src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25
  26 import javax.swing.*;
  27
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.GroupUrlLink;
  34 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  35 import jalview.util.MessageManager;\r
  36 import jalview.util.UrlLink;
  37
  38 /**
  39  * DOCUMENT ME!
  40  *
  41  * @author $author$
  42  * @version $Revision: 1.118 $
  43  */
  44 public class PopupMenu extends JPopupMenu
  45 {
  46   JMenu groupMenu = new JMenu();
  47
  48   JMenuItem groupName = new JMenuItem();
  49
  50   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  51
  52   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  65
  66   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  67
  68   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  71
  72   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  73
  74   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  75   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  76
  77   // protected JRadioButtonMenuItem covariationColour = new
  78   // JRadioButtonMenuItem();
  79
  80   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  81
  82   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  83
  84   AlignmentPanel ap;
  85
  86   JMenu sequenceMenu = new JMenu();
  87
  88   JMenuItem sequenceName = new JMenuItem();
  89
  90   JMenuItem sequenceDetails = new JMenuItem();
  91
  92   JMenuItem sequenceSelDetails = new JMenuItem();
  93
  94   SequenceI sequence;
  95   JMenuItem createGroupMenuItem = new JMenuItem();
  96   JMenuItem unGroupMenuItem = new JMenuItem();
  97
  98   JMenuItem outline = new JMenuItem();
  99
 100   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 101
 102   JMenu colourMenu = new JMenu();
 103
 104   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 105
 106   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 107
 108   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 109
 110   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 111
 112   JMenu editMenu = new JMenu();
 113
 114   JMenuItem cut = new JMenuItem();
 115
 116   JMenuItem copy = new JMenuItem();
 117
 118   JMenuItem upperCase = new JMenuItem();
 119
 120   JMenuItem lowerCase = new JMenuItem();
 121
 122   JMenuItem toggle = new JMenuItem();
 123
 124   JMenu pdbMenu = new JMenu();
 125
 126   JMenuItem pdbFromFile = new JMenuItem();
 127     // JBPNote: Commented these out - Should add these services via the web services menu system.
 128     // JMenuItem ContraFold = new JMenuItem();
 129
 130     // JMenuItem RNAFold = new JMenuItem();
 131
 132   JMenuItem enterPDB = new JMenuItem();
 133
 134   JMenuItem discoverPDB = new JMenuItem();
 135
 136   JMenu outputMenu = new JMenu();
 137
 138   JMenuItem sequenceFeature = new JMenuItem();
 139
 140   JMenuItem textColour = new JMenuItem();
 141
 142   JMenu jMenu1 = new JMenu();
 143
 144   JMenu structureMenu = new JMenu();
 145
 146   JMenu viewStructureMenu = new JMenu();
 147
 148   // JMenu colStructureMenu = new JMenu();
 149   JMenuItem editSequence = new JMenuItem();
 150
 151   // JMenuItem annotationMenuItem = new JMenuItem();
 152
 153   JMenu groupLinksMenu;
 154
 155   /**
 156    * Creates a new PopupMenu object.
 157    *
 158    * @param ap
 159    *          DOCUMENT ME!
 160    * @param seq
 161    *          DOCUMENT ME!
 162    */
 163   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 164   {
 165     this(ap, seq, links, null);
 166   }
 167
 168   /**
 169    *
 170    * @param ap
 171    * @param seq
 172    * @param links
 173    * @param groupLinks
 174    */
 175   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 176           Vector links, Vector groupLinks)
 177   {
 178     // /////////////////////////////////////////////////////////
 179     // If this is activated from the sequence panel, the user may want to
 180     // edit or annotate a particular residue. Therefore display the residue menu
 181     //
 182     // If from the IDPanel, we must display the sequence menu
 183     // ////////////////////////////////////////////////////////
 184     this.ap = ap;
 185     sequence = seq;
 186
 187     ButtonGroup colours = new ButtonGroup();
 188     colours.add(noColourmenuItem);
 189     colours.add(clustalColour);
 190     colours.add(zappoColour);
 191     colours.add(taylorColour);
 192     colours.add(hydrophobicityColour);
 193     colours.add(helixColour);
 194     colours.add(strandColour);
 195     colours.add(turnColour);
 196     colours.add(buriedColour);
 197     colours.add(abovePIDColour);
 198     colours.add(userDefinedColour);
 199     colours.add(PIDColour);
 200     colours.add(BLOSUM62Colour);
 201     colours.add(purinePyrimidineColour);
 202     colours.add(RNAInteractionColour);
 203     // colours.add(covariationColour);
 204
 205     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 206     {
 207       JMenuItem item = new JMenuItem(
 208               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 209
 210       item.addActionListener(new java.awt.event.ActionListener()
 211       {
 212         public void actionPerformed(ActionEvent e)
 213         {
 214           outputText_actionPerformed(e);
 215         }
 216       });
 217
 218       outputMenu.add(item);
 219     }
 220
 221     try
 222     {
 223       jbInit();
 224     } catch (Exception e)
 225     {
 226       e.printStackTrace();
 227     }
 228
 229     JMenuItem menuItem;
 230     if (seq != null)
 231     {
 232       sequenceMenu.setText(sequence.getName());
 233
 234       if (seq.getDatasetSequence().getPDBId() != null
 235               && seq.getDatasetSequence().getPDBId().size() > 0)
 236       {
 237         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 238                 .elements();
 239
 240         while (e.hasMoreElements())
 241         {
 242           final PDBEntry pdb = (PDBEntry) e.nextElement();
 243
 244           menuItem = new JMenuItem();
 245           menuItem.setText(pdb.getId());
 246           menuItem.addActionListener(new java.awt.event.ActionListener()
 247           {
 248             public void actionPerformed(ActionEvent e)
 249             {
 250               // TODO re JAL-860: optionally open dialog or provide a menu entry
 251               // allowing user to open just one structure per sequence
 252               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 253               { pdb })[0], null, ap);
 254               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 255             }
 256
 257           });
 258           viewStructureMenu.add(menuItem);
 259
 260           /*
 261            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 262            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 263            * public void actionPerformed(ActionEvent e) {
 264            * colourByStructure(pdb.getId()); } });
 265            * colStructureMenu.add(menuItem);
 266            */
 267         }
 268       }
 269       else
 270       {
 271         if (ap.av.getAlignment().isNucleotide() == false)
 272         {
 273           structureMenu.remove(viewStructureMenu);
 274         }
 275         // structureMenu.remove(colStructureMenu);
 276       }
 277
 278       if (ap.av.getAlignment().isNucleotide() == true)
 279       {
 280         AlignmentAnnotation[] aa = ap.av.getAlignment()
 281                 .getAlignmentAnnotation();
 282         for (int i = 0; i < aa.length; i++)
 283         {
 284           if (aa[i].getRNAStruc() != null)
 285           {
 286             final String rnastruc = aa[i].getRNAStruc();
 287             final String structureLine = aa[i].label;
 288             menuItem = new JMenuItem();
 289             menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
 290             menuItem.addActionListener(new java.awt.event.ActionListener()
 291
 292             {
 293               public void actionPerformed(ActionEvent e)
 294               {
 295                         //System.out.println("1:"+structureLine);
 296                         System.out.println("1:sname"+seq.getName());
 297                         System.out.println("2:seq"+seq);
 298
 299                         //System.out.println("3:"+seq.getSequenceAsString());
 300                         System.out.println("3:strucseq"+rnastruc);
 301                         //System.out.println("4:struc"+seq.getRNA());
 302                         System.out.println("5:name"+seq.getName());
 303                         System.out.println("6:ap"+ap);
