src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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
  42     extends JPopupMenu
  43 {
  44   JMenu groupMenu = new JMenu();
  45   JMenuItem groupName = new JMenuItem();
  46   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  47   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  48   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  49   protected JRadioButtonMenuItem hydrophobicityColour = new
  50       JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  54   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  55   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  56   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  58   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  59   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  60   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  61   AlignmentPanel ap;
  62   JMenu sequenceMenu = new JMenu();
  63   JMenuItem sequenceName = new JMenuItem();
  64   Sequence sequence;
  65   JMenuItem unGroupMenuItem = new JMenuItem();
  66   JMenuItem outline = new JMenuItem();
  67   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  68   JMenu colourMenu = new JMenu();
  69   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  70   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  71   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  72   JMenu editMenu = new JMenu();
  73   JMenuItem cut = new JMenuItem();
  74   JMenuItem copy = new JMenuItem();
  75   JMenuItem upperCase = new JMenuItem();
  76   JMenuItem lowerCase = new JMenuItem();
  77   JMenuItem toggle = new JMenuItem();
  78   JMenu pdbMenu = new JMenu();
  79   JMenuItem pdbFromFile = new JMenuItem();
  80   JMenuItem enterPDB = new JMenuItem();
  81   JMenuItem discoverPDB = new JMenuItem();
  82   JMenu outputMenu = new JMenu();
  83   JMenuItem sequenceFeature = new JMenuItem();
  84   JMenuItem textColour = new JMenuItem();
  85   JMenu jMenu1 = new JMenu();
  86   JMenu structureMenu = new JMenu();
  87   JMenu viewStructureMenu = new JMenu();
  88  // JMenu colStructureMenu = new JMenu();
  89   JMenuItem editSequence = new JMenuItem();
  90  // JMenuItem annotationMenuItem = new JMenuItem();
  91
  92   /**
  93    * Creates a new PopupMenu object.
  94    *
  95    * @param ap DOCUMENT ME!
  96    * @param seq DOCUMENT ME!
  97    */
  98   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
  99   {
 100     ///////////////////////////////////////////////////////////
 101     // If this is activated from the sequence panel, the user may want to
 102     // edit or annotate a particular residue. Therefore display the residue menu
 103     //
 104     // If from the IDPanel, we must display the sequence menu
 105     //////////////////////////////////////////////////////////
 106     this.ap = ap;
 107     sequence = seq;
 108
 109     ButtonGroup colours = new ButtonGroup();
 110     colours.add(noColourmenuItem);
 111     colours.add(clustalColour);
 112     colours.add(zappoColour);
 113     colours.add(taylorColour);
 114     colours.add(hydrophobicityColour);
 115     colours.add(helixColour);
 116     colours.add(strandColour);
 117     colours.add(turnColour);
 118     colours.add(buriedColour);
 119     colours.add(abovePIDColour);
 120     colours.add(userDefinedColour);
 121     colours.add(PIDColour);
 122     colours.add(BLOSUM62Colour);
 123
 124     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 125     {
 126       JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
 127                                      i]);
 128
 129       item.addActionListener(new java.awt.event.ActionListener()
 130       {
 131         public void actionPerformed(ActionEvent e)
 132         {
 133           outputText_actionPerformed(e);
 134         }
 135       });
 136
 137       outputMenu.add(item);
 138     }
 139
 140     try
 141     {
 142       jbInit();
 143     }
 144     catch (Exception e)
 145     {
 146       e.printStackTrace();
 147     }
 148
 149     if (seq != null)
 150     {
 151       sequenceMenu.setText(sequence.getName());
 152
 153       JMenuItem menuItem;
 154       if (seq.getDatasetSequence().getPDBId() != null
 155           && seq.getDatasetSequence().getPDBId().size()>0)
 156       {
 157         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
 158             elements();
 159
 160         while (e.hasMoreElements())
 161         {
 162           final PDBEntry pdb = (PDBEntry) e.nextElement();
 163
 164           menuItem = new JMenuItem();
 165           menuItem.setText(pdb.getId());
 166           menuItem.addActionListener(new java.awt.event.ActionListener()
 167           {
 168             public void actionPerformed(ActionEvent e)
 169             {
 170               Vector seqs = new Vector();
 171               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 172               {
 173                 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
 174                 if(pdbs==null)
 175                   continue;
 176
 177                 for(int p=0; p<pdbs.size(); p++)
 178                 {
 179                   PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
 180                   if(p1.getId().equals(pdb.getId()))
 181                   {
 182                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 183                         seqs.addElement(ap.av.alignment.getSequenceAt(i));
 184
 185                       continue;
 186                   }
 187                 }
 188               }
 189
 190               SequenceI [] seqs2 = new SequenceI[seqs.size()];
 191               seqs.toArray(seqs2);
 192
 193               new AppJmol(pdb, seqs2, null, ap);
 194               //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 195             }
 196           });
