1274     {
1275       sg.setOutlineColour(col);
1276     }
1277
1278     refresh();
1279   }
1280
1281   /**
1282    * DOCUMENT ME!
1283    *
1284    * @param e
1285    *                DOCUMENT ME!
1286    */
1287   public void showBoxes_actionPerformed()
1288   {
1289     getGroup().setDisplayBoxes(showBoxes.isSelected());
1290     refresh();
1291   }
1292
1293   /**
1294    * DOCUMENT ME!
1295    *
1296    * @param e
1297    *                DOCUMENT ME!
1298    */
1299   public void showText_actionPerformed()
1300   {
1301     getGroup().setDisplayText(showText.isSelected());
1302     refresh();
1303   }
1304
1305   /**
1306    * DOCUMENT ME!
1307    *
1308    * @param e
1309    *                DOCUMENT ME!
1310    */
1311   public void showColourText_actionPerformed()
1312   {
1313     getGroup().setColourText(showColourText.isSelected());
1314     refresh();
1315   }
1316
1317   public void showLink(String url)
1318   {
1319     try
1320     {
1321       jalview.util.BrowserLauncher.openURL(url);
1322     } catch (Exception ex)
1323     {
1324       JOptionPane
1325               .showInternalMessageDialog(
1326                       Desktop.desktop,
1327                       "Unixers: Couldn't find default web browser."
1328                               + "\nAdd the full path to your browser in Preferences.",
1329                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1330
1331       ex.printStackTrace();
1332     }
1333   }
1334
1335   void hideSequences(boolean representGroup)
1336   {
1337     SequenceGroup sg = ap.av.getSelectionGroup();
1338     if (sg == null || sg.getSize() < 1)
1339     {
1340       ap.av.hideSequence(new SequenceI[]
1341       { sequence });
1342       return;
1343     }
1344
1345     ap.av.setSelectionGroup(null);
1346
1347     if (representGroup)
1348     {
1349       ap.av.hideRepSequences(sequence, sg);
1350
1351       return;
1352     }
1353
1354     int gsize = sg.getSize();
1355     SequenceI[] hseqs;
1356
1357     hseqs = new SequenceI[gsize];
1358
1359     int index = 0;
1360     for (int i = 0; i < gsize; i++)
1361     {
1362       hseqs[index++] = sg.getSequenceAt(i);
1363     }
1364
1365     ap.av.hideSequence(hseqs);
1366   }
1367
1368   public void copy_actionPerformed()
1369   {
1370     ap.alignFrame.copy_actionPerformed(null);
1371   }
1372
1373   public void cut_actionPerformed()
1374   {
1375     ap.alignFrame.cut_actionPerformed(null);
1376   }
1377
1378   void changeCase(ActionEvent e)
1379   {
1380     Object source = e.getSource();
1381     SequenceGroup sg = ap.av.getSelectionGroup();
1382
1383     if (sg != null)
1384     {
1385       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1386               sg.getEndRes() + 1);
1387
1388       String description;
1389       int caseChange;
1390
1391       if (source == toggle)
1392       {
1393         description = "Toggle Case";
1394         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1395       }
1396       else if (source == upperCase)
1397       {
1398         description = "To Upper Case";
1399         caseChange = ChangeCaseCommand.TO_UPPER;
1400       }
1401       else
1402       {
1403         description = "To Lower Case";
1404         caseChange = ChangeCaseCommand.TO_LOWER;
1405       }
1406
1407       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1408               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1409               caseChange);
1410
1411       ap.alignFrame.addHistoryItem(caseCommand);
1412
1413       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1414               .getSequences());
1415
1416     }
1417   }
1418
1419   public void outputText_actionPerformed(ActionEvent e)
1420   {
1421     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1422     cap.setForInput(null);
1423     Desktop.addInternalFrame(cap, "Alignment output - "
1424             + e.getActionCommand(), 600, 500);
1425
1426     String[] omitHidden = null;
1427
1428     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1429                                             // or we simply trust the user wants
1430                                             // wysiwig behaviour
1431     SequenceGroup sg = ap.av.getSelectionGroup();
1432     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1433     omitHidden = ap.av.getViewAsString(true);
1434     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1435     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1436     for (int i = 0; i < nala.length; i++)
1437     {
1438       AlignmentAnnotation na = nala[i];
1439       oal.addAnnotation(na);
1440     }
1441     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1442             oal, omitHidden, csel, sg));
1443     oal = null;
1444   }
1445
1446   public void pdbFromFile_actionPerformed()
1447   {
1448     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1449             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1450     chooser.setFileView(new jalview.io.JalviewFileView());
1451     chooser.setDialogTitle("Select a PDB file");
1452     chooser.setToolTipText("Load a PDB file");
1453
1454     int value = chooser.showOpenDialog(null);
1455
1456     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1457     {
1458       PDBEntry entry = new PDBEntry();
1459       String choice = chooser.getSelectedFile().getPath();
1460       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1461       try
1462       {
1463         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1464                 jalview.io.AppletFormatAdapter.FILE);
1465
1466         if (pdbfile.id == null)
1467         {
1468           String reply = JOptionPane
1469                   .showInternalInputDialog(
1470                           Desktop.desktop,
1471                           "Couldn't find a PDB id in the file supplied."