 304                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 305                             .getName(), ap);
 306                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 307                         System.out.println("end");
 308               }
 309             });
 310             viewStructureMenu.add(menuItem);
 311           }
 312         }
 313
 314         // SequenceFeatures[] test = seq.getSequenceFeatures();
 315
 316         if (seq.getAnnotation() != null)
 317         {
 318           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 319           for (int i = 0; i < seqAnno.length; i++)
 320           {
 321             if (seqAnno[i].getRNAStruc() != null)
 322             {
 323               final String rnastruc = seqAnno[i].getRNAStruc();
 324
 325               // TODO: make rnastrucF a bit more nice
 326               menuItem = new JMenuItem();
 327               menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
 328               menuItem.addActionListener(new java.awt.event.ActionListener()
 329               {
 330                 public void actionPerformed(ActionEvent e)
 331                 {
 332                   // TODO: VARNA does'nt print gaps in the sequence
 333
 334                   new AppVarna(seq.getName() + " structure", seq, seq
 335                           .getSequenceAsString(), rnastruc, seq.getName(),
 336                           ap);
 337                 }
 338               });
 339               viewStructureMenu.add(menuItem);
 340             }
 341           }
 342         }
 343
 344       }
 345
 346       menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
 347       menuItem.addActionListener(new java.awt.event.ActionListener()
 348       {
 349         public void actionPerformed(ActionEvent e)
 350         {
 351           hideSequences(false);
 352         }
 353       });
 354       add(menuItem);
 355
 356       if (ap.av.getSelectionGroup() != null
 357               && ap.av.getSelectionGroup().getSize() > 1)
 358       {
 359         menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
 360         menuItem.addActionListener(new java.awt.event.ActionListener()
 361         {
 362           public void actionPerformed(ActionEvent e)
 363           {
 364             hideSequences(true);
 365           }
 366         });
 367         sequenceMenu.add(menuItem);
 368       }
 369
 370       if (ap.av.hasHiddenRows())
 371       {
 372         final int index = ap.av.getAlignment().findIndex(seq);
 373
 374         if (ap.av.adjustForHiddenSeqs(index)
 375                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 376         {
 377           menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
 378           menuItem.addActionListener(new ActionListener()
 379           {
 380             public void actionPerformed(ActionEvent e)
 381             {
 382               ap.av.showSequence(index);
 383               if (ap.overviewPanel != null)
 384               {
 385                 ap.overviewPanel.updateOverviewImage();
 386               }
 387             }
 388           });
 389           add(menuItem);
 390         }
 391       }
 392     }
 393     // for the case when no sequences are even visible
 394     if (ap.av.hasHiddenRows())
 395     {
 396       {
 397         menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
 398         menuItem.addActionListener(new ActionListener()
 399         {
 400           public void actionPerformed(ActionEvent e)
 401           {
 402             ap.av.showAllHiddenSeqs();
 403             if (ap.overviewPanel != null)
 404             {
 405               ap.overviewPanel.updateOverviewImage();
 406             }
 407           }
 408         });
 409
 410         add(menuItem);
 411       }
 412
 413     }
 414
 415     SequenceGroup sg = ap.av.getSelectionGroup();
 416     boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
 417
 418     if (sg != null && sg.getSize() > 0)
 419     {
 420       groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
 421       groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
 422
 423       if (sg.cs instanceof ZappoColourScheme)
 424       {
 425         zappoColour.setSelected(true);
 426       }
 427       else if (sg.cs instanceof TaylorColourScheme)
 428       {
 429         taylorColour.setSelected(true);
 430       }
 431       else if (sg.cs instanceof PIDColourScheme)
 432       {
 433         PIDColour.setSelected(true);
 434       }
 435       else if (sg.cs instanceof Blosum62ColourScheme)
 436       {
 437         BLOSUM62Colour.setSelected(true);
 438       }
 439       else if (sg.cs instanceof UserColourScheme)
 440       {
 441         userDefinedColour.setSelected(true);
 442       }
 443       else if (sg.cs instanceof HydrophobicColourScheme)
 444       {
 445         hydrophobicityColour.setSelected(true);
 446       }
 447       else if (sg.cs instanceof HelixColourScheme)
 448       {
 449         helixColour.setSelected(true);
 450       }
 451       else if (sg.cs instanceof StrandColourScheme)
 452       {
 453         strandColour.setSelected(true);
 454       }
 455       else if (sg.cs instanceof TurnColourScheme)
 456       {
 457         turnColour.setSelected(true);
 458       }
 459       else if (sg.cs instanceof BuriedColourScheme)
 460       {
 461         buriedColour.setSelected(true);
 462       }
 463       else if (sg.cs instanceof ClustalxColourScheme)
 464       {
 465         clustalColour.setSelected(true);
 466       }
 467       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 468       {
 469         purinePyrimidineColour.setSelected(true);
 470       }
 471
 472
 473       /*
 474        * else if (sg.cs instanceof CovariationColourScheme) {
 475        * covariationColour.setSelected(true); }
 476        */
 477       else
 478       {
 479         noColourmenuItem.setSelected(true);
 480       }
 481
 482       if (sg.cs != null && sg.cs.conservationApplied())
 483       {
 484         conservationMenuItem.setSelected(true);
 485       }
 486       displayNonconserved.setSelected(sg.getShowNonconserved());
 487       showText.setSelected(sg.getDisplayText());
 488       showColourText.setSelected(sg.getColourText());
 489       showBoxes.setSelected(sg.getDisplayBoxes());
 490       // add any groupURLs to the groupURL submenu and make it visible
 491       if (groupLinks != null && groupLinks.size() > 0)
 492       {
 493         buildGroupURLMenu(sg, groupLinks);
 494       }
 495       // Add a 'show all structures' for the current selection
 496       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 497       SequenceI sqass = null;
 498       for (SequenceI sq : ap.av.getSequenceSelection())
 499       {
 500         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 501                 .getPDBId();
 502         if (pes != null)
 503         {
 504           for (PDBEntry pe : pes)
 505           {
 506             pdbe.put(pe.getId(), pe);
 507             if (sqass == null)
 508             {
 509               sqass = sq;
 510             }
 511           }
 512         }
 513       }
 514       if (pdbe.size() > 0)
 515       {
 516         final PDBEntry[] pe = pdbe.values().toArray(
 517                 new PDBEntry[pdbe.size()]);
 518         final JMenuItem gpdbview;
 519         if (pdbe.size() == 1)
 520         {
 521           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
 522         }
 523         else
 524         {
 525           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
 526         }
 527         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
 528         gpdbview.addActionListener(new ActionListener()
 529         {
 530
 531           @Override
 532           public void actionPerformed(ActionEvent e)
 533           {
 534             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 535           }
 536         });
 537       }
 538     }
 539     else
 540     {
 541       groupMenu.setVisible(false);
 542       editMenu.setVisible(false);
 543     }
 544
 545     if (!isDefinedGroup)
 546     {
 547       createGroupMenuItem.setVisible(true);
 548       unGroupMenuItem.setVisible(false);
 549       jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
 550     } else {
 551       createGroupMenuItem.setVisible(false);
 552       unGroupMenuItem.setVisible(true);
 553       jMenu1.setText(MessageManager.getString("action.edit_group"));\r
 554     }
 555
 556     if (seq == null)
 557     {
