src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   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>(),reppdb=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           reppdb.put(pes.get(0).getId(),pes.get(0));
 505           for (PDBEntry pe : pes)
 506           {
 507             pdbe.put(pe.getId(), pe);
 508             if (sqass == null)
 509             {
 510               sqass = sq;
 511             }
 512           }
 513         }
 514       }
 515       if (pdbe.size() > 0)
 516       {
 517         final PDBEntry[] pe = pdbe.values().toArray(
 518                 new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
 519                         new PDBEntry[reppdb.size()]);
 520         final JMenuItem gpdbview,rpdbview;
 521         if (pdbe.size() == 1)
 522         {
 523           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
 524         }
 525         else
 526         {
 527           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));          \r
 528         }
 529         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
 530         gpdbview.addActionListener(new ActionListener()
 531         {
 532
 533           @Override
 534           public void actionPerformed(ActionEvent e)
 535           {
 536             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 537           }
 538         });
 539         if (reppdb.size()>1 && reppdb.size()<pdbe.size())
 540         {
 541           structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
 542           rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
 543           rpdbview.addActionListener(new ActionListener()
 544           {
 545
 546             @Override
 547             public void actionPerformed(ActionEvent e)
 548             {
 549               new AppJmol(ap, pr, ap.av.collateForPDB(pr));
 550             }
 551           });
 552         }
 553       }
 554     }
 555     else
 556     {
 557       groupMenu.setVisible(false);
 558       editMenu.setVisible(false);
 559     }
 560
 561     if (!isDefinedGroup)
 562     {
 563       createGroupMenuItem.setVisible(true);
 564       unGroupMenuItem.setVisible(false);
 565       jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
 566     } else {
 567       createGroupMenuItem.setVisible(false);
 568       unGroupMenuItem.setVisible(true);
 569       jMenu1.setText(MessageManager.getString("action.edit_group"));\r
 570     }
 571
 572     if (seq == null)
 573     {
 574       sequenceMenu.setVisible(false);
 575       structureMenu.setVisible(false);
 576     }
 577
 578     if (links != null && links.size() > 0)
 579     {
 580
 581       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
 582       Vector linkset = new Vector();
 583       for (int i = 0; i < links.size(); i++)
 584       {
 585         String link = links.elementAt(i).toString();
 586         UrlLink urlLink = null;
 587         try
 588         {
 589           urlLink = new UrlLink(link);
 590         } catch (Exception foo)
 591         {
 592           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 593                   + "'", foo);
 594           continue;
 595         }
 596         ;
 597         if (!urlLink.isValid())
 598         {
 599           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 600           continue;
 601         }
 602         final String label = urlLink.getLabel();
 603         if (seq != null && urlLink.isDynamic())
 604         {
 605
 606           // collect matching db-refs
 607           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 608                   seq.getDBRef(), new String[]
 609                   { urlLink.getTarget() });
 610           // collect id string too
 611           String id = seq.getName();
 612           String descr = seq.getDescription();
 613           if (descr != null && descr.length() < 1)
 614           {
 615             descr = null;
 616           }
 617
 618           if (dbr != null)
 619           {
 620             for (int r = 0; r < dbr.length; r++)
 621             {
 622               if (id != null && dbr[r].getAccessionId().equals(id))
 623               {
 624                 // suppress duplicate link creation for the bare sequence ID
 625                 // string with this link
 626                 id = null;
 627               }
 628               // create Bare ID link for this RUL
 629               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 630                       true);
 631               if (urls != null)
 632               {
 633                 for (int u = 0; u < urls.length; u += 2)
 634                 {
 635                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 636                   {
 637                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 638                     addshowLink(linkMenu, label + "|" + urls[u],
 639                             urls[u + 1]);
 640                   }
 641                 }
 642               }
 643             }
 644           }
 645           if (id != null)
 646           {
 647             // create Bare ID link for this RUL
 648             String[] urls = urlLink.makeUrls(id, true);
 649             if (urls != null)
 650             {
 651               for (int u = 0; u < urls.length; u += 2)
 652               {
 653                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 654                 {
 655                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 656                   addshowLink(linkMenu, label, urls[u + 1]);
 657                 }
 658               }
 659             }
 660           }
 661           // Create urls from description but only for URL links which are regex
 662           // links
 663           if (descr != null && urlLink.getRegexReplace() != null)
 664           {
 665             // create link for this URL from description where regex matches
 666             String[] urls = urlLink.makeUrls(descr, true);
 667             if (urls != null)
 668             {
 669               for (int u = 0; u < urls.length; u += 2)
 670               {
 671                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 672                 {
 673                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 674                   addshowLink(linkMenu, label, urls[u + 1]);
 675                 }
 676               }
 677             }
 678           }
 679         }
 680         else
 681         {
 682           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 683           {
 684             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 685             // Add a non-dynamic link
 686             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 687           }
 688         }
 689       }
 690       if (sequence != null)
 691       {
 692         sequenceMenu.add(linkMenu);
 693       }
 694       else
 695       {
 696         add(linkMenu);
 697       }
 698     }
 699   }
 700
 701   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 702   {
 703
 704     // TODO: usability: thread off the generation of group url content so root
 705     // menu appears asap
 706     // sequence only URLs
 707     // ID/regex match URLs
 708     groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 709     JMenu[] linkMenus = new JMenu[]
 710     { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
 711         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
 712                                           // created.