 197           viewStructureMenu.add(menuItem);
 198
 199        /*   menuItem = new JMenuItem();
 200           menuItem.setText(pdb.getId());
 201           menuItem.addActionListener(new java.awt.event.ActionListener()
 202           {
 203             public void actionPerformed(ActionEvent e)
 204             {
 205               colourByStructure(pdb.getId());
 206             }
 207           });
 208           colStructureMenu.add(menuItem);*/
 209         }
 210       }
 211       else
 212       {
 213         structureMenu.remove(viewStructureMenu);
 214        // structureMenu.remove(colStructureMenu);
 215       }
 216
 217       menuItem = new JMenuItem("Hide Sequences");
 218       menuItem.addActionListener(new java.awt.event.ActionListener()
 219       {
 220         public void actionPerformed(ActionEvent e)
 221         {
 222           hideSequences(false);
 223         }
 224       });
 225       add(menuItem);
 226
 227       if (ap.av.getSelectionGroup() != null
 228           && ap.av.getSelectionGroup().getSize() > 1)
 229       {
 230         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 231         menuItem.addActionListener(new java.awt.event.ActionListener()
 232         {
 233           public void actionPerformed(ActionEvent e)
 234           {
 235             hideSequences(true);
 236           }
 237         });
 238         sequenceMenu.add(menuItem);
 239       }
 240
 241       if (ap.av.hasHiddenRows)
 242       {
 243         final int index = ap.av.alignment.findIndex(seq);
 244
 245         if (ap.av.adjustForHiddenSeqs(index) -
 246             ap.av.adjustForHiddenSeqs(index - 1) > 1)
 247         {
 248           menuItem = new JMenuItem("Reveal Sequences");
 249           menuItem.addActionListener(new ActionListener()
 250           {
 251             public void actionPerformed(ActionEvent e)
 252             {
 253               ap.av.showSequence(index);
 254               if (ap.overviewPanel != null)
 255               {
 256                 ap.overviewPanel.updateOverviewImage();
 257               }
 258             }
 259           });
 260           add(menuItem);
 261         }
 262
 263         menuItem = new JMenuItem("Reveal All");
 264         menuItem.addActionListener(new ActionListener()
 265         {
 266           public void actionPerformed(ActionEvent e)
 267           {
 268             ap.av.showAllHiddenSeqs();
 269             if (ap.overviewPanel != null)
 270             {
 271               ap.overviewPanel.updateOverviewImage();
 272             }
 273           }
 274         });
 275
 276         add(menuItem);
 277       }
 278
 279     }
 280
 281     SequenceGroup sg = ap.av.getSelectionGroup();
 282
 283     if (sg != null)
 284     {
 285       groupName.setText(sg.getName());
 286
 287       if (sg.cs instanceof ZappoColourScheme)
 288       {
 289         zappoColour.setSelected(true);
 290       }
 291       else if (sg.cs instanceof TaylorColourScheme)
 292       {
 293         taylorColour.setSelected(true);
 294       }
 295       else if (sg.cs instanceof PIDColourScheme)
 296       {
 297         PIDColour.setSelected(true);
 298       }
 299       else if (sg.cs instanceof Blosum62ColourScheme)
 300       {
 301         BLOSUM62Colour.setSelected(true);
 302       }
 303       else if (sg.cs instanceof UserColourScheme)
 304       {
 305         userDefinedColour.setSelected(true);
 306       }
 307       else if (sg.cs instanceof HydrophobicColourScheme)
 308       {
 309         hydrophobicityColour.setSelected(true);
 310       }
 311       else if (sg.cs instanceof HelixColourScheme)
 312       {
 313         helixColour.setSelected(true);
 314       }
 315       else if (sg.cs instanceof StrandColourScheme)
 316       {
 317         strandColour.setSelected(true);
 318       }
 319       else if (sg.cs instanceof TurnColourScheme)
 320       {
 321         turnColour.setSelected(true);
 322       }
 323       else if (sg.cs instanceof BuriedColourScheme)
 324       {
 325         buriedColour.setSelected(true);
 326       }
 327       else if (sg.cs instanceof ClustalxColourScheme)
 328       {
 329         clustalColour.setSelected(true);
 330       }
 331       else
 332       {
 333         noColourmenuItem.setSelected(true);
 334       }
 335
 336       if (sg.cs != null && sg.cs.conservationApplied())
 337       {
 338         conservationMenuItem.setSelected(true);
 339       }
 340
 341       showText.setSelected(sg.getDisplayText());
 342       showColourText.setSelected(sg.getColourText());
 343       showBoxes.setSelected(sg.getDisplayBoxes());
 344     }
 345     else
 346     {
 347       groupMenu.setVisible(false);
 348       editMenu.setVisible(false);
 349     }
 350
 351     if (!ap.av.alignment.getGroups().contains(sg))
 352     {
 353       unGroupMenuItem.setVisible(false);
 354     }
 355
 356     if (seq == null)
 357     {
 358       sequenceMenu.setVisible(false);
 359       structureMenu.setVisible(false);
 360     }
 361
 362     if (links != null && links.size() > 0)
 363     {
 364       JMenu linkMenu = new JMenu("Link");
 365
 366       for (int i = 0; i < links.size(); i++)
 367       {
 368         String link = links.elementAt(i).toString();
 369         UrlLink urlLink = null;
 370         try {
 371           urlLink = new UrlLink(link);
 372         } catch (Exception foo) {
 373           jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo);
 374           continue;
 375         };
 376         if (!urlLink.isValid())
 377         {
 378           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 379           continue;
 380         }
 381         final String label = urlLink.getLabel();
 382         if (urlLink.isDynamic())
 383         {
 384
 385           // collect matching db-refs
 386           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