 558       sequenceMenu.setVisible(false);
 559       structureMenu.setVisible(false);
 560     }
 561
 562     if (links != null && links.size() > 0)
 563     {
 564
 565       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
 566       Vector linkset = new Vector();
 567       for (int i = 0; i < links.size(); i++)
 568       {
 569         String link = links.elementAt(i).toString();
 570         UrlLink urlLink = null;
 571         try
 572         {
 573           urlLink = new UrlLink(link);
 574         } catch (Exception foo)
 575         {
 576           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 577                   + "'", foo);
 578           continue;
 579         }
 580         ;
 581         if (!urlLink.isValid())
 582         {
 583           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 584           continue;
 585         }
 586         final String label = urlLink.getLabel();
 587         if (seq != null && urlLink.isDynamic())
 588         {
 589
 590           // collect matching db-refs
 591           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 592                   seq.getDBRef(), new String[]
 593                   { urlLink.getTarget() });
 594           // collect id string too
 595           String id = seq.getName();
 596           String descr = seq.getDescription();
 597           if (descr != null && descr.length() < 1)
 598           {
 599             descr = null;
 600           }
 601
 602           if (dbr != null)
 603           {
 604             for (int r = 0; r < dbr.length; r++)
 605             {
 606               if (id != null && dbr[r].getAccessionId().equals(id))
 607               {
 608                 // suppress duplicate link creation for the bare sequence ID
 609                 // string with this link
 610                 id = null;
 611               }
 612               // create Bare ID link for this RUL
 613               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 614                       true);
 615               if (urls != null)
 616               {
 617                 for (int u = 0; u < urls.length; u += 2)
 618                 {
 619                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 620                   {
 621                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 622                     addshowLink(linkMenu, label + "|" + urls[u],
 623                             urls[u + 1]);
 624                   }
 625                 }
 626               }
 627             }
 628           }
 629           if (id != null)
 630           {
 631             // create Bare ID link for this RUL
 632             String[] urls = urlLink.makeUrls(id, true);
 633             if (urls != null)
 634             {
 635               for (int u = 0; u < urls.length; u += 2)
 636               {
 637                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 638                 {
 639                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 640                   addshowLink(linkMenu, label, urls[u + 1]);
 641                 }
 642               }
 643             }
 644           }
 645           // Create urls from description but only for URL links which are regex
 646           // links
 647           if (descr != null && urlLink.getRegexReplace() != null)
 648           {
 649             // create link for this URL from description where regex matches
 650             String[] urls = urlLink.makeUrls(descr, true);
 651             if (urls != null)
 652             {
 653               for (int u = 0; u < urls.length; u += 2)
 654               {
 655                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 656                 {
 657                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 658                   addshowLink(linkMenu, label, urls[u + 1]);
 659                 }
 660               }
 661             }
 662           }
 663         }
 664         else
 665         {
 666           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 667           {
 668             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 669             // Add a non-dynamic link
 670             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 671           }
 672         }
 673       }
 674       if (sequence != null)
 675       {
 676         sequenceMenu.add(linkMenu);
 677       }
 678       else
 679       {
 680         add(linkMenu);
 681       }
 682     }
 683   }
 684
 685   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 686   {
 687
 688     // TODO: usability: thread off the generation of group url content so root
 689     // menu appears asap
 690     // sequence only URLs
 691     // ID/regex match URLs
 692     groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 693     JMenu[] linkMenus = new JMenu[]
 694     { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
 695         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
 696                                           // created.
 697     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 698     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 699     Hashtable commonDbrefs = new Hashtable();
 700     for (int sq = 0; sq < seqs.length; sq++)
 701     {
 702
 703       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 704               .findPosition(sg.getEndRes());
 705       // just collect ids from dataset sequence
 706       // TODO: check if IDs collected from selecton group intersects with the
 707       // current selection, too
 708       SequenceI sqi = seqs[sq];
 709       while (sqi.getDatasetSequence() != null)
 710       {
 711         sqi = sqi.getDatasetSequence();
 712       }
 713       DBRefEntry[] dbr = sqi.getDBRef();
 714       if (dbr != null && dbr.length > 0)
 715       {
 716         for (int d = 0; d < dbr.length; d++)
 717         {
 718           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 719           Object[] sarray = (Object[]) commonDbrefs.get(src);
 720           if (sarray == null)
 721           {
 722             sarray = new Object[2];
 723             sarray[0] = new int[]
 724             { 0 };
 725             sarray[1] = new String[seqs.length];
 726
 727             commonDbrefs.put(src, sarray);
 728           }
 729
 730           if (((String[]) sarray[1])[sq] == null)
 731           {
 732             if (!dbr[d].hasMap()
 733                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 734             {
 735               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 736               ((int[]) sarray[0])[0]++;
 737             }
 738           }
 739         }
 740       }
 741     }
 742     // now create group links for all distinct ID/sequence sets.
 743     boolean addMenu = false; // indicates if there are any group links to give
 744                              // to user
 745     for (int i = 0; i < groupLinks.size(); i++)
 746     {
 747       String link = groupLinks.elementAt(i).toString();
 748       GroupUrlLink urlLink = null;
 749       try
 750       {
 751         urlLink = new GroupUrlLink(link);
 752       } catch (Exception foo)
 753       {
 754         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 755                 + "'", foo);
 756         continue;
 757       }
 758       ;
 759       if (!urlLink.isValid())
 760       {
 761         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 762         continue;
 763       }
 764       final String label = urlLink.getLabel();
 765       boolean usingNames = false;
 766       // Now see which parts of the group apply for this URL
 767       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 768       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 769       String[] seqstr, ids; // input to makeUrl
 770       if (idset != null)
 771       {
 772         int numinput = ((int[]) idset[0])[0];
 773         String[] allids = ((String[]) idset[1]);
 774         seqstr = new String[numinput];
 775         ids = new String[numinput];
 776         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 777         {
 778           if (allids[sq] != null)
 779           {
 780             ids[idcount] = allids[sq];
 781             seqstr[idcount++] = idandseqs[1][sq];
 782           }
 783         }
 784       }
 785       else
 786       {
 787         // just use the id/seq set
 788         seqstr = idandseqs[1];
 789         ids = idandseqs[0];
 790         usingNames = true;
 791       }
 792       // and try and make the groupURL!