 713     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 714     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 715     Hashtable commonDbrefs = new Hashtable();
 716     for (int sq = 0; sq < seqs.length; sq++)
 717     {
 718
 719       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 720               .findPosition(sg.getEndRes());
 721       // just collect ids from dataset sequence
 722       // TODO: check if IDs collected from selecton group intersects with the
 723       // current selection, too
 724       SequenceI sqi = seqs[sq];
 725       while (sqi.getDatasetSequence() != null)
 726       {
 727         sqi = sqi.getDatasetSequence();
 728       }
 729       DBRefEntry[] dbr = sqi.getDBRef();
 730       if (dbr != null && dbr.length > 0)
 731       {
 732         for (int d = 0; d < dbr.length; d++)
 733         {
 734           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 735           Object[] sarray = (Object[]) commonDbrefs.get(src);
 736           if (sarray == null)
 737           {
 738             sarray = new Object[2];
 739             sarray[0] = new int[]
 740             { 0 };
 741             sarray[1] = new String[seqs.length];
 742
 743             commonDbrefs.put(src, sarray);
 744           }
 745
 746           if (((String[]) sarray[1])[sq] == null)
 747           {
 748             if (!dbr[d].hasMap()
 749                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 750             {
 751               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 752               ((int[]) sarray[0])[0]++;
 753             }
 754           }
 755         }
 756       }
 757     }
 758     // now create group links for all distinct ID/sequence sets.
 759     boolean addMenu = false; // indicates if there are any group links to give
 760                              // to user
 761     for (int i = 0; i < groupLinks.size(); i++)
 762     {
 763       String link = groupLinks.elementAt(i).toString();
 764       GroupUrlLink urlLink = null;
 765       try
 766       {
 767         urlLink = new GroupUrlLink(link);
 768       } catch (Exception foo)
 769       {
 770         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 771                 + "'", foo);
 772         continue;
 773       }
 774       ;
 775       if (!urlLink.isValid())
 776       {
 777         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 778         continue;
 779       }
 780       final String label = urlLink.getLabel();
 781       boolean usingNames = false;
 782       // Now see which parts of the group apply for this URL
 783       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 784       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 785       String[] seqstr, ids; // input to makeUrl
 786       if (idset != null)
 787       {
 788         int numinput = ((int[]) idset[0])[0];
 789         String[] allids = ((String[]) idset[1]);
 790         seqstr = new String[numinput];
 791         ids = new String[numinput];
 792         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 793         {
 794           if (allids[sq] != null)
 795           {
 796             ids[idcount] = allids[sq];
 797             seqstr[idcount++] = idandseqs[1][sq];
 798           }
 799         }
 800       }
 801       else
 802       {
 803         // just use the id/seq set
 804         seqstr = idandseqs[1];
 805         ids = idandseqs[0];
 806         usingNames = true;
 807       }
 808       // and try and make the groupURL!
 809
 810       Object[] urlset = null;
 811       try
 812       {
 813         urlset = urlLink.makeUrlStubs(ids, seqstr,
 814                 "FromJalview" + System.currentTimeMillis(), false);
 815       } catch (UrlStringTooLongException e)
 816       {
 817       }
 818       if (urlset != null)
 819       {
 820         int type = urlLink.getGroupURLType() & 3;
 821         // System.out.println(urlLink.getGroupURLType()
 822         // +" "+((String[])urlset[3])[0]);
 823         // first two bits ofurlLink type bitfield are sequenceids and sequences
 824         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 825         addshowLink(linkMenus[type], label
 826                 + (((type & 1) == 1) ? ("("
 827                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 828                 urlLink, urlset);
 829         addMenu = true;
 830       }
 831     }
 832     if (addMenu)
 833     {
 834       groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 835       for (int m = 0; m < linkMenus.length; m++)
 836       {
 837         if (linkMenus[m] != null
 838                 && linkMenus[m].getMenuComponentCount() > 0)
 839         {
 840           groupLinksMenu.add(linkMenus[m]);
 841         }
 842       }
 843
 844       groupMenu.add(groupLinksMenu);
 845     }
 846   }
 847
 848   /**
 849    * add a show URL menu item to the given linkMenu
 850    *
 851    * @param linkMenu
 852    * @param label
 853    *          - menu label string
 854    * @param url
 855    *          - url to open
 856    */
 857   private void addshowLink(JMenu linkMenu, String label, final String url)
 858   {
 859     JMenuItem item = new JMenuItem(label);
 860     item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
 861     item.addActionListener(new java.awt.event.ActionListener()
 862     {
 863       public void actionPerformed(ActionEvent e)
 864       {
 865         new Thread(new Runnable()
 866         {
 867
 868           public void run()
 869           {
 870             showLink(url);
 871           }
 872
 873         }).start();
 874       }
 875     });
 876
 877     linkMenu.add(item);
 878   }
 879
 880   /**
 881    * add a late bound groupURL item to the given linkMenu
 882    *
 883    * @param linkMenu
 884    * @param label
 885    *          - menu label string
 886    * @param urlgenerator
 887    *          GroupURLLink used to generate URL
 888    * @param urlstub
 889    *          Object array returned from the makeUrlStubs function.
 890    */
 891   private void addshowLink(JMenu linkMenu, String label,
 892           final GroupUrlLink urlgenerator, final Object[] urlstub)
 893   {
 894     JMenuItem item = new JMenuItem(label);
 895     item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
 896     // TODO: put in info about what is being sent.\r
 897     item.addActionListener(new java.awt.event.ActionListener()
 898     {
 899       public void actionPerformed(ActionEvent e)
 900       {
 901         new Thread(new Runnable()
 902         {
 903
 904           public void run()
 905           {
 906             try
 907             {
 908               showLink(urlgenerator.constructFrom(urlstub));
 909             } catch (UrlStringTooLongException e)
 910             {
 911             }
 912           }
 913
 914         }).start();
 915       }
 916     });
 917
 918     linkMenu.add(item);
 919   }
 920
 921   /**
 922    * DOCUMENT ME!