 387           // collect id string too
 388           String id = seq.getName();
 389           if (dbr!=null)
 390           {
 391             for (int r=0;r<dbr.length; r++)
 392             {
 393               if (id!=null && dbr[r].getAccessionId().equals(id))
 394               {
 395                 // suppress duplicate link creation for the bare sequence ID string with this link
 396                 id = null;
 397               }
 398               // create Bare ID link for this RUL
 399               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
 400               if (urls!=null)
 401               {
 402                 for (int u=0; u<urls.length; u+=2)
 403                 {
 404                   addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
 405                 }
 406               }
 407             }
 408           }
 409           if (id!=null)
 410           {
 411             // create Bare ID link for this RUL
 412             String[] urls = urlLink.makeUrls(id, true);
 413             if (urls!=null)
 414             {
 415               for (int u=0; u<urls.length; u+=2)
 416               {
 417                 addshowLink(linkMenu, label,  urls[u+1]);
 418               }
 419             }
 420           }
 421         } else
 422         {
 423           // Add a non-dynamic link
 424           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 425         }
 426       }
 427       if (sequence != null)
 428       {
 429         sequenceMenu.add(linkMenu);
 430       }
 431       else
 432       {
 433         add(linkMenu);
 434       }
 435     }
 436   }
 437
 438   /**
 439    * add a show URL menu item to the given linkMenu
 440    * @param linkMenu
 441    * @param label - menu label string
 442    * @param url - url to open
 443    */
 444   private void addshowLink(JMenu linkMenu, String label, final String url)
 445   {
 446     JMenuItem item = new JMenuItem(label);
 447     item.setToolTipText("open URL: "+url);
 448     item.addActionListener(new java.awt.event.ActionListener()
 449     {
 450       public void actionPerformed(ActionEvent e)
 451       {
 452         new Thread(new Runnable() {
 453
 454           public void run()
 455           {
 456             showLink(url);
 457           }
 458
 459         }).start();
 460       }
 461     });
 462
 463     linkMenu.add(item);
 464   }
 465
 466   /**
 467    * DOCUMENT ME!
 468    *
 469    * @throws Exception DOCUMENT ME!
 470    */
 471   private void jbInit()
 472       throws Exception
 473   {
 474     groupMenu.setText("Group");
 475     groupMenu.setText("Selection");
 476     groupName.setText("Name");
 477     groupName.addActionListener(new java.awt.event.ActionListener()
 478     {
 479       public void actionPerformed(ActionEvent e)
 480       {
 481         groupName_actionPerformed();
 482       }
 483     });
 484     sequenceMenu.setText("Sequence");
 485     sequenceName.setText("Edit Name/Description");
 486     sequenceName.addActionListener(new java.awt.event.ActionListener()
 487     {
 488       public void actionPerformed(ActionEvent e)
 489       {
 490         sequenceName_actionPerformed();
 491       }
 492     });
 493     PIDColour.setFocusPainted(false);
 494     unGroupMenuItem.setText("Remove Group");
 495     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 496     {
 497       public void actionPerformed(ActionEvent e)
 498       {
 499         unGroupMenuItem_actionPerformed();
 500       }
 501     });
 502
 503     outline.setText("Border colour");
 504     outline.addActionListener(new java.awt.event.ActionListener()
 505     {
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         outline_actionPerformed();
 509       }
 510     });
 511     nucleotideMenuItem.setText("Nucleotide");
 512     nucleotideMenuItem.addActionListener(new ActionListener()
 513     {
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         nucleotideMenuItem_actionPerformed();
 517       }
 518     });
 519     colourMenu.setText("Group Colour");
 520     showBoxes.setText("Boxes");
 521     showBoxes.setState(true);
 522     showBoxes.addActionListener(new ActionListener()
 523     {
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         showBoxes_actionPerformed();
 527       }
 528     });
 529     showText.setText("Text");
 530     showText.setState(true);
 531     showText.addActionListener(new ActionListener()
 532     {
 533       public void actionPerformed(ActionEvent e)
 534       {
 535         showText_actionPerformed();
 536       }
 537     });
 538     showColourText.setText("Colour Text");
 539     showColourText.addActionListener(new ActionListener()
 540     {
 541       public void actionPerformed(ActionEvent e)
 542       {
 543         showColourText_actionPerformed();
 544       }
 545     });
 546     editMenu.setText("Edit");
 547     cut.setText("Cut");
 548     cut.addActionListener(new ActionListener()
 549     {
 550       public void actionPerformed(ActionEvent e)
 551       {
 552         cut_actionPerformed();
 553       }
 554     });
 555     upperCase.setText("To Upper Case");
 556     upperCase.addActionListener(new ActionListener()
 557     {
 558       public void actionPerformed(ActionEvent e)
 559       {
 560         changeCase(e);
 561       }
 562     });
 563     copy.setText("Copy");
 564     copy.addActionListener(new ActionListener()
 565     {
 566       public void actionPerformed(ActionEvent e)
 567       {
 568         copy_actionPerformed();
 569       }
 570     });
 571     lowerCase.setText("To Lower Case");
 572     lowerCase.addActionListener(new ActionListener()
 573     {
 574       public void actionPerformed(ActionEvent e)
 575       {
 576         changeCase(e);
 577       }
 578     });
 579     toggle.setText("Toggle Case");