 793
 794       Object[] urlset = null;
 795       try
 796       {
 797         urlset = urlLink.makeUrlStubs(ids, seqstr,
 798                 "FromJalview" + System.currentTimeMillis(), false);
 799       } catch (UrlStringTooLongException e)
 800       {
 801       }
 802       if (urlset != null)
 803       {
 804         int type = urlLink.getGroupURLType() & 3;
 805         // System.out.println(urlLink.getGroupURLType()
 806         // +" "+((String[])urlset[3])[0]);
 807         // first two bits ofurlLink type bitfield are sequenceids and sequences
 808         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 809         addshowLink(linkMenus[type], label
 810                 + (((type & 1) == 1) ? ("("
 811                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 812                 urlLink, urlset);
 813         addMenu = true;
 814       }
 815     }
 816     if (addMenu)
 817     {
 818       groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 819       for (int m = 0; m < linkMenus.length; m++)
 820       {
 821         if (linkMenus[m] != null
 822                 && linkMenus[m].getMenuComponentCount() > 0)
 823         {
 824           groupLinksMenu.add(linkMenus[m]);
 825         }
 826       }
 827
 828       groupMenu.add(groupLinksMenu);
 829     }
 830   }
 831
 832   /**
 833    * add a show URL menu item to the given linkMenu
 834    *
 835    * @param linkMenu
 836    * @param label
 837    *          - menu label string
 838    * @param url
 839    *          - url to open
 840    */
 841   private void addshowLink(JMenu linkMenu, String label, final String url)
 842   {
 843     JMenuItem item = new JMenuItem(label);
 844     item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
 845     item.addActionListener(new java.awt.event.ActionListener()
 846     {
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         new Thread(new Runnable()
 850         {
 851
 852           public void run()
 853           {
 854             showLink(url);
 855           }
 856
 857         }).start();
 858       }
 859     });
 860
 861     linkMenu.add(item);
 862   }
 863
 864   /**
 865    * add a late bound groupURL item to the given linkMenu
 866    *
 867    * @param linkMenu
 868    * @param label
 869    *          - menu label string
 870    * @param urlgenerator
 871    *          GroupURLLink used to generate URL
 872    * @param urlstub
 873    *          Object array returned from the makeUrlStubs function.
 874    */
 875   private void addshowLink(JMenu linkMenu, String label,
 876           final GroupUrlLink urlgenerator, final Object[] urlstub)
 877   {
 878     JMenuItem item = new JMenuItem(label);
 879     item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
 880     // TODO: put in info about what is being sent.\r
 881     item.addActionListener(new java.awt.event.ActionListener()
 882     {
 883       public void actionPerformed(ActionEvent e)
 884       {
 885         new Thread(new Runnable()
 886         {
 887
 888           public void run()
 889           {
 890             try
 891             {
 892               showLink(urlgenerator.constructFrom(urlstub));
 893             } catch (UrlStringTooLongException e)
 894             {
 895             }
 896           }
 897
 898         }).start();
 899       }
 900     });
 901
 902     linkMenu.add(item);
 903   }
 904
 905   /**
 906    * DOCUMENT ME!
 907    *
 908    * @throws Exception
 909    *           DOCUMENT ME!
 910    */
 911   private void jbInit() throws Exception
 912   {
 913     groupMenu.setText(MessageManager.getString("label.group"));\r
 914     groupMenu.setText(MessageManager.getString("label.selection"));\r
 915     groupName.setText(MessageManager.getString("label.name"));\r
 916     groupName.addActionListener(new java.awt.event.ActionListener()
 917     {
 918       public void actionPerformed(ActionEvent e)
 919       {
 920         groupName_actionPerformed();
 921       }
 922     });
 923     sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
 924     sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
 925     sequenceName.addActionListener(new java.awt.event.ActionListener()
 926     {
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         sequenceName_actionPerformed();
 930       }
 931     });
 932     sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 933     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         sequenceDetails_actionPerformed();
 938       }
 939     });
 940     sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 941     sequenceSelDetails
 942             .addActionListener(new java.awt.event.ActionListener()
 943             {
 944               public void actionPerformed(ActionEvent e)
 945               {
 946                 sequenceSelectionDetails_actionPerformed();
 947               }
 948             });
 949     PIDColour.setFocusPainted(false);
 950     unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
 951     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 952     {
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         unGroupMenuItem_actionPerformed();
 956       }
 957     });
 958     createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
 959     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         createGroupMenuItem_actionPerformed();
 964       }
 965     });
 966
 967     outline.setText(MessageManager.getString("action.border_colour"));\r
 968     outline.addActionListener(new java.awt.event.ActionListener()
 969     {
 970       public void actionPerformed(ActionEvent e)
 971       {
 972         outline_actionPerformed();
 973       }
 974     });
 975     nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
 976     nucleotideMenuItem.addActionListener(new ActionListener()
 977     {
 978       public void actionPerformed(ActionEvent e)
 979       {
 980         nucleotideMenuItem_actionPerformed();
 981       }
 982     });
 983     colourMenu.setText(MessageManager.getString("label.group_colour"));\r
 984     showBoxes.setText(MessageManager.getString("action.boxes"));\r
 985     showBoxes.setState(true);
 986     showBoxes.addActionListener(new ActionListener()
 987     {
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         showBoxes_actionPerformed();
 991       }
 992     });
 993     showText.setText(MessageManager.getString("action.text"));\r
 994     showText.setState(true);
 995     showText.addActionListener(new ActionListener()
 996     {
 997       public void actionPerformed(ActionEvent e)
 998       {
 999         showText_actionPerformed();
1000       }
1001     });
1002     showColourText.setText(MessageManager.getString("label.colour_text"));\r
1003     showColourText.addActionListener(new ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         showColourText_actionPerformed();
1008       }
1009     });
1010     displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
1011     displayNonconserved.setState(true);
1012     displayNonconserved.addActionListener(new ActionListener()
1013     {
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         showNonconserved_actionPerformed();
1017       }
1018     });
1019     editMenu.setText(MessageManager.getString("action.edit"));\r
1020     cut.setText(MessageManager.getString("action.cut"));\r
1021     cut.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         cut_actionPerformed();
1026       }
1027     });
1028     upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
1029     upperCase.addActionListener(new ActionListener()
1030     {
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         changeCase(e);
1034       }
1035     });
1036     copy.setText(MessageManager.getString("action.copy"));\r
1037     copy.addActionListener(new ActionListener()
1038     {
1039       public void actionPerformed(ActionEvent e)
1040       {
1041         copy_actionPerformed();
1042       }
1043     });
1044     lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
1045     lowerCase.addActionListener(new ActionListener()
1046     {
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         changeCase(e);
1050       }
1051     });
1052     toggle.setText(MessageManager.getString("label.toggle_case"));\r
1053     toggle.addActionListener(new ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         changeCase(e);
1058       }
1059     });
1060     pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
1061     pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