 923    *
 924    * @throws Exception
 925    *           DOCUMENT ME!
 926    */
 927   private void jbInit() throws Exception
 928   {
 929     groupMenu.setText(MessageManager.getString("label.group"));\r
 930     groupMenu.setText(MessageManager.getString("label.selection"));\r
 931     groupName.setText(MessageManager.getString("label.name"));\r
 932     groupName.addActionListener(new java.awt.event.ActionListener()
 933     {
 934       public void actionPerformed(ActionEvent e)
 935       {
 936         groupName_actionPerformed();
 937       }
 938     });
 939     sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
 940     sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
 941     sequenceName.addActionListener(new java.awt.event.ActionListener()
 942     {
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         sequenceName_actionPerformed();
 946       }
 947     });
 948     sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 949     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 950     {
 951       public void actionPerformed(ActionEvent e)
 952       {
 953         sequenceDetails_actionPerformed();
 954       }
 955     });
 956     sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 957     sequenceSelDetails
 958             .addActionListener(new java.awt.event.ActionListener()
 959             {
 960               public void actionPerformed(ActionEvent e)
 961               {
 962                 sequenceSelectionDetails_actionPerformed();
 963               }
 964             });
 965     PIDColour.setFocusPainted(false);
 966     unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
 967     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 968     {
 969       public void actionPerformed(ActionEvent e)
 970       {
 971         unGroupMenuItem_actionPerformed();
 972       }
 973     });
 974     createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
 975     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 976     {
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         createGroupMenuItem_actionPerformed();
 980       }
 981     });
 982
 983     outline.setText(MessageManager.getString("action.border_colour"));\r
 984     outline.addActionListener(new java.awt.event.ActionListener()
 985     {
 986       public void actionPerformed(ActionEvent e)
 987       {
 988         outline_actionPerformed();
 989       }
 990     });
 991     nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
 992     nucleotideMenuItem.addActionListener(new ActionListener()
 993     {
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         nucleotideMenuItem_actionPerformed();
 997       }
 998     });
 999     colourMenu.setText(MessageManager.getString("label.group_colour"));\r
1000     showBoxes.setText(MessageManager.getString("action.boxes"));\r
1001     showBoxes.setState(true);
1002     showBoxes.addActionListener(new ActionListener()
1003     {
1004       public void actionPerformed(ActionEvent e)
1005       {
1006         showBoxes_actionPerformed();
1007       }
1008     });
1009     showText.setText(MessageManager.getString("action.text"));\r
1010     showText.setState(true);
1011     showText.addActionListener(new ActionListener()
1012     {
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         showText_actionPerformed();
1016       }
1017     });
1018     showColourText.setText(MessageManager.getString("label.colour_text"));\r
1019     showColourText.addActionListener(new ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         showColourText_actionPerformed();
1024       }
1025     });
1026     displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
1027     displayNonconserved.setState(true);
1028     displayNonconserved.addActionListener(new ActionListener()
1029     {
1030       public void actionPerformed(ActionEvent e)
1031       {
1032         showNonconserved_actionPerformed();
1033       }
1034     });
1035     editMenu.setText(MessageManager.getString("action.edit"));\r
1036     cut.setText(MessageManager.getString("action.cut"));\r
1037     cut.addActionListener(new ActionListener()
1038     {
1039       public void actionPerformed(ActionEvent e)
1040       {
1041         cut_actionPerformed();
1042       }
1043     });
1044     upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
1045     upperCase.addActionListener(new ActionListener()
1046     {
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         changeCase(e);
1050       }
1051     });
1052     copy.setText(MessageManager.getString("action.copy"));\r
1053     copy.addActionListener(new ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         copy_actionPerformed();
1058       }
1059     });
1060     lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
1061     lowerCase.addActionListener(new ActionListener()
1062     {
1063       public void actionPerformed(ActionEvent e)
1064       {
1065         changeCase(e);
1066       }
1067     });
1068     toggle.setText(MessageManager.getString("label.toggle_case"));\r
1069     toggle.addActionListener(new ActionListener()
1070     {
1071       public void actionPerformed(ActionEvent e)
1072       {
1073         changeCase(e);
1074       }
1075     });
1076     pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
1077     pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
1078     pdbFromFile.addActionListener(new ActionListener()
1079     {
1080       public void actionPerformed(ActionEvent e)
1081       {
1082         pdbFromFile_actionPerformed();
1083       }
1084     });
1085 //    RNAFold.setText("From RNA Fold with predict2D");
1086 //    RNAFold.addActionListener(new ActionListener()
1087 //    {
1088 //      public void actionPerformed(ActionEvent e)
1089 //      {
1090 //        try {
1091 //                      RNAFold_actionPerformed();
1092 //              } catch (Exception e1) {
1093 //                      // TODO Auto-generated catch block
1094 //                      e1.printStackTrace();
1095 //              }
1096 //      }
1097 //    });
1098 //    ContraFold.setText("From Contra Fold with predict2D");
1099 //    ContraFold.addActionListener(new ActionListener()
1100 //    {
1101 //      public void actionPerformed(ActionEvent e)
1102 //      {
1103 //        try {
1104 //                      ContraFold_actionPerformed();
1105 //              } catch (Exception e1) {
1106 //                      // TODO Auto-generated catch block
1107 //                      e1.printStackTrace();
1108 //              }
1109 //      }
1110 //    });