 580     toggle.addActionListener(new ActionListener()
 581     {
 582       public void actionPerformed(ActionEvent e)
 583       {
 584         changeCase(e);
 585       }
 586     });
 587     pdbMenu.setText("Associate Structure with Sequence");
 588     pdbFromFile.setText("From File");
 589     pdbFromFile.addActionListener(new ActionListener()
 590     {
 591       public void actionPerformed(ActionEvent e)
 592       {
 593         pdbFromFile_actionPerformed();
 594       }
 595     });
 596     enterPDB.setText("Enter PDB Id");
 597     enterPDB.addActionListener(new ActionListener()
 598     {
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         enterPDB_actionPerformed();
 602       }
 603     });
 604     discoverPDB.setText("Discover PDB ids");
 605     discoverPDB.addActionListener(new ActionListener()
 606     {
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         discoverPDB_actionPerformed();
 610       }
 611     });
 612     outputMenu.setText("Output to Textbox...");
 613     sequenceFeature.setText("Create Sequence Feature");
 614     sequenceFeature.addActionListener(new ActionListener()
 615     {
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         sequenceFeature_actionPerformed();
 619       }
 620     });
 621     textColour.setText("Text Colour");
 622     textColour.addActionListener(new ActionListener()
 623     {
 624       public void actionPerformed(ActionEvent e)
 625       {
 626         textColour_actionPerformed();
 627       }
 628     });
 629     jMenu1.setText("Group");
 630     structureMenu.setText("Structure");
 631     viewStructureMenu.setText("View Structure");
 632   //  colStructureMenu.setText("Colour By Structure");
 633     editSequence.setText("Edit Sequence...");
 634     editSequence.addActionListener(new ActionListener()
 635     {
 636       public void actionPerformed(ActionEvent actionEvent)
 637       {
 638         editSequence_actionPerformed(actionEvent);
 639       }
 640     });
 641    /* annotationMenuItem.setText("By Annotation");
 642     annotationMenuItem.addActionListener(new ActionListener()
 643     {
 644       public void actionPerformed(ActionEvent actionEvent)
 645       {
 646         annotationMenuItem_actionPerformed(actionEvent);
 647       }
 648     });*/
 649
 650     add(groupMenu);
 651
 652     add(sequenceMenu);
 653     this.add(structureMenu);
 654     groupMenu.add(editMenu);
 655     groupMenu.add(outputMenu);
 656     groupMenu.add(sequenceFeature);
 657     groupMenu.add(jMenu1);
 658     sequenceMenu.add(sequenceName);
 659     colourMenu.add(textColour);
 660     colourMenu.add(noColourmenuItem);
 661     colourMenu.add(clustalColour);
 662     colourMenu.add(BLOSUM62Colour);
 663     colourMenu.add(PIDColour);
 664     colourMenu.add(zappoColour);
 665     colourMenu.add(taylorColour);
 666     colourMenu.add(hydrophobicityColour);
 667     colourMenu.add(helixColour);
 668     colourMenu.add(strandColour);
 669     colourMenu.add(turnColour);
 670     colourMenu.add(buriedColour);
 671     colourMenu.add(nucleotideMenuItem);
 672     colourMenu.add(userDefinedColour);
 673
 674     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 675     {
 676       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 677           getUserColourSchemes().keys();
 678
 679       while (userColours.hasMoreElements())
 680       {
 681         JMenuItem item = new JMenuItem(userColours.
 682                                        nextElement().toString());
 683         item.addActionListener(new ActionListener()
 684         {
 685           public void actionPerformed(ActionEvent evt)
 686           {
 687             userDefinedColour_actionPerformed(evt);
 688           }
 689         });
 690         colourMenu.add(item);
 691       }
 692     }
 693
 694     colourMenu.addSeparator();
 695     colourMenu.add(abovePIDColour);
 696     colourMenu.add(conservationMenuItem);
 697     //colourMenu.add(annotationMenuItem);
 698     editMenu.add(copy);
 699     editMenu.add(cut);
 700     editMenu.add(editSequence);
 701     editMenu.add(upperCase);
 702     editMenu.add(lowerCase);
 703     editMenu.add(toggle);
 704     pdbMenu.add(pdbFromFile);
 705     pdbMenu.add(enterPDB);
 706     pdbMenu.add(discoverPDB);
 707     jMenu1.add(groupName);
 708     jMenu1.add(unGroupMenuItem);
 709     jMenu1.add(colourMenu);
 710     jMenu1.add(showBoxes);
 711     jMenu1.add(showText);
 712     jMenu1.add(showColourText);
 713     jMenu1.add(outline);
 714     structureMenu.add(pdbMenu);
 715     structureMenu.add(viewStructureMenu);
 716    // structureMenu.add(colStructureMenu);
 717     noColourmenuItem.setText("None");
 718     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 719     {
 720       public void actionPerformed(ActionEvent e)
 721       {
 722         noColourmenuItem_actionPerformed();
 723       }
 724     });
 725
 726     clustalColour.setText("Clustalx colours");
 727     clustalColour.addActionListener(new java.awt.event.ActionListener()
 728     {
 729       public void actionPerformed(ActionEvent e)
 730       {
 731         clustalColour_actionPerformed();
 732       }
 733     });
 734     zappoColour.setText("Zappo");
 735     zappoColour.addActionListener(new java.awt.event.ActionListener()
 736     {
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         zappoColour_actionPerformed();
 740       }
 741     });
 742     taylorColour.setText("Taylor");
 743     taylorColour.addActionListener(new java.awt.event.ActionListener()
 744     {
 745       public void actionPerformed(ActionEvent e)
 746       {
 747         taylorColour_actionPerformed();
 748       }
 749     });
 750     hydrophobicityColour.setText("Hydrophobicity");
 751     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 752     {
 753       public void actionPerformed(ActionEvent e)