1062     pdbFromFile.addActionListener(new ActionListener()
1063     {
1064       public void actionPerformed(ActionEvent e)
1065       {
1066         pdbFromFile_actionPerformed();
1067       }
1068     });
1069 //    RNAFold.setText("From RNA Fold with predict2D");
1070 //    RNAFold.addActionListener(new ActionListener()
1071 //    {
1072 //      public void actionPerformed(ActionEvent e)
1073 //      {
1074 //        try {
1075 //                      RNAFold_actionPerformed();
1076 //              } catch (Exception e1) {
1077 //                      // TODO Auto-generated catch block
1078 //                      e1.printStackTrace();
1079 //              }
1080 //      }
1081 //    });
1082 //    ContraFold.setText("From Contra Fold with predict2D");
1083 //    ContraFold.addActionListener(new ActionListener()
1084 //    {
1085 //      public void actionPerformed(ActionEvent e)
1086 //      {
1087 //        try {
1088 //                      ContraFold_actionPerformed();
1089 //              } catch (Exception e1) {
1090 //                      // TODO Auto-generated catch block
1091 //                      e1.printStackTrace();
1092 //              }
1093 //      }
1094 //    });
1095     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
1096     enterPDB.addActionListener(new ActionListener()
1097     {
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         enterPDB_actionPerformed();
1101       }
1102     });
1103     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
1104     discoverPDB.addActionListener(new ActionListener()
1105     {
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         discoverPDB_actionPerformed();
1109       }
1110     });
1111     outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
1112     sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
1113     sequenceFeature.addActionListener(new ActionListener()
1114     {
1115       public void actionPerformed(ActionEvent e)
1116       {
1117         sequenceFeature_actionPerformed();
1118       }
1119     });
1120     textColour.setText(MessageManager.getString("label.text_colour"));\r
1121     textColour.addActionListener(new ActionListener()
1122     {
1123       public void actionPerformed(ActionEvent e)
1124       {
1125         textColour_actionPerformed();
1126       }
1127     });
1128     jMenu1.setText(MessageManager.getString("label.group"));\r
1129     structureMenu.setText(MessageManager.getString("label.structure"));\r
1130     viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
1131     // colStructureMenu.setText("Colour By Structure");
1132     editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
1133     editSequence.addActionListener(new ActionListener()
1134     {
1135       public void actionPerformed(ActionEvent actionEvent)
1136       {
1137         editSequence_actionPerformed(actionEvent);
1138       }
1139     });
1140
1141     /*
1142      * annotationMenuItem.setText("By Annotation");
1143      * annotationMenuItem.addActionListener(new ActionListener() { public void
1144      * actionPerformed(ActionEvent actionEvent) {
1145      * annotationMenuItem_actionPerformed(actionEvent); } });
1146      */
1147     groupMenu.add(sequenceSelDetails);
1148     add(groupMenu);
1149     add(sequenceMenu);
1150     this.add(structureMenu);
1151     groupMenu.add(editMenu);
1152     groupMenu.add(outputMenu);
1153     groupMenu.add(sequenceFeature);
1154     groupMenu.add(createGroupMenuItem);
1155     groupMenu.add(unGroupMenuItem);
1156     groupMenu.add(jMenu1);
1157     sequenceMenu.add(sequenceName);
1158     sequenceMenu.add(sequenceDetails);
1159     colourMenu.add(textColour);
1160     colourMenu.add(noColourmenuItem);
1161     colourMenu.add(clustalColour);
1162     colourMenu.add(BLOSUM62Colour);
1163     colourMenu.add(PIDColour);
1164     colourMenu.add(zappoColour);
1165     colourMenu.add(taylorColour);
1166     colourMenu.add(hydrophobicityColour);
1167     colourMenu.add(helixColour);
1168     colourMenu.add(strandColour);
1169     colourMenu.add(turnColour);
1170     colourMenu.add(buriedColour);
1171     colourMenu.add(nucleotideMenuItem);
1172     if (ap.getAlignment().isNucleotide()) {
1173         // JBPNote - commented since the colourscheme isn't functional
1174         //  colourMenu.add(RNAInteractionColour);
1175         colourMenu.add(purinePyrimidineColour);
1176     }
1177     // colourMenu.add(covariationColour);
1178     colourMenu.add(userDefinedColour);
1179
1180     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1181     {
1182       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1183               .getUserColourSchemes().keys();
1184
1185       while (userColours.hasMoreElements())
1186       {
1187         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1188         item.addActionListener(new ActionListener()
1189         {
1190           public void actionPerformed(ActionEvent evt)
1191           {
1192             userDefinedColour_actionPerformed(evt);
1193           }
1194         });
1195         colourMenu.add(item);
1196       }
1197     }
1198
1199     colourMenu.addSeparator();
1200     colourMenu.add(abovePIDColour);
1201     colourMenu.add(conservationMenuItem);
1202     // colourMenu.add(annotationMenuItem);
1203     editMenu.add(copy);
1204     editMenu.add(cut);
1205     editMenu.add(editSequence);
1206     editMenu.add(upperCase);
1207     editMenu.add(lowerCase);
1208     editMenu.add(toggle);
1209     pdbMenu.add(pdbFromFile);
1210     // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1211     //    pdbMenu.add(RNAFold);
1212     //    pdbMenu.add(ContraFold);
1213     pdbMenu.add(enterPDB);
1214     pdbMenu.add(discoverPDB);
1215     jMenu1.add(groupName);
1216     jMenu1.add(colourMenu);
1217     jMenu1.add(showBoxes);
1218     jMenu1.add(showText);
1219     jMenu1.add(showColourText);
1220     jMenu1.add(outline);
1221     jMenu1.add(displayNonconserved);
1222     structureMenu.add(pdbMenu);
1223     structureMenu.add(viewStructureMenu);
1224     // structureMenu.add(colStructureMenu);
1225     noColourmenuItem.setText(MessageManager.getString("label.none"));\r
1226     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1227     {
1228       public void actionPerformed(ActionEvent e)
1229       {
1230         noColourmenuItem_actionPerformed();
1231       }
1232     });
1233
1234     clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
1235     clustalColour.addActionListener(new java.awt.event.ActionListener()
1236     {
1237       public void actionPerformed(ActionEvent e)
1238       {
1239         clustalColour_actionPerformed();
1240       }
1241     });
1242     zappoColour.setText(MessageManager.getString("label.zappo"));\r
1243     zappoColour.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         zappoColour_actionPerformed();
1248       }
1249     });
1250     taylorColour.setText(MessageManager.getString("label.taylor"));\r
1251     taylorColour.addActionListener(new java.awt.event.ActionListener()
1252     {
1253       public void actionPerformed(ActionEvent e)
1254       {
1255         taylorColour_actionPerformed();
1256       }
1257     });
1258     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
1259     hydrophobicityColour
1260             .addActionListener(new java.awt.event.ActionListener()
1261             {
1262               public void actionPerformed(ActionEvent e)
1263               {
1264                 hydrophobicityColour_actionPerformed();
1265               }
1266             });
1267     helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
1268     helixColour.addActionListener(new java.awt.event.ActionListener()
1269     {
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         helixColour_actionPerformed();
1273       }
1274     });
1275     strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
1276     strandColour.addActionListener(new java.awt.event.ActionListener()
1277     {
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         strandColour_actionPerformed();
1281       }
1282     });
1283     turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
1284     turnColour.addActionListener(new java.awt.event.ActionListener()
1285     {
1286       public void actionPerformed(ActionEvent e)
1287       {
1288         turnColour_actionPerformed();
1289       }
1290     });
1291     buriedColour.setText(MessageManager.getString("label.buried_index"));\r
1292     buriedColour.addActionListener(new java.awt.event.ActionListener()