1111     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
1112     enterPDB.addActionListener(new ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         enterPDB_actionPerformed();
1117       }
1118     });
1119     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
1120     discoverPDB.addActionListener(new ActionListener()
1121     {
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         discoverPDB_actionPerformed();
1125       }
1126     });
1127     outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
1128     sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
1129     sequenceFeature.addActionListener(new ActionListener()
1130     {
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         sequenceFeature_actionPerformed();
1134       }
1135     });
1136     textColour.setText(MessageManager.getString("label.text_colour"));\r
1137     textColour.addActionListener(new ActionListener()
1138     {
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         textColour_actionPerformed();
1142       }
1143     });
1144     jMenu1.setText(MessageManager.getString("label.group"));\r
1145     structureMenu.setText(MessageManager.getString("label.structure"));\r
1146     viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
1147     // colStructureMenu.setText("Colour By Structure");
1148     editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
1149     editSequence.addActionListener(new ActionListener()
1150     {
1151       public void actionPerformed(ActionEvent actionEvent)
1152       {
1153         editSequence_actionPerformed(actionEvent);
1154       }
1155     });
1156
1157     /*
1158      * annotationMenuItem.setText("By Annotation");
1159      * annotationMenuItem.addActionListener(new ActionListener() { public void
1160      * actionPerformed(ActionEvent actionEvent) {
1161      * annotationMenuItem_actionPerformed(actionEvent); } });
1162      */
1163     groupMenu.add(sequenceSelDetails);
1164     add(groupMenu);
1165     add(sequenceMenu);
1166     this.add(structureMenu);
1167     groupMenu.add(editMenu);
1168     groupMenu.add(outputMenu);
1169     groupMenu.add(sequenceFeature);
1170     groupMenu.add(createGroupMenuItem);
1171     groupMenu.add(unGroupMenuItem);
1172     groupMenu.add(jMenu1);
1173     sequenceMenu.add(sequenceName);
1174     sequenceMenu.add(sequenceDetails);
1175     colourMenu.add(textColour);
1176     colourMenu.add(noColourmenuItem);
1177     colourMenu.add(clustalColour);
1178     colourMenu.add(BLOSUM62Colour);
1179     colourMenu.add(PIDColour);
1180     colourMenu.add(zappoColour);
1181     colourMenu.add(taylorColour);
1182     colourMenu.add(hydrophobicityColour);
1183     colourMenu.add(helixColour);
1184     colourMenu.add(strandColour);
1185     colourMenu.add(turnColour);
1186     colourMenu.add(buriedColour);
1187     colourMenu.add(nucleotideMenuItem);
1188     if (ap.getAlignment().isNucleotide()) {
1189         // JBPNote - commented since the colourscheme isn't functional
1190         //  colourMenu.add(RNAInteractionColour);
1191         colourMenu.add(purinePyrimidineColour);
1192     }
1193     // colourMenu.add(covariationColour);
1194     colourMenu.add(userDefinedColour);
1195
1196     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1197     {
1198       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1199               .getUserColourSchemes().keys();
1200
1201       while (userColours.hasMoreElements())
1202       {
1203         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1204         item.addActionListener(new ActionListener()
1205         {
1206           public void actionPerformed(ActionEvent evt)
1207           {
1208             userDefinedColour_actionPerformed(evt);
1209           }
1210         });
1211         colourMenu.add(item);
1212       }
1213     }
1214
1215     colourMenu.addSeparator();
1216     colourMenu.add(abovePIDColour);
1217     colourMenu.add(conservationMenuItem);
1218     // colourMenu.add(annotationMenuItem);
1219     editMenu.add(copy);
1220     editMenu.add(cut);
1221     editMenu.add(editSequence);
1222     editMenu.add(upperCase);
1223     editMenu.add(lowerCase);
1224     editMenu.add(toggle);
1225     pdbMenu.add(pdbFromFile);
1226     // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1227     //    pdbMenu.add(RNAFold);
1228     //    pdbMenu.add(ContraFold);
1229     pdbMenu.add(enterPDB);
1230     pdbMenu.add(discoverPDB);
1231     jMenu1.add(groupName);
1232     jMenu1.add(colourMenu);
1233     jMenu1.add(showBoxes);
1234     jMenu1.add(showText);
1235     jMenu1.add(showColourText);
1236     jMenu1.add(outline);
1237     jMenu1.add(displayNonconserved);
1238     structureMenu.add(pdbMenu);
1239     structureMenu.add(viewStructureMenu);
1240     // structureMenu.add(colStructureMenu);
1241     noColourmenuItem.setText(MessageManager.getString("label.none"));\r
1242     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1243     {
1244       public void actionPerformed(ActionEvent e)
1245       {
1246         noColourmenuItem_actionPerformed();
1247       }
1248     });
1249
1250     clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
1251     clustalColour.addActionListener(new java.awt.event.ActionListener()
1252     {
1253       public void actionPerformed(ActionEvent e)
1254       {
1255         clustalColour_actionPerformed();
1256       }
1257     });
1258     zappoColour.setText(MessageManager.getString("label.zappo"));\r
1259     zappoColour.addActionListener(new java.awt.event.ActionListener()
1260     {
1261       public void actionPerformed(ActionEvent e)
1262       {
1263         zappoColour_actionPerformed();
1264       }
1265     });
1266     taylorColour.setText(MessageManager.getString("label.taylor"));\r
1267     taylorColour.addActionListener(new java.awt.event.ActionListener()
1268     {
1269       public void actionPerformed(ActionEvent e)
1270       {
1271         taylorColour_actionPerformed();
1272       }
1273     });
1274     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
1275     hydrophobicityColour
1276             .addActionListener(new java.awt.event.ActionListener()
1277             {
1278               public void actionPerformed(ActionEvent e)
1279               {
1280                 hydrophobicityColour_actionPerformed();
1281               }
1282             });
1283     helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
1284     helixColour.addActionListener(new java.awt.event.ActionListener()
1285     {
1286       public void actionPerformed(ActionEvent e)
1287       {