 754       {
 755         hydrophobicityColour_actionPerformed();
 756       }
 757     });
 758     helixColour.setText("Helix propensity");
 759     helixColour.addActionListener(new java.awt.event.ActionListener()
 760     {
 761       public void actionPerformed(ActionEvent e)
 762       {
 763         helixColour_actionPerformed();
 764       }
 765     });
 766     strandColour.setText("Strand propensity");
 767     strandColour.addActionListener(new java.awt.event.ActionListener()
 768     {
 769       public void actionPerformed(ActionEvent e)
 770       {
 771         strandColour_actionPerformed();
 772       }
 773     });
 774     turnColour.setText("Turn propensity");
 775     turnColour.addActionListener(new java.awt.event.ActionListener()
 776     {
 777       public void actionPerformed(ActionEvent e)
 778       {
 779         turnColour_actionPerformed();
 780       }
 781     });
 782     buriedColour.setText("Buried Index");
 783     buriedColour.addActionListener(new java.awt.event.ActionListener()
 784     {
 785       public void actionPerformed(ActionEvent e)
 786       {
 787         buriedColour_actionPerformed();
 788       }
 789     });
 790     abovePIDColour.setText("Above % Identity");
 791     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 792     {
 793       public void actionPerformed(ActionEvent e)
 794       {
 795         abovePIDColour_actionPerformed();
 796       }
 797     });
 798     userDefinedColour.setText("User Defined...");
 799     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 800     {
 801       public void actionPerformed(ActionEvent e)
 802       {
 803         userDefinedColour_actionPerformed(e);
 804       }
 805     });
 806     PIDColour.setText("Percentage Identity");
 807     PIDColour.addActionListener(new java.awt.event.ActionListener()
 808     {
 809       public void actionPerformed(ActionEvent e)
 810       {
 811         PIDColour_actionPerformed();
 812       }
 813     });
 814     BLOSUM62Colour.setText("BLOSUM62");
 815     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 816     {
 817       public void actionPerformed(ActionEvent e)
 818       {
 819         BLOSUM62Colour_actionPerformed();
 820       }
 821     });
 822     conservationMenuItem.setText("Conservation");
 823     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 824     {
 825       public void actionPerformed(ActionEvent e)
 826       {
 827         conservationMenuItem_actionPerformed();
 828       }
 829     });
 830   }
 831
 832   /**
 833    * DOCUMENT ME!
 834    */
 835   void refresh()
 836   {
 837     ap.paintAlignment(true);
 838
 839     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 840   }
 841
 842   /**
 843    * DOCUMENT ME!
 844    *
 845    * @param e DOCUMENT ME!
 846    */
 847   protected void clustalColour_actionPerformed()
 848   {
 849     SequenceGroup sg = getGroup();
 850     sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
 851                                      ap.av.alignment.getWidth());
 852     refresh();
 853   }
 854
 855   /**
 856    * DOCUMENT ME!
 857    *
 858    * @param e DOCUMENT ME!
 859    */
 860   protected void zappoColour_actionPerformed()
 861   {
 862     getGroup().cs = new ZappoColourScheme();
 863     refresh();
 864   }
 865
 866   /**
 867    * DOCUMENT ME!
 868    *
 869    * @param e DOCUMENT ME!
 870    */
 871   protected void taylorColour_actionPerformed()
 872   {
 873     getGroup().cs = new TaylorColourScheme();
 874     refresh();
 875   }
 876
 877   /**
 878    * DOCUMENT ME!
 879    *
 880    * @param e DOCUMENT ME!
 881    */
 882   protected void hydrophobicityColour_actionPerformed()
 883   {
 884     getGroup().cs = new HydrophobicColourScheme();
 885     refresh();
 886   }
 887
 888   /**
 889    * DOCUMENT ME!
 890    *
 891    * @param e DOCUMENT ME!
 892    */
 893   protected void helixColour_actionPerformed()
 894   {
 895     getGroup().cs = new HelixColourScheme();
 896     refresh();
 897   }
 898
 899   /**
 900    * DOCUMENT ME!
 901    *
 902    * @param e DOCUMENT ME!
 903    */
 904   protected void strandColour_actionPerformed()
 905   {
 906     getGroup().cs = new StrandColourScheme();
 907     refresh();
 908   }
 909
 910   /**
 911    * DOCUMENT ME!
 912    *
 913    * @param e DOCUMENT ME!
 914    */
 915   protected void turnColour_actionPerformed()
 916   {
 917     getGroup().cs = new TurnColourScheme();
 918     refresh();
 919   }
 920
 921   /**
 922    * DOCUMENT ME!
 923    *
 924    * @param e DOCUMENT ME!
 925    */
 926   protected void buriedColour_actionPerformed()
 927   {
 928     getGroup().cs = new BuriedColourScheme();
 929     refresh();
 930   }
 931
 932   /**
 933    * DOCUMENT ME!
 934    *
 935    * @param e DOCUMENT ME!
 936    */
 937   public void nucleotideMenuItem_actionPerformed()
 938   {
 939     getGroup().cs = new NucleotideColourScheme();
 940     refresh();
 941   }
 942
 943   /**
 944    * DOCUMENT ME!
 945    *
 946    * @param e DOCUMENT ME!
 947    */
 948   protected void abovePIDColour_actionPerformed()
 949   {
 950     SequenceGroup sg = getGroup();
 951     if (sg.cs == null)
 952     {
 953       return;
 954     }
 955
 956     if (abovePIDColour.isSelected())
 957     {
 958       sg.cs.setConsensus(AAFrequency.calculate(
 959           sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
 960           sg.getEndRes() + 1));
 961
 962       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
 963           getGroup().getName());
 964
 965       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 966
 967       SliderPanel.showPIDSlider();
 968     }
 969     else // remove PIDColouring
 970     {
 971       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 972     }
 973
 974     refresh();
 975   }
 976
 977   /**
 978    * DOCUMENT ME!