1293     {
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         buriedColour_actionPerformed();
1297       }
1298     });
1299     abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
1300     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1301     {
1302       public void actionPerformed(ActionEvent e)
1303       {
1304         abovePIDColour_actionPerformed();
1305       }
1306     });
1307     userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
1308     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1309     {
1310       public void actionPerformed(ActionEvent e)
1311       {
1312         userDefinedColour_actionPerformed(e);
1313       }
1314     });
1315     PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
1316     PIDColour.addActionListener(new java.awt.event.ActionListener()
1317     {
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         PIDColour_actionPerformed();
1321       }
1322     });
1323     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
1324     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1325     {
1326       public void actionPerformed(ActionEvent e)
1327       {
1328         BLOSUM62Colour_actionPerformed();
1329       }
1330     });
1331     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
1332     purinePyrimidineColour
1333             .addActionListener(new java.awt.event.ActionListener()
1334             {
1335               public void actionPerformed(ActionEvent e)
1336               {
1337                 purinePyrimidineColour_actionPerformed();
1338               }
1339             });
1340
1341
1342     /*
1343      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1344      * public void actionPerformed(ActionEvent e) {
1345      * covariationColour_actionPerformed(); } });
1346      */
1347
1348     conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
1349     conservationMenuItem
1350             .addActionListener(new java.awt.event.ActionListener()
1351             {
1352               public void actionPerformed(ActionEvent e)
1353               {
1354                 conservationMenuItem_actionPerformed();
1355               }
1356             });
1357   }
1358
1359   protected void sequenceSelectionDetails_actionPerformed()
1360   {
1361     createSequenceDetailsReport(ap.av.getSequenceSelection());
1362   }
1363
1364   protected void sequenceDetails_actionPerformed()
1365   {
1366     createSequenceDetailsReport(new SequenceI[]
1367     { sequence });
1368   }
1369
1370   public void createSequenceDetailsReport(SequenceI[] sequences)
1371   {
1372     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1373     StringBuffer contents = new StringBuffer();
1374     for (SequenceI seq : sequences)
1375     {
1376       contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
1377               + "</h2></p><p>");
1378       new SequenceAnnotationReport(null)
1379               .createSequenceAnnotationReport(
1380                       contents,
1381                       seq,
1382                       true,
1383                       true,
1384                       false,
1385                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1386                               : null);
1387       contents.append("</p>");
1388     }
1389     cap.setText("<html>" + contents.toString() + "</html>");
1390
1391     Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
1392                 ,500, 400);\r
1393
1394   }
1395
1396   protected void showNonconserved_actionPerformed()
1397   {
1398     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1399     refresh();
1400   }
1401
1402   /**
1403    * call to refresh view after settings change
1404    */
1405   void refresh()
1406   {
1407     ap.updateAnnotation();
1408     ap.paintAlignment(true);
1409
1410     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1411   }
1412
1413   /**
1414    * DOCUMENT ME!
1415    *
1416    * @param e
1417    *          DOCUMENT ME!
1418    */
1419   protected void clustalColour_actionPerformed()
1420   {
1421     SequenceGroup sg = getGroup();
1422     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1423     refresh();
1424   }
1425
1426   /**
1427    * DOCUMENT ME!
1428    *
1429    * @param e
1430    *          DOCUMENT ME!
1431    */
1432   protected void zappoColour_actionPerformed()
1433   {
1434     getGroup().cs = new ZappoColourScheme();
1435     refresh();
1436   }
1437
1438   /**
1439    * DOCUMENT ME!
1440    *
1441    * @param e
1442    *          DOCUMENT ME!
1443    */
1444   protected void taylorColour_actionPerformed()
1445   {
1446     getGroup().cs = new TaylorColourScheme();
1447     refresh();
1448   }
1449
1450   /**
1451    * DOCUMENT ME!
1452    *
1453    * @param e
1454    *          DOCUMENT ME!
1455    */
1456   protected void hydrophobicityColour_actionPerformed()
1457   {
1458     getGroup().cs = new HydrophobicColourScheme();
1459     refresh();
1460   }
1461
1462   /**
1463    * DOCUMENT ME!
1464    *
1465    * @param e
1466    *          DOCUMENT ME!
1467    */
1468   protected void helixColour_actionPerformed()
1469   {
1470     getGroup().cs = new HelixColourScheme();
1471     refresh();
1472   }
1473
1474   /**
1475    * DOCUMENT ME!
1476    *
1477    * @param e
1478    *          DOCUMENT ME!
1479    */
1480   protected void strandColour_actionPerformed()
1481   {
1482     getGroup().cs = new StrandColourScheme();
1483     refresh();
1484   }
1485
1486   /**
1487    * DOCUMENT ME!
1488    *
1489    * @param e
1490    *          DOCUMENT ME!
1491    */
1492   protected void turnColour_actionPerformed()
1493   {
1494     getGroup().cs = new TurnColourScheme();
1495     refresh();
1496   }
1497
1498   /**
1499    * DOCUMENT ME!
1500    *
1501    * @param e
1502    *          DOCUMENT ME!
1503    */
1504   protected void buriedColour_actionPerformed()
1505   {
1506     getGroup().cs = new BuriedColourScheme();
1507     refresh();
1508   }
1509
1510   /**
1511    * DOCUMENT ME!
1512    *
1513    * @param e
1514    *          DOCUMENT ME!
1515    */
1516   public void nucleotideMenuItem_actionPerformed()
1517   {
1518     getGroup().cs = new NucleotideColourScheme();
1519     refresh();
1520   }
1521
1522   protected void purinePyrimidineColour_actionPerformed()
1523   {
1524     getGroup().cs = new PurinePyrimidineColourScheme();
1525     refresh();
1526   }
1527
1528
1529   /*
1530    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1531    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1532    */
1533   /**
1534    * DOCUMENT ME!
1535    *
1536    * @param e
1537    *          DOCUMENT ME!
1538    */
1539   protected void abovePIDColour_actionPerformed()
1540   {
1541     SequenceGroup sg = getGroup();
1542     if (sg.cs == null)
1543     {
1544       return;
1545     }
1546
1547     if (abovePIDColour.isSelected())
1548     {
1549       sg.cs.setConsensus(AAFrequency.calculate(
1550               sg.getSequences(ap.av.getHiddenRepSequences()),
1551               sg.getStartRes(), sg.getEndRes() + 1));
1552
1553       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1554               .getName());
1555
1556       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1557
1558       SliderPanel.showPIDSlider();
1559     }
1560     else
1561     // remove PIDColouring
1562     {
1563       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1564     }
1565
1566     refresh();
1567   }
1568
1569   /**
1570    * DOCUMENT ME!
1571    *
1572    * @param e
1573    *          DOCUMENT ME!
1574    */
1575   protected void userDefinedColour_actionPerformed(ActionEvent e)
1576   {
1577     SequenceGroup sg = getGroup();
1578
1579     if (e.getSource().equals(userDefinedColour))\r
1580     {
1581       new UserDefinedColours(ap, sg);
1582     }
1583     else
1584     {
1585       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1586               .getUserColourSchemes().get(e.getActionCommand());
1587
1588       sg.cs = udc;
1589     }
1590     refresh();
1591   }
1592
1593   /**
1594    * DOCUMENT ME!
1595    *
1596    * @param e
1597    *          DOCUMENT ME!
1598    */
1599   protected void PIDColour_actionPerformed()
1600   {
1601     SequenceGroup sg = getGroup();
1602     sg.cs = new PIDColourScheme();
1603     sg.cs.setConsensus(AAFrequency.calculate(
1604             sg.getSequences(ap.av.getHiddenRepSequences()),
1605             sg.getStartRes(), sg.getEndRes() + 1));
1606     refresh();
1607   }
1608
1609   /**
1610    * DOCUMENT ME!