1288         helixColour_actionPerformed();
1289       }
1290     });
1291     strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
1292     strandColour.addActionListener(new java.awt.event.ActionListener()
1293     {
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         strandColour_actionPerformed();
1297       }
1298     });
1299     turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
1300     turnColour.addActionListener(new java.awt.event.ActionListener()
1301     {
1302       public void actionPerformed(ActionEvent e)
1303       {
1304         turnColour_actionPerformed();
1305       }
1306     });
1307     buriedColour.setText(MessageManager.getString("label.buried_index"));\r
1308     buriedColour.addActionListener(new java.awt.event.ActionListener()
1309     {
1310       public void actionPerformed(ActionEvent e)
1311       {
1312         buriedColour_actionPerformed();
1313       }
1314     });
1315     abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
1316     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1317     {
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         abovePIDColour_actionPerformed();
1321       }
1322     });
1323     userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
1324     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1325     {
1326       public void actionPerformed(ActionEvent e)
1327       {
1328         userDefinedColour_actionPerformed(e);
1329       }
1330     });
1331     PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
1332     PIDColour.addActionListener(new java.awt.event.ActionListener()
1333     {
1334       public void actionPerformed(ActionEvent e)
1335       {
1336         PIDColour_actionPerformed();
1337       }
1338     });
1339     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
1340     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1341     {
1342       public void actionPerformed(ActionEvent e)
1343       {
1344         BLOSUM62Colour_actionPerformed();
1345       }
1346     });
1347     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
1348     purinePyrimidineColour
1349             .addActionListener(new java.awt.event.ActionListener()
1350             {
1351               public void actionPerformed(ActionEvent e)
1352               {
1353                 purinePyrimidineColour_actionPerformed();
1354               }
1355             });
1356
1357
1358     /*
1359      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1360      * public void actionPerformed(ActionEvent e) {
1361      * covariationColour_actionPerformed(); } });
1362      */
1363
1364     conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
1365     conservationMenuItem
1366             .addActionListener(new java.awt.event.ActionListener()
1367             {
1368               public void actionPerformed(ActionEvent e)
1369               {
1370                 conservationMenuItem_actionPerformed();
1371               }
1372             });
1373   }
1374
1375   protected void sequenceSelectionDetails_actionPerformed()
1376   {
1377     createSequenceDetailsReport(ap.av.getSequenceSelection());
1378   }
1379
1380   protected void sequenceDetails_actionPerformed()
1381   {
1382     createSequenceDetailsReport(new SequenceI[]
1383     { sequence });
1384   }
1385
1386   public void createSequenceDetailsReport(SequenceI[] sequences)
1387   {
1388     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1389     StringBuffer contents = new StringBuffer();
1390     for (SequenceI seq : sequences)
1391     {
1392       contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
1393               + "</h2></p><p>");
1394       new SequenceAnnotationReport(null)
1395               .createSequenceAnnotationReport(
1396                       contents,
1397                       seq,
1398                       true,
1399                       true,
1400                       false,
1401                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1402                               : null);
1403       contents.append("</p>");
1404     }
1405     cap.setText("<html>" + contents.toString() + "</html>");
1406
1407     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
1408                 ,500, 400);\r
1409
1410   }
1411
1412   protected void showNonconserved_actionPerformed()
1413   {
1414     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1415     refresh();
1416   }
1417
1418   /**
1419    * call to refresh view after settings change
1420    */
1421   void refresh()
1422   {
1423     ap.updateAnnotation();
1424     ap.paintAlignment(true);
1425
1426     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1427   }
1428
1429   /**
1430    * DOCUMENT ME!
1431    *
1432    * @param e
1433    *          DOCUMENT ME!
1434    */
1435   protected void clustalColour_actionPerformed()
1436   {
1437     SequenceGroup sg = getGroup();
1438     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1439     refresh();
1440   }
1441
1442   /**
1443    * DOCUMENT ME!
1444    *
1445    * @param e
1446    *          DOCUMENT ME!
1447    */
1448   protected void zappoColour_actionPerformed()
1449   {
1450     getGroup().cs = new ZappoColourScheme();
1451     refresh();
1452   }
1453
1454   /**
1455    * DOCUMENT ME!
1456    *
1457    * @param e
1458    *          DOCUMENT ME!
1459    */
1460   protected void taylorColour_actionPerformed()
1461   {
1462     getGroup().cs = new TaylorColourScheme();
1463     refresh();
1464   }
1465
1466   /**
1467    * DOCUMENT ME!
1468    *
1469    * @param e
1470    *          DOCUMENT ME!
1471    */
1472   protected void hydrophobicityColour_actionPerformed()
1473   {
1474     getGroup().cs = new HydrophobicColourScheme();
1475     refresh();
1476   }
1477
1478   /**
1479    * DOCUMENT ME!
1480    *
1481    * @param e
1482    *          DOCUMENT ME!
1483    */
1484   protected void helixColour_actionPerformed()
1485   {
1486     getGroup().cs = new HelixColourScheme();
1487     refresh();
1488   }
1489
1490   /**
1491    * DOCUMENT ME!
1492    *
1493    * @param e
1494    *          DOCUMENT ME!
1495    */
1496   protected void strandColour_actionPerformed()
1497   {
1498     getGroup().cs = new StrandColourScheme();
1499     refresh();
1500   }
1501
1502   /**
1503    * DOCUMENT ME!
1504    *
1505    * @param e
1506    *          DOCUMENT ME!
1507    */
1508   protected void turnColour_actionPerformed()
1509   {
1510     getGroup().cs = new TurnColourScheme();
1511     refresh();
1512   }
1513
1514   /**
1515    * DOCUMENT ME!
1516    *
1517    * @param e
1518    *          DOCUMENT ME!