 979    *
 980    * @param e DOCUMENT ME!
 981    */
 982   protected void userDefinedColour_actionPerformed(ActionEvent e)
 983   {
 984     SequenceGroup sg = getGroup();
 985
 986     if (e.getActionCommand().equals("User Defined..."))
 987     {
 988       new UserDefinedColours(ap, sg);
 989     }
 990     else
 991     {
 992       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 993           getUserColourSchemes().get(e.getActionCommand());
 994
 995       sg.cs = udc;
 996     }
 997     refresh();
 998   }
 999
1000   /**
1001    * DOCUMENT ME!
1002    *
1003    * @param e DOCUMENT ME!
1004    */
1005   protected void PIDColour_actionPerformed()
1006   {
1007     SequenceGroup sg = getGroup();
1008     sg.cs = new PIDColourScheme();
1009     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1010         hiddenRepSequences),
1011                                              sg.getStartRes(),
1012                                              sg.getEndRes() + 1));
1013     refresh();
1014   }
1015
1016   /**
1017    * DOCUMENT ME!
1018    *
1019    * @param e DOCUMENT ME!
1020    */
1021   protected void BLOSUM62Colour_actionPerformed()
1022   {
1023     SequenceGroup sg = getGroup();
1024
1025     sg.cs = new Blosum62ColourScheme();
1026
1027     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1028         hiddenRepSequences),
1029                                              sg.getStartRes(),
1030                                              sg.getEndRes() + 1));
1031
1032     refresh();
1033   }
1034
1035   /**
1036    * DOCUMENT ME!
1037    *
1038    * @param e DOCUMENT ME!
1039    */
1040   protected void noColourmenuItem_actionPerformed()
1041   {
1042     getGroup().cs = null;
1043     refresh();
1044   }
1045
1046   /**
1047    * DOCUMENT ME!
1048    *
1049    * @param e DOCUMENT ME!
1050    */
1051   protected void conservationMenuItem_actionPerformed()
1052   {
1053     SequenceGroup sg = getGroup();
1054     if (sg.cs == null)
1055     {
1056       return;
1057     }
1058
1059     if (conservationMenuItem.isSelected())
1060     {
1061       Conservation c = new Conservation("Group",
1062                                         ResidueProperties.propHash, 3,
1063                                         sg.getSequences(ap.av.
1064           hiddenRepSequences),
1065                                         sg.getStartRes(),
1066                                         sg.getEndRes() + 1);
1067
1068       c.calculate();
1069       c.verdict(false, ap.av.ConsPercGaps);
1070
1071       sg.cs.setConservation(c);
1072
1073       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1074       SliderPanel.showConservationSlider();
1075     }
1076     else // remove ConservationColouring
1077     {
1078       sg.cs.setConservation(null);
1079     }
1080
1081     refresh();
1082   }
1083
1084   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1085   {
1086     SequenceGroup sg = getGroup();
1087     if (sg == null)
1088     {
1089       return;
1090     }
1091
1092     AnnotationColourGradient acg = new AnnotationColourGradient(
1093         sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
1094
1095     acg.predefinedColours = true;
1096     sg.cs = acg;
1097
1098     refresh();
1099   }
1100
1101   /**
1102    * DOCUMENT ME!
1103    *
1104    * @param e DOCUMENT ME!
1105    */
1106   protected void groupName_actionPerformed()
1107   {
1108
1109     SequenceGroup sg = getGroup();
1110     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1111                                                sg.getDescription(),
1112                                                "       Group Name ",
1113                                                "Group Description ",
1114                                                "Edit Group Name/Description");
1115
1116     if (!dialog.accept)
1117     {
1118       return;
1119     }
1120
1121     sg.setName(dialog.getName());
1122     sg.setDescription(dialog.getDescription());
1123   }
1124
1125   /**
1126    * DOCUMENT ME!
1127    *
1128    * @return DOCUMENT ME!
1129    */
1130   SequenceGroup getGroup()
1131   {
1132     SequenceGroup sg = ap.av.getSelectionGroup();
1133     // this method won't add a new group if it already exists
1134     if (sg != null)
1135     {
1136       ap.av.alignment.addGroup(sg);
1137     }
1138
1139     return sg;
1140   }
1141
1142   /**
1143    * DOCUMENT ME!
1144    *
1145    * @param e DOCUMENT ME!
1146    */
1147   void sequenceName_actionPerformed()
1148   {
1149     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1150                                                sequence.getDescription(),
1151                                                "       Sequence Name ",
1152                                                "Sequence Description ",
1153                                                "Edit Sequence Name/Description");
1154
1155     if (!dialog.accept)
1156     {
1157       return;
1158     }
1159
1160     if (dialog.getName() != null)
1161     {
1162       if (dialog.getName().indexOf(" ") > -1)
1163       {
1164         JOptionPane.showMessageDialog(ap,
1165                                       "Spaces have been converted to \"_\"",
1166                                       "No spaces allowed in Sequence Name",
1167                                       JOptionPane.WARNING_MESSAGE);
1168       }
1169
1170       sequence.setName(dialog.getName().replace(' ', '_'));
1171       ap.paintAlignment(false);
1172     }
1173
1174     sequence.setDescription(dialog.getDescription());
1175
1176     ap.av.firePropertyChange("alignment", null,
1177                              ap.av.getAlignment().getSequences());
1178
1179   }
1180
1181   /**
1182    * DOCUMENT ME!