1611    *
1612    * @param e
1613    *          DOCUMENT ME!
1614    */
1615   protected void BLOSUM62Colour_actionPerformed()
1616   {
1617     SequenceGroup sg = getGroup();
1618
1619     sg.cs = new Blosum62ColourScheme();
1620
1621     sg.cs.setConsensus(AAFrequency.calculate(
1622             sg.getSequences(ap.av.getHiddenRepSequences()),
1623             sg.getStartRes(), sg.getEndRes() + 1));
1624
1625     refresh();
1626   }
1627
1628   /**
1629    * DOCUMENT ME!
1630    *
1631    * @param e
1632    *          DOCUMENT ME!
1633    */
1634   protected void noColourmenuItem_actionPerformed()
1635   {
1636     getGroup().cs = null;
1637     refresh();
1638   }
1639
1640   /**
1641    * DOCUMENT ME!
1642    *
1643    * @param e
1644    *          DOCUMENT ME!
1645    */
1646   protected void conservationMenuItem_actionPerformed()
1647   {
1648     SequenceGroup sg = getGroup();
1649     if (sg.cs == null)
1650     {
1651       return;
1652     }
1653
1654     if (conservationMenuItem.isSelected())
1655     {
1656     // JBPNote: Conservation name shouldn't be i18n translated
1657       Conservation c = new Conservation("Group",
1658               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1659                       .getHiddenRepSequences()), sg.getStartRes(),
1660               sg.getEndRes() + 1);
1661
1662       c.calculate();
1663       c.verdict(false, ap.av.getConsPercGaps());
1664
1665       sg.cs.setConservation(c);
1666
1667       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1668       SliderPanel.showConservationSlider();
1669     }
1670     else
1671     // remove ConservationColouring
1672     {
1673       sg.cs.setConservation(null);
1674     }
1675
1676     refresh();
1677   }
1678
1679   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1680   {
1681     SequenceGroup sg = getGroup();
1682     if (sg == null)
1683     {
1684       return;
1685     }
1686
1687     AnnotationColourGradient acg = new AnnotationColourGradient(
1688             sequence.getAnnotation()[0], null,
1689             AnnotationColourGradient.NO_THRESHOLD);
1690
1691     acg.setPredefinedColours(true);
1692     sg.cs = acg;
1693
1694     refresh();
1695   }
1696
1697   /**
1698    * DOCUMENT ME!
1699    *
1700    * @param e
1701    *          DOCUMENT ME!
1702    */
1703   protected void groupName_actionPerformed()
1704   {
1705
1706     SequenceGroup sg = getGroup();
1707     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1708             sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",\r
1709             MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
1710             ap.alignFrame);
1711
1712     if (!dialog.accept)
1713     {
1714       return;
1715     }
1716
1717     sg.setName(dialog.getName());
1718     sg.setDescription(dialog.getDescription());
1719     refresh();
1720   }
1721
1722   /**
1723    * Get selection group - adding it to the alignment if necessary.
1724    *
1725    * @return sequence group to operate on
1726    */
1727   SequenceGroup getGroup()
1728   {
1729     SequenceGroup sg = ap.av.getSelectionGroup();
1730     // this method won't add a new group if it already exists
1731     if (sg != null)
1732     {
1733       ap.av.getAlignment().addGroup(sg);
1734     }
1735
1736     return sg;
1737   }
1738
1739   /**
1740    * DOCUMENT ME!
1741    *
1742    * @param e
1743    *          DOCUMENT ME!
1744    */
1745   void sequenceName_actionPerformed()
1746   {
1747     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1748             sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",\r
1749             MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
1750             ap.alignFrame);
1751
1752     if (!dialog.accept)
1753     {
1754       return;
1755     }
1756
1757     if (dialog.getName() != null)
1758     {
1759       if (dialog.getName().indexOf(" ") > -1)
1760       {
1761         JOptionPane.showMessageDialog(ap,
1762                 MessageManager.getString("label.spaces_converted_to_backslashes"),\r
1763                 MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
1764                 JOptionPane.WARNING_MESSAGE);
1765       }
1766
1767       sequence.setName(dialog.getName().replace(' ', '_'));
1768       ap.paintAlignment(false);
1769     }
1770
1771     sequence.setDescription(dialog.getDescription());
1772
1773     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1774             .getSequences());
1775
1776   }
1777
1778   /**
1779    * DOCUMENT ME!
1780    *
1781    * @param e
1782    *          DOCUMENT ME!
1783    */
1784   void unGroupMenuItem_actionPerformed()
1785   {
1786     SequenceGroup sg = ap.av.getSelectionGroup();
1787     ap.av.getAlignment().deleteGroup(sg);
1788     ap.av.setSelectionGroup(null);
1789     refresh();
1790   }
1791   void createGroupMenuItem_actionPerformed()
1792   {
1793     getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
1794     refresh();
1795   }
1796
1797   /**
1798    * DOCUMENT ME!
1799    *
1800    * @param e
1801    *          DOCUMENT ME!
1802    */
1803   protected void outline_actionPerformed()
1804   {
1805     SequenceGroup sg = getGroup();
1806     Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
1807             Color.BLUE);
1808
1809     if (col != null)
1810     {
1811       sg.setOutlineColour(col);
1812     }
1813
1814     refresh();
1815   }
1816
1817   /**
1818    * DOCUMENT ME!
1819    *
1820    * @param e
1821    *          DOCUMENT ME!
1822    */
1823   public void showBoxes_actionPerformed()
1824   {
1825     getGroup().setDisplayBoxes(showBoxes.isSelected());
1826     refresh();
1827   }
1828
1829   /**
1830    * DOCUMENT ME!
1831    *
1832    * @param e
1833    *          DOCUMENT ME!
1834    */
1835   public void showText_actionPerformed()
1836   {
1837     getGroup().setDisplayText(showText.isSelected());
1838     refresh();
1839   }
1840
1841   /**
1842    * DOCUMENT ME!
1843    *
1844    * @param e
1845    *          DOCUMENT ME!
1846    */
1847   public void showColourText_actionPerformed()
1848   {
1849     getGroup().setColourText(showColourText.isSelected());
1850     refresh();
1851   }
1852
1853   public void showLink(String url)
1854   {
1855     try
1856     {
1857       jalview.util.BrowserLauncher.openURL(url);
1858     } catch (Exception ex)
1859     {
1860       JOptionPane
1861               .showInternalMessageDialog(
1862                       Desktop.desktop,
1863                       MessageManager.getString("label.web_browser_not_found_unix"),\r
1864                       MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
1865
1866       ex.printStackTrace();
1867     }
1868   }
1869
1870   void hideSequences(boolean representGroup)
1871   {
1872     SequenceGroup sg = ap.av.getSelectionGroup();
1873     if (sg == null || sg.getSize() < 1)
1874     {
1875       ap.av.hideSequence(new SequenceI[]
1876       { sequence });
1877       return;
1878     }
1879
1880     ap.av.setSelectionGroup(null);
1881
1882     if (representGroup)
1883     {
1884       ap.av.hideRepSequences(sequence, sg);
1885
1886       return;
1887     }
1888
1889     int gsize = sg.getSize();
1890     SequenceI[] hseqs;
1891
1892     hseqs = new SequenceI[gsize];
1893
1894     int index = 0;
1895     for (int i = 0; i < gsize; i++)
1896     {
1897       hseqs[index++] = sg.getSequenceAt(i);
1898     }
1899
1900     ap.av.hideSequence(hseqs);
1901     // refresh(); TODO: ? needed ?