1519    */
1520   protected void buriedColour_actionPerformed()
1521   {
1522     getGroup().cs = new BuriedColourScheme();
1523     refresh();
1524   }
1525
1526   /**
1527    * DOCUMENT ME!
1528    *
1529    * @param e
1530    *          DOCUMENT ME!
1531    */
1532   public void nucleotideMenuItem_actionPerformed()
1533   {
1534     getGroup().cs = new NucleotideColourScheme();
1535     refresh();
1536   }
1537
1538   protected void purinePyrimidineColour_actionPerformed()
1539   {
1540     getGroup().cs = new PurinePyrimidineColourScheme();
1541     refresh();
1542   }
1543
1544
1545   /*
1546    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1547    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1548    */
1549   /**
1550    * DOCUMENT ME!
1551    *
1552    * @param e
1553    *          DOCUMENT ME!
1554    */
1555   protected void abovePIDColour_actionPerformed()
1556   {
1557     SequenceGroup sg = getGroup();
1558     if (sg.cs == null)
1559     {
1560       return;
1561     }
1562
1563     if (abovePIDColour.isSelected())
1564     {
1565       sg.cs.setConsensus(AAFrequency.calculate(
1566               sg.getSequences(ap.av.getHiddenRepSequences()),
1567               sg.getStartRes(), sg.getEndRes() + 1));
1568
1569       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1570               .getName());
1571
1572       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1573
1574       SliderPanel.showPIDSlider();
1575     }
1576     else
1577     // remove PIDColouring
1578     {
1579       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1580     }
1581
1582     refresh();
1583   }
1584
1585   /**
1586    * DOCUMENT ME!
1587    *
1588    * @param e
1589    *          DOCUMENT ME!
1590    */
1591   protected void userDefinedColour_actionPerformed(ActionEvent e)
1592   {
1593     SequenceGroup sg = getGroup();
1594
1595     if (e.getSource().equals(userDefinedColour))\r
1596     {
1597       new UserDefinedColours(ap, sg);
1598     }
1599     else
1600     {
1601       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1602               .getUserColourSchemes().get(e.getActionCommand());
1603
1604       sg.cs = udc;
1605     }
1606     refresh();
1607   }
1608
1609   /**
1610    * DOCUMENT ME!
1611    *
1612    * @param e
1613    *          DOCUMENT ME!
1614    */
1615   protected void PIDColour_actionPerformed()
1616   {
1617     SequenceGroup sg = getGroup();
1618     sg.cs = new PIDColourScheme();
1619     sg.cs.setConsensus(AAFrequency.calculate(
1620             sg.getSequences(ap.av.getHiddenRepSequences()),
1621             sg.getStartRes(), sg.getEndRes() + 1));
1622     refresh();
1623   }
1624
1625   /**
1626    * DOCUMENT ME!
1627    *
1628    * @param e
1629    *          DOCUMENT ME!
1630    */
1631   protected void BLOSUM62Colour_actionPerformed()
1632   {
1633     SequenceGroup sg = getGroup();
1634
1635     sg.cs = new Blosum62ColourScheme();
1636
1637     sg.cs.setConsensus(AAFrequency.calculate(
1638             sg.getSequences(ap.av.getHiddenRepSequences()),
1639             sg.getStartRes(), sg.getEndRes() + 1));
1640
1641     refresh();
1642   }
1643
1644   /**
1645    * DOCUMENT ME!
1646    *
1647    * @param e
1648    *          DOCUMENT ME!
1649    */
1650   protected void noColourmenuItem_actionPerformed()
1651   {
1652     getGroup().cs = null;
1653     refresh();
1654   }
1655
1656   /**
1657    * DOCUMENT ME!
1658    *
1659    * @param e
1660    *          DOCUMENT ME!
1661    */
1662   protected void conservationMenuItem_actionPerformed()
1663   {
1664     SequenceGroup sg = getGroup();
1665     if (sg.cs == null)
1666     {
1667       return;
1668     }
1669
1670     if (conservationMenuItem.isSelected())
1671     {
1672     // JBPNote: Conservation name shouldn't be i18n translated
1673       Conservation c = new Conservation("Group",
1674               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1675                       .getHiddenRepSequences()), sg.getStartRes(),
1676               sg.getEndRes() + 1);
1677
1678       c.calculate();
1679       c.verdict(false, ap.av.getConsPercGaps());
1680
1681       sg.cs.setConservation(c);
1682
1683       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1684       SliderPanel.showConservationSlider();
1685     }
1686     else
1687     // remove ConservationColouring
1688     {
1689       sg.cs.setConservation(null);
1690     }
1691
1692     refresh();
1693   }
1694
1695   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1696   {
1697     SequenceGroup sg = getGroup();
1698     if (sg == null)
1699     {
1700       return;
1701     }
1702
1703     AnnotationColourGradient acg = new AnnotationColourGradient(
1704             sequence.getAnnotation()[0], null,
1705             AnnotationColourGradient.NO_THRESHOLD);
1706
1707     acg.setPredefinedColours(true);
1708     sg.cs = acg;
1709
1710     refresh();
1711   }
1712
1713   /**
1714    * DOCUMENT ME!
1715    *
1716    * @param e
1717    *          DOCUMENT ME!
1718    */
1719   protected void groupName_actionPerformed()
1720   {
1721
1722     SequenceGroup sg = getGroup();
1723     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1724             sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",\r
1725             MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
1726             ap.alignFrame);
1727
1728     if (!dialog.accept)
1729     {
1730       return;
1731     }
1732
1733     sg.setName(dialog.getName());
1734     sg.setDescription(dialog.getDescription());
1735     refresh();
1736   }
1737
1738   /**
1739    * Get selection group - adding it to the alignment if necessary.