1183    *
1184    * @param e DOCUMENT ME!
1185    */
1186   void unGroupMenuItem_actionPerformed()
1187   {
1188     SequenceGroup sg = ap.av.getSelectionGroup();
1189     ap.av.alignment.deleteGroup(sg);
1190     ap.av.setSelectionGroup(null);
1191     refresh();
1192   }
1193
1194   /**
1195    * DOCUMENT ME!
1196    *
1197    * @param e DOCUMENT ME!
1198    */
1199   protected void outline_actionPerformed()
1200   {
1201     SequenceGroup sg = getGroup();
1202     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1203                                          Color.BLUE);
1204
1205     if (col != null)
1206     {
1207       sg.setOutlineColour(col);
1208     }
1209
1210     refresh();
1211   }
1212
1213   /**
1214    * DOCUMENT ME!
1215    *
1216    * @param e DOCUMENT ME!
1217    */
1218   public void showBoxes_actionPerformed()
1219   {
1220     getGroup().setDisplayBoxes(showBoxes.isSelected());
1221     refresh();
1222   }
1223
1224   /**
1225    * DOCUMENT ME!
1226    *
1227    * @param e DOCUMENT ME!
1228    */
1229   public void showText_actionPerformed()
1230   {
1231     getGroup().setDisplayText(showText.isSelected());
1232     refresh();
1233   }
1234
1235   /**
1236    * DOCUMENT ME!
1237    *
1238    * @param e DOCUMENT ME!
1239    */
1240   public void showColourText_actionPerformed()
1241   {
1242     getGroup().setColourText(showColourText.isSelected());
1243     refresh();
1244   }
1245
1246   public void showLink(String url)
1247   {
1248     try
1249     {
1250       jalview.util.BrowserLauncher.openURL(url);
1251     }
1252     catch (Exception ex)
1253     {
1254       JOptionPane.showInternalMessageDialog(Desktop.desktop,
1255                                             "Unixers: Couldn't find default web browser."
1256                                             +
1257           "\nAdd the full path to your browser in Preferences.",
1258                                             "Web browser not found",
1259                                             JOptionPane.WARNING_MESSAGE);
1260
1261       ex.printStackTrace();
1262     }
1263   }
1264
1265   void hideSequences(boolean representGroup)
1266   {
1267     SequenceGroup sg = ap.av.getSelectionGroup();
1268     if (sg == null || sg.getSize() < 1)
1269     {
1270       ap.av.hideSequence(new SequenceI[]
1271                          {sequence});
1272       return;
1273     }
1274
1275     ap.av.setSelectionGroup(null);
1276
1277     if (representGroup)
1278     {
1279       ap.av.hideRepSequences(sequence, sg);
1280
1281       return;
1282     }
1283
1284     int gsize = sg.getSize();
1285     SequenceI[] hseqs;
1286
1287     hseqs = new SequenceI[gsize];
1288
1289     int index = 0;
1290     for (int i = 0; i < gsize; i++)
1291     {
1292       hseqs[index++] = sg.getSequenceAt(i);
1293     }
1294
1295     ap.av.hideSequence(hseqs);
1296   }
1297
1298   public void copy_actionPerformed()
1299   {
1300     ap.alignFrame.copy_actionPerformed(null);
1301   }
1302
1303   public void cut_actionPerformed()
1304   {
1305     ap.alignFrame.cut_actionPerformed(null);
1306   }
1307
1308   void changeCase(ActionEvent e)
1309   {
1310     Object source = e.getSource();
1311     SequenceGroup sg = ap.av.getSelectionGroup();
1312
1313     if (sg != null)
1314     {
1315       int[][] startEnd = ap.av.getVisibleRegionBoundaries(
1316           sg.getStartRes(), sg.getEndRes() + 1);
1317
1318       String description;
1319       int caseChange;
1320
1321       if (source == toggle)
1322       {
1323         description = "Toggle Case";
1324         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1325       }
1326       else if (source == upperCase)
1327       {
1328         description = "To Upper Case";
1329         caseChange = ChangeCaseCommand.TO_UPPER;
1330       }
1331       else
1332       {
1333         description = "To Lower Case";
1334         caseChange = ChangeCaseCommand.TO_LOWER;
1335       }
1336
1337       ChangeCaseCommand caseCommand = new ChangeCaseCommand(
1338           description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1339           startEnd, caseChange
1340           );
1341
1342       ap.alignFrame.addHistoryItem(caseCommand);
1343
1344       ap.av.firePropertyChange("alignment", null,
1345                                ap.av.getAlignment().getSequences());
1346
1347     }
1348   }
1349
1350   public void outputText_actionPerformed(ActionEvent e)
1351   {
1352     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1353     cap.setForInput(null);
1354     Desktop.addInternalFrame(cap,
1355                              "Alignment output - " + e.getActionCommand(), 600,
1356                              500);
1357
1358     String[] omitHidden = null;
1359
1360     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
1361     SequenceGroup sg = ap.av.getSelectionGroup();
1362     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1363     omitHidden = ap.av.getViewAsString(true);
1364     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1365     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1366     for (int i=0; i<nala.length; i++)
1367     {
1368       AlignmentAnnotation na =nala[i];
1369       oal.addAnnotation(na);
1370     }
1371     cap.setText(new FormatAdapter().formatSequences(
1372             e.getActionCommand(),
1373             oal,
1374             omitHidden, csel, sg));
1375     oal=null;
1376   }
1377
1378   public void pdbFromFile_actionPerformed()
1379   {
1380     jalview.io.JalviewFileChooser chooser
1381         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1382                                             getProperty(
1383                                                 "LAST_DIRECTORY"));
1384     chooser.setFileView(new jalview.io.JalviewFileView());
1385     chooser.setDialogTitle("Select a PDB file");
1386     chooser.setToolTipText("Load a PDB file");
1387
1388     int value = chooser.showOpenDialog(null);
1389
1390     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1391     {
1392       PDBEntry entry = new PDBEntry();
1393       String choice = chooser.getSelectedFile().getPath();
1394       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1395       try
1396       {
1397         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1398             jalview.io.AppletFormatAdapter.FILE);
1399
1400         if (pdbfile.id == null)
1401         {
1402           String reply = JOptionPane.showInternalInputDialog(
1403               Desktop.desktop,
1404               "Couldn't find a PDB id in the file supplied."