1902     ap.av.sendSelection();
1903   }
1904
1905   public void copy_actionPerformed()
1906   {
1907     ap.alignFrame.copy_actionPerformed(null);
1908   }
1909
1910   public void cut_actionPerformed()
1911   {
1912     ap.alignFrame.cut_actionPerformed(null);
1913   }
1914
1915   void changeCase(ActionEvent e)
1916   {
1917     Object source = e.getSource();
1918     SequenceGroup sg = ap.av.getSelectionGroup();
1919
1920     if (sg != null)
1921     {
1922       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1923               sg.getEndRes() + 1);
1924
1925       String description;
1926       int caseChange;
1927
1928       if (source == toggle)
1929       {
1930         description = MessageManager.getString("label.toggle_case");\r
1931         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1932       }
1933       else if (source == upperCase)
1934       {
1935         description = MessageManager.getString("label.to_upper_case");\r
1936         caseChange = ChangeCaseCommand.TO_UPPER;
1937       }
1938       else
1939       {
1940         description = MessageManager.getString("label.to_lower_case");\r
1941         caseChange = ChangeCaseCommand.TO_LOWER;
1942       }
1943
1944       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1945               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1946               startEnd, caseChange);
1947
1948       ap.alignFrame.addHistoryItem(caseCommand);
1949
1950       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1951               .getSequences());
1952
1953     }
1954   }
1955
1956   public void outputText_actionPerformed(ActionEvent e)
1957   {
1958     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1959     cap.setForInput(null);
1960     Desktop.addInternalFrame(cap,
1961             MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
1962
1963     String[] omitHidden = null;
1964
1965     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1966     // or we simply trust the user wants
1967     // wysiwig behaviour
1968     SequenceGroup sg = ap.av.getSelectionGroup();
1969     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1970     omitHidden = ap.av.getViewAsString(true);
1971     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1972     AlignmentAnnotation[] nala = ap.av.getAlignment()
1973             .getAlignmentAnnotation();
1974     if (nala != null)
1975     {
1976       for (int i = 0; i < nala.length; i++)
1977       {
1978         AlignmentAnnotation na = nala[i];
1979         oal.addAnnotation(na);
1980       }
1981     }
1982     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1983             oal, omitHidden, csel, sg));
1984     oal = null;
1985   }
1986
1987   public void pdbFromFile_actionPerformed()
1988   {
1989     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1990             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1991     chooser.setFileView(new jalview.io.JalviewFileView());
1992     chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
1993     chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
1994
1995     int value = chooser.showOpenDialog(null);
1996
1997     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1998     {
1999       String choice = chooser.getSelectedFile().getPath();
2000       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2001       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2002               jalview.io.AppletFormatAdapter.FILE, sequence, true);
2003     }
2004
2005   }
2006     // JBNote: commented out - these won't be instantiated here...!
2007 //  public void RNAFold_actionPerformed() throws Exception
2008 //  {
2009 //        Predict2D P2D = new Predict2D();
2010 //        P2D.getStructure2DFromRNAFold("toto");
2011 //  }
2012 //
2013 //  public void ContraFold_actionPerformed() throws Exception
2014 //  {
2015 //        Predict2D P2D = new Predict2D();
2016 //        P2D.getStructure2DFromContraFold("toto");
2017 //  }
2018   public void enterPDB_actionPerformed()
2019   {
2020     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2021             MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
2022
2023     if (id != null && id.length() > 0)
2024     {
2025       PDBEntry entry = new PDBEntry();
2026       entry.setId(id.toUpperCase());
2027       sequence.getDatasetSequence().addPDBId(entry);
2028     }
2029   }
2030
2031   public void discoverPDB_actionPerformed()
2032   {
2033
2034     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2035     { sequence }
2036             : ap.av.getSequenceSelection());
2037     Thread discpdb = new Thread(new Runnable()
2038     {
2039       public void run()
2040       {
2041
2042         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2043                 .fetchDBRefs(false);
2044       }
2045
2046     });
2047     discpdb.start();
2048   }
2049
2050   public void sequenceFeature_actionPerformed()
2051   {
2052     SequenceGroup sg = ap.av.getSelectionGroup();
2053     if (sg == null)
2054     {
2055       return;
2056     }
2057
2058     int rsize = 0, gSize = sg.getSize();
2059     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2060     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2061
2062     for (int i = 0; i < gSize; i++)
2063     {
2064       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2065       int end = sg.findEndRes(sg.getSequenceAt(i));
2066       if (start <= end)
2067       {
2068         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2069         features[rsize] = new SequenceFeature(null, null, null, start, end,
2070                 "Jalview");
2071         rsize++;
2072       }
2073     }
2074     rseqs = new SequenceI[rsize];
2075     tfeatures = new SequenceFeature[rsize];
2076     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2077     System.arraycopy(features, 0, tfeatures, 0, rsize);
2078     features = tfeatures;
2079     seqs = rseqs;
2080     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2081             features, true, ap))
2082     {
2083       ap.alignFrame.setShowSeqFeatures(true);
2084       ap.highlightSearchResults(null);
2085     }
2086   }
2087
2088   public void textColour_actionPerformed()
2089   {
2090     SequenceGroup sg = getGroup();
2091     if (sg != null)
2092     {
2093       new TextColourChooser().chooseColour(ap, sg);
2094     }
2095   }
2096
2097   public void colourByStructure(String pdbid)
2098   {
2099     Annotation[] anots = ap.av.getStructureSelectionManager()
2100             .colourSequenceFromStructure(sequence, pdbid);
2101
2102     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2103             "Coloured by " + pdbid, anots);
2104
2105     ap.av.getAlignment().addAnnotation(an);
2106     an.createSequenceMapping(sequence, 0, true);
2107     // an.adjustForAlignment();
2108     ap.av.getAlignment().setAnnotationIndex(an, 0);
2109
2110     ap.adjustAnnotationHeight();
2111
2112     sequence.addAlignmentAnnotation(an);
2113
2114   }
2115
2116   public void editSequence_actionPerformed(ActionEvent actionEvent)
2117   {
2118     SequenceGroup sg = ap.av.getSelectionGroup();
2119
2120     if (sg != null)
2121     {
2122       if (sequence == null)
2123         sequence = (Sequence) sg.getSequenceAt(0);
2124
2125       EditNameDialog dialog = new EditNameDialog(
2126               sequence.getSequenceAsString(sg.getStartRes(),
2127                       sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
2128                       MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
2129
2130       if (dialog.accept)
2131       {
2132         EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
2133                 EditCommand.REPLACE, dialog.getName().replace(' ',
2134                         ap.av.getGapCharacter()),
2135                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2136                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2137
2138         ap.alignFrame.addHistoryItem(editCommand);
2139
2140         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2141                 .getSequences());
2142       }
2143     }
2144   }
2145
2146 }