1472                                   + "Please enter an Id to identify this structure.",
1473                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1474           if (reply == null)
1475           {
1476             return;
1477           }
1478
1479           entry.setId(reply);
1480         }
1481         else
1482         {
1483           entry.setId(pdbfile.id);
1484         }
1485       } catch (java.io.IOException ex)
1486       {
1487         ex.printStackTrace();
1488       }
1489
1490       entry.setFile(choice);
1491       sequence.getDatasetSequence().addPDBId(entry);
1492     }
1493
1494   }
1495
1496   public void enterPDB_actionPerformed()
1497   {
1498     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1499             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1500
1501     if (id != null && id.length() > 0)
1502     {
1503       PDBEntry entry = new PDBEntry();
1504       entry.setId(id.toUpperCase());
1505       sequence.getDatasetSequence().addPDBId(entry);
1506     }
1507   }
1508
1509   public void discoverPDB_actionPerformed()
1510   {
1511
1512     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1513     { sequence }
1514             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1515     Thread discpdb = new Thread(new Runnable()
1516     {
1517       public void run()
1518       {
1519
1520         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1521                 .fetchDBRefs(false);
1522       }
1523
1524     });
1525     discpdb.start();
1526   }
1527
1528   public void sequenceFeature_actionPerformed()
1529   {
1530     SequenceGroup sg = ap.av.getSelectionGroup();
1531     if (sg == null)
1532     {
1533       return;
1534     }
1535
1536     int gSize = sg.getSize();
1537     SequenceI[] seqs = new SequenceI[gSize];
1538     SequenceFeature[] features = new SequenceFeature[gSize];
1539
1540     for (int i = 0; i < gSize; i++)
1541     {
1542       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1543       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1544       int end = sg.findEndRes(sg.getSequenceAt(i));
1545       features[i] = new SequenceFeature(null, null, null, start, end,
1546               "Jalview");
1547     }
1548
1549     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1550             features, true, ap))
1551     {
1552       ap.alignFrame.showSeqFeatures.setSelected(true);
1553       ap.av.setShowSequenceFeatures(true);
1554       ap.highlightSearchResults(null);
1555     }
1556   }
1557
1558   public void textColour_actionPerformed()
1559   {
1560     SequenceGroup sg = getGroup();
1561     if (sg != null)
1562     {
1563       new TextColourChooser().chooseColour(ap, sg);
1564     }
1565   }
1566
1567   public void colourByStructure(String pdbid)
1568   {
1569     Annotation[] anots = jalview.structure.StructureSelectionManager
1570             .getStructureSelectionManager().colourSequenceFromStructure(
1571                     sequence, pdbid);
1572
1573     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1574             "Coloured by " + pdbid, anots);
1575
1576     ap.av.alignment.addAnnotation(an);
1577     an.createSequenceMapping(sequence, 0, true);
1578     // an.adjustForAlignment();
1579     ap.av.alignment.setAnnotationIndex(an, 0);
1580
1581     ap.adjustAnnotationHeight();
1582
1583     sequence.addAlignmentAnnotation(an);
1584
1585   }
1586
1587   public void editSequence_actionPerformed(ActionEvent actionEvent)
1588   {
1589     SequenceGroup sg = ap.av.getSelectionGroup();
1590
1591     if (sg != null)
1592     {
1593       if (sequence == null)
1594         sequence = (Sequence) sg.getSequenceAt(0);
1595
1596       EditNameDialog dialog = new EditNameDialog(sequence
1597               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1598               null, "Edit Sequence ", null, "Edit Sequence");
1599
1600       if (dialog.accept)
1601       {
1602         EditCommand editCommand = new EditCommand("Edit Sequences",
1603                 EditCommand.REPLACE, dialog.getName().replace(' ',
1604                         ap.av.getGapCharacter()), sg
1605                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1606                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1607
1608         ap.alignFrame.addHistoryItem(editCommand);
1609
1610         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1611                 .getSequences());
1612       }
1613     }
1614   }
1615
1616 }