1405               + "Please enter an Id to identify this structure.",
1406               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1407           if (reply == null)
1408           {
1409             return;
1410           }
1411
1412           entry.setId(reply);
1413         }
1414         else
1415         {
1416           entry.setId(pdbfile.id);
1417         }
1418       }
1419       catch (java.io.IOException ex)
1420       {
1421         ex.printStackTrace();
1422       }
1423
1424       entry.setFile(choice);
1425       sequence.getDatasetSequence().addPDBId(entry);
1426     }
1427
1428   }
1429
1430   public void enterPDB_actionPerformed()
1431   {
1432     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1433         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1434
1435     if (id != null && id.length() > 0)
1436     {
1437       PDBEntry entry = new PDBEntry();
1438       entry.setId(id.toUpperCase());
1439       sequence.getDatasetSequence()
1440           .addPDBId(entry);
1441     }
1442   }
1443
1444   public void discoverPDB_actionPerformed()
1445   {
1446
1447     final SequenceI[] sequences =
1448       ((ap.av.selectionGroup == null)
1449               ?  new Sequence[]{sequence}
1450       : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1451     Thread discpdb = new Thread(new Runnable() {
1452       public void run()
1453       {
1454
1455         new jalview.ws.DBRefFetcher(sequences,
1456                 ap.alignFrame).fetchDBRefs(false);
1457       }
1458
1459     });
1460     discpdb.start();
1461   }
1462
1463   public void sequenceFeature_actionPerformed()
1464   {
1465     SequenceGroup sg = ap.av.getSelectionGroup();
1466     if (sg == null)
1467     {
1468       return;
1469     }
1470
1471     int gSize = sg.getSize();
1472     SequenceI[] seqs = new SequenceI[gSize];
1473     SequenceFeature[] features = new SequenceFeature[gSize];
1474
1475     for (int i = 0; i < gSize; i++)
1476     {
1477       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1478       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1479       int end = sg.findEndRes(sg.getSequenceAt(i));
1480       features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
1481     }
1482
1483     if (ap.seqPanel.seqCanvas.getFeatureRenderer()
1484         .amendFeatures(seqs, features, true, ap))
1485     {
1486       ap.alignFrame.showSeqFeatures.setSelected(true);
1487       ap.av.setShowSequenceFeatures(true);
1488       ap.highlightSearchResults(null);
1489     }
1490   }
1491
1492   public void textColour_actionPerformed()
1493   {
1494     SequenceGroup sg = getGroup();
1495     if (sg != null)
1496     {
1497       new TextColourChooser().chooseColour(ap, sg);
1498     }
1499   }
1500
1501   public void colourByStructure(String pdbid)
1502   {
1503     Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
1504         .colourSequenceFromStructure(sequence, pdbid);
1505
1506     AlignmentAnnotation an = new AlignmentAnnotation(
1507       "Structure", "Coloured by "+pdbid, anots);
1508
1509     ap.av.alignment.addAnnotation(an);
1510     an.createSequenceMapping(sequence, 0, true);
1511     //an.adjustForAlignment();
1512     ap.av.alignment.setAnnotationIndex(an,0);
1513
1514     ap.adjustAnnotationHeight();
1515
1516     sequence.addAlignmentAnnotation(an);
1517
1518     }
1519
1520   public void editSequence_actionPerformed(ActionEvent actionEvent)
1521   {
1522       SequenceGroup sg = ap.av.getSelectionGroup();
1523
1524       if(sg!=null)
1525       {
1526         if (sequence == null)
1527           sequence = (Sequence) sg.getSequenceAt(0);
1528
1529         EditNameDialog dialog = new EditNameDialog(
1530             sequence.getSequenceAsString(
1531                 sg.getStartRes(),
1532                 sg.getEndRes() + 1),
1533             null,
1534             "Edit Sequence ",
1535             null,
1536             "Edit Sequence");
1537
1538         if (dialog.accept)
1539         {
1540           EditCommand editCommand = new EditCommand(
1541               "Edit Sequences", EditCommand.REPLACE,
1542               dialog.getName().replace(' ', ap.av.getGapCharacter()),
1543               sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1544               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
1545               );
1546
1547           ap.alignFrame.addHistoryItem(editCommand);
1548
1549           ap.av.firePropertyChange("alignment", null,
1550                                    ap.av.getAlignment().getSequences());
1551         }
1552       }
1553   }
1554
1555
1556 }