1740    *
1741    * @return sequence group to operate on
1742    */
1743   SequenceGroup getGroup()
1744   {
1745     SequenceGroup sg = ap.av.getSelectionGroup();
1746     // this method won't add a new group if it already exists
1747     if (sg != null)
1748     {
1749       ap.av.getAlignment().addGroup(sg);
1750     }
1751
1752     return sg;
1753   }
1754
1755   /**
1756    * DOCUMENT ME!
1757    *
1758    * @param e
1759    *          DOCUMENT ME!
1760    */
1761   void sequenceName_actionPerformed()
1762   {
1763     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1764             sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",\r
1765             MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
1766             ap.alignFrame);
1767
1768     if (!dialog.accept)
1769     {
1770       return;
1771     }
1772
1773     if (dialog.getName() != null)
1774     {
1775       if (dialog.getName().indexOf(" ") > -1)
1776       {
1777         JOptionPane.showMessageDialog(ap,
1778                 MessageManager.getString("label.spaces_converted_to_backslashes"),\r
1779                 MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
1780                 JOptionPane.WARNING_MESSAGE);
1781       }
1782
1783       sequence.setName(dialog.getName().replace(' ', '_'));
1784       ap.paintAlignment(false);
1785     }
1786
1787     sequence.setDescription(dialog.getDescription());
1788
1789     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1790             .getSequences());
1791
1792   }
1793
1794   /**
1795    * DOCUMENT ME!
1796    *
1797    * @param e
1798    *          DOCUMENT ME!
1799    */
1800   void unGroupMenuItem_actionPerformed()
1801   {
1802     SequenceGroup sg = ap.av.getSelectionGroup();
1803     ap.av.getAlignment().deleteGroup(sg);
1804     ap.av.setSelectionGroup(null);
1805     refresh();
1806   }
1807   void createGroupMenuItem_actionPerformed()
1808   {
1809     getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
1810     refresh();
1811   }
1812
1813   /**
1814    * DOCUMENT ME!
1815    *
1816    * @param e
1817    *          DOCUMENT ME!
1818    */
1819   protected void outline_actionPerformed()
1820   {
1821     SequenceGroup sg = getGroup();
1822     Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
1823             Color.BLUE);
1824
1825     if (col != null)
1826     {
1827       sg.setOutlineColour(col);
1828     }
1829
1830     refresh();
1831   }
1832
1833   /**
1834    * DOCUMENT ME!
1835    *
1836    * @param e
1837    *          DOCUMENT ME!
1838    */
1839   public void showBoxes_actionPerformed()
1840   {
1841     getGroup().setDisplayBoxes(showBoxes.isSelected());
1842     refresh();
1843   }
1844
1845   /**
1846    * DOCUMENT ME!
1847    *
1848    * @param e
1849    *          DOCUMENT ME!
1850    */
1851   public void showText_actionPerformed()
1852   {
1853     getGroup().setDisplayText(showText.isSelected());
1854     refresh();
1855   }
1856
1857   /**
1858    * DOCUMENT ME!
1859    *
1860    * @param e
1861    *          DOCUMENT ME!
1862    */
1863   public void showColourText_actionPerformed()
1864   {
1865     getGroup().setColourText(showColourText.isSelected());
1866     refresh();
1867   }
1868
1869   public void showLink(String url)
1870   {
1871     try
1872     {
1873       jalview.util.BrowserLauncher.openURL(url);
1874     } catch (Exception ex)
1875     {
1876       JOptionPane
1877               .showInternalMessageDialog(
1878                       Desktop.desktop,
1879                       MessageManager.getString("label.web_browser_not_found_unix"),\r
1880                       MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
1881
1882       ex.printStackTrace();
1883     }
1884   }
1885
1886   void hideSequences(boolean representGroup)
1887   {
1888     SequenceGroup sg = ap.av.getSelectionGroup();
1889     if (sg == null || sg.getSize() < 1)
1890     {
1891       ap.av.hideSequence(new SequenceI[]
1892       { sequence });
1893       return;
1894     }
1895
1896     ap.av.setSelectionGroup(null);
1897
1898     if (representGroup)
1899     {
1900       ap.av.hideRepSequences(sequence, sg);
1901
1902       return;
1903     }
1904
1905     int gsize = sg.getSize();
1906     SequenceI[] hseqs;
1907
1908     hseqs = new SequenceI[gsize];
1909
1910     int index = 0;
1911     for (int i = 0; i < gsize; i++)
1912     {
1913       hseqs[index++] = sg.getSequenceAt(i);
1914     }
1915
1916     ap.av.hideSequence(hseqs);
1917     // refresh(); TODO: ? needed ?
1918     ap.av.sendSelection();
1919   }
1920
1921   public void copy_actionPerformed()
1922   {
1923     ap.alignFrame.copy_actionPerformed(null);
1924   }
1925
1926   public void cut_actionPerformed()
1927   {
1928     ap.alignFrame.cut_actionPerformed(null);
1929   }
1930
1931   void changeCase(ActionEvent e)
1932   {
1933     Object source = e.getSource();
1934     SequenceGroup sg = ap.av.getSelectionGroup();
1935
1936     if (sg != null)
1937     {
1938       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1939               sg.getEndRes() + 1);
1940
1941       String description;
1942       int caseChange;
1943
1944       if (source == toggle)
1945       {
1946         description = MessageManager.getString("label.toggle_case");\r
1947         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1948       }
1949       else if (source == upperCase)
1950       {
1951         description = MessageManager.getString("label.to_upper_case");\r
1952         caseChange = ChangeCaseCommand.TO_UPPER;
1953       }
1954       else
1955       {
1956         description = MessageManager.getString("label.to_lower_case");\r
1957         caseChange = ChangeCaseCommand.TO_LOWER;
1958       }
1959
1960       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1961               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1962               startEnd, caseChange);
1963
1964       ap.alignFrame.addHistoryItem(caseCommand);
1965
1966       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1967               .getSequences());
1968
1969     }
1970   }
1971
1972   public void outputText_actionPerformed(ActionEvent e)
1973   {
1974     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1975     cap.setForInput(null);
1976     Desktop.addInternalFrame(cap,
1977             MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
1978
1979     String[] omitHidden = null;
1980
1981     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1982     // or we simply trust the user wants
1983     // wysiwig behaviour
1984     SequenceGroup sg = ap.av.getSelectionGroup();
1985     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1986     omitHidden = ap.av.getViewAsString(true);
1987     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1988     AlignmentAnnotation[] nala = ap.av.getAlignment()
1989             .getAlignmentAnnotation();
1990     if (nala != null)
1991     {
1992       for (int i = 0; i < nala.length; i++)
1993       {
1994         AlignmentAnnotation na = nala[i];
1995         oal.addAnnotation(na);
1996       }
1997     }
1998     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1999             oal, omitHidden, csel, sg));
2000     oal = null;
2001   }
2002
2003   public void pdbFromFile_actionPerformed()
2004   {
2005     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2006             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2007     chooser.setFileView(new jalview.io.JalviewFileView());
2008     chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
2009     chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
2010
2011     int value = chooser.showOpenDialog(null);
2012
2013     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2014     {
2015       String choice = chooser.getSelectedFile().getPath();
2016       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2017       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2018               jalview.io.AppletFormatAdapter.FILE, sequence, true);
2019     }
2020
2021   }
2022     // JBNote: commented out - these won't be instantiated here...!
2023 //  public void RNAFold_actionPerformed() throws Exception
2024 //  {
2025 //        Predict2D P2D = new Predict2D();
2026 //        P2D.getStructure2DFromRNAFold("toto");
2027 //  }
2028 //
2029 //  public void ContraFold_actionPerformed() throws Exception
2030 //  {
2031 //        Predict2D P2D = new Predict2D();
2032 //        P2D.getStructure2DFromContraFold("toto");
2033 //  }
2034   public void enterPDB_actionPerformed()
2035   {
2036     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2037             MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
2038
2039     if (id != null && id.length() > 0)
2040     {
2041       PDBEntry entry = new PDBEntry();
2042       entry.setId(id.toUpperCase());
2043       sequence.getDatasetSequence().addPDBId(entry);
2044     }
2045   }
2046
2047   public void discoverPDB_actionPerformed()
2048   {
2049
2050     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2051     { sequence }
2052             : ap.av.getSequenceSelection());
2053     Thread discpdb = new Thread(new Runnable()
2054     {
2055       public void run()
2056       {
2057
2058         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2059                 .fetchDBRefs(false);
2060       }
2061
2062     });
2063     discpdb.start();
2064   }
2065
2066   public void sequenceFeature_actionPerformed()
2067   {
2068     SequenceGroup sg = ap.av.getSelectionGroup();
2069     if (sg == null)
2070     {
2071       return;
2072     }
2073
2074     int rsize = 0, gSize = sg.getSize();
2075     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2076     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2077
2078     for (int i = 0; i < gSize; i++)
2079     {
2080       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2081       int end = sg.findEndRes(sg.getSequenceAt(i));
2082       if (start <= end)
2083       {
2084         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2085         features[rsize] = new SequenceFeature(null, null, null, start, end,
2086                 "Jalview");
2087         rsize++;
2088       }
2089     }
2090     rseqs = new SequenceI[rsize];
2091     tfeatures = new SequenceFeature[rsize];
2092     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2093     System.arraycopy(features, 0, tfeatures, 0, rsize);
2094     features = tfeatures;
2095     seqs = rseqs;
2096     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2097             features, true, ap))
2098     {
2099       ap.alignFrame.setShowSeqFeatures(true);
2100       ap.highlightSearchResults(null);
2101     }
2102   }
2103
2104   public void textColour_actionPerformed()
2105   {
2106     SequenceGroup sg = getGroup();
2107     if (sg != null)
2108     {
2109       new TextColourChooser().chooseColour(ap, sg);
2110     }
2111   }
2112
2113   public void colourByStructure(String pdbid)
2114   {
2115     Annotation[] anots = ap.av.getStructureSelectionManager()
2116             .colourSequenceFromStructure(sequence, pdbid);
2117
2118     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2119             "Coloured by " + pdbid, anots);
2120
2121     ap.av.getAlignment().addAnnotation(an);
2122     an.createSequenceMapping(sequence, 0, true);
2123     // an.adjustForAlignment();
2124     ap.av.getAlignment().setAnnotationIndex(an, 0);
2125
2126     ap.adjustAnnotationHeight();
2127
2128     sequence.addAlignmentAnnotation(an);
2129
2130   }
2131
2132   public void editSequence_actionPerformed(ActionEvent actionEvent)
2133   {
2134     SequenceGroup sg = ap.av.getSelectionGroup();
2135
2136     if (sg != null)
2137     {
2138       if (sequence == null)
2139         sequence = (Sequence) sg.getSequenceAt(0);
2140
2141       EditNameDialog dialog = new EditNameDialog(
2142               sequence.getSequenceAsString(sg.getStartRes(),
2143                       sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
2144                       MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
2145
2146       if (dialog.accept)
2147       {
2148         EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
2149                 EditCommand.REPLACE, dialog.getName().replace(' ',
2150                         ap.av.getGapCharacter()),
2151                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2152                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2153
2154         ap.alignFrame.addHistoryItem(editCommand);
2155
2156         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2157                 .getSequences());
2158       }
2159     }
2160   }
2161
2162 }