src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27
  28 import javax.swing.*;
  29
  30 import jalview.analysis.*;
  31 import jalview.commands.*;
  32 import jalview.datamodel.*;
  33 import jalview.io.*;
  34 import jalview.schemes.*;
  35 import jalview.util.GroupUrlLink;
  36 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  37 import jalview.util.MessageManager;
  38 import jalview.util.UrlLink;
  39
  40 /**
  41  * DOCUMENT ME!
  42  *
  43  * @author $author$
  44  * @version $Revision: 1.118 $
  45  */
  46 public class PopupMenu extends JPopupMenu
  47 {
  48   JMenu groupMenu = new JMenu();
  49
  50   JMenuItem groupName = new JMenuItem();
  51
  52   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  65
  66   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  67
  68   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  69
  70   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  71
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  73
  74   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  75
  76   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  77   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  78
  79   // protected JRadioButtonMenuItem covariationColour = new
  80   // JRadioButtonMenuItem();
  81
  82   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  83
  84   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  85
  86   AlignmentPanel ap;
  87
  88   JMenu sequenceMenu = new JMenu();
  89
  90   JMenuItem sequenceName = new JMenuItem();
  91
  92   JMenuItem sequenceDetails = new JMenuItem();
  93
  94   JMenuItem sequenceSelDetails = new JMenuItem();
  95
  96   SequenceI sequence;
  97   JMenuItem createGroupMenuItem = new JMenuItem();
  98   JMenuItem unGroupMenuItem = new JMenuItem();
  99
 100   JMenuItem outline = new JMenuItem();
 101
 102   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 103
 104   JMenu colourMenu = new JMenu();
 105
 106   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 107
 108   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 109
 110   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 111
 112   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 113
 114   JMenu editMenu = new JMenu();
 115
 116   JMenuItem cut = new JMenuItem();
 117
 118   JMenuItem copy = new JMenuItem();
 119
 120   JMenuItem upperCase = new JMenuItem();
 121
 122   JMenuItem lowerCase = new JMenuItem();
 123
 124   JMenuItem toggle = new JMenuItem();
 125
 126   JMenu pdbMenu = new JMenu();
 127
 128   JMenuItem pdbFromFile = new JMenuItem();
 129     // JBPNote: Commented these out - Should add these services via the web services menu system.
 130     // JMenuItem ContraFold = new JMenuItem();
 131
 132     // JMenuItem RNAFold = new JMenuItem();
 133
 134   JMenuItem enterPDB = new JMenuItem();
 135
 136   JMenuItem discoverPDB = new JMenuItem();
 137
 138   JMenu outputMenu = new JMenu();
 139
 140   JMenuItem sequenceFeature = new JMenuItem();
 141
 142   JMenuItem textColour = new JMenuItem();
 143
 144   JMenu jMenu1 = new JMenu();
 145
 146   JMenu structureMenu = new JMenu();
 147
 148   JMenu viewStructureMenu = new JMenu();
 149
 150   // JMenu colStructureMenu = new JMenu();
 151   JMenuItem editSequence = new JMenuItem();
 152
 153   // JMenuItem annotationMenuItem = new JMenuItem();
 154
 155   JMenu groupLinksMenu;
 156
 157   /**
 158    * Creates a new PopupMenu object.
 159    *
 160    * @param ap
 161    *          DOCUMENT ME!
 162    * @param seq
 163    *          DOCUMENT ME!
 164    */
 165   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 166   {
 167     this(ap, seq, links, null);
 168   }
 169
 170   /**
 171    *
 172    * @param ap
 173    * @param seq
 174    * @param links
 175    * @param groupLinks
 176    */
 177   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 178           Vector links, Vector groupLinks)
 179   {
 180     // /////////////////////////////////////////////////////////
 181     // If this is activated from the sequence panel, the user may want to
 182     // edit or annotate a particular residue. Therefore display the residue menu
 183     //
 184     // If from the IDPanel, we must display the sequence menu
 185     // ////////////////////////////////////////////////////////
 186     this.ap = ap;
 187     sequence = seq;
 188
 189     ButtonGroup colours = new ButtonGroup();
 190     colours.add(noColourmenuItem);
 191     colours.add(clustalColour);
 192     colours.add(zappoColour);
 193     colours.add(taylorColour);
 194     colours.add(hydrophobicityColour);
 195     colours.add(helixColour);
 196     colours.add(strandColour);
 197     colours.add(turnColour);
 198     colours.add(buriedColour);
 199     colours.add(abovePIDColour);
 200     colours.add(userDefinedColour);
 201     colours.add(PIDColour);
 202     colours.add(BLOSUM62Colour);
 203     colours.add(purinePyrimidineColour);
 204     colours.add(RNAInteractionColour);
 205     // colours.add(covariationColour);
 206
 207     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 208     {
 209       JMenuItem item = new JMenuItem(
 210               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 211
 212       item.addActionListener(new java.awt.event.ActionListener()
 213       {
 214         public void actionPerformed(ActionEvent e)
 215         {
 216           outputText_actionPerformed(e);
 217         }
 218       });
 219
 220       outputMenu.add(item);
 221     }
 222
 223     try
 224     {
 225       jbInit();
 226     } catch (Exception e)
 227     {
 228       e.printStackTrace();
 229     }
 230
 231     JMenuItem menuItem;
 232     if (seq != null)
 233     {
 234       sequenceMenu.setText(sequence.getName());
 235
 236       if (seq.getDatasetSequence().getPDBId() != null
 237               && seq.getDatasetSequence().getPDBId().size() > 0)
 238       {
 239         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 240                 .elements();
 241
 242         while (e.hasMoreElements())
 243         {
 244           final PDBEntry pdb = (PDBEntry) e.nextElement();
 245
 246           menuItem = new JMenuItem();
 247           menuItem.setText(pdb.getId());
 248           menuItem.addActionListener(new java.awt.event.ActionListener()
 249           {
 250             public void actionPerformed(ActionEvent e)
 251             {
 252               // TODO re JAL-860: optionally open dialog or provide a menu entry
 253               // allowing user to open just one structure per sequence
 254               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 255               { pdb })[0], null, ap);
 256               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 257             }
 258
 259           });
 260           viewStructureMenu.add(menuItem);
 261
 262           /*
 263            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 264            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 265            * public void actionPerformed(ActionEvent e) {
 266            * colourByStructure(pdb.getId()); } });
 267            * colStructureMenu.add(menuItem);
 268            */
 269         }
 270       }
 271       else
 272       {
 273         if (ap.av.getAlignment().isNucleotide() == false)
 274         {
 275           structureMenu.remove(viewStructureMenu);
 276         }
 277         // structureMenu.remove(colStructureMenu);
 278       }
 279
 280       if (ap.av.getAlignment().isNucleotide() == true)
 281       {
 282         AlignmentAnnotation[] aa = ap.av.getAlignment()
 283                 .getAlignmentAnnotation();
 284         for (int i = 0; i < aa.length; i++)
 285         {
 286           if (aa[i].getRNAStruc() != null)
 287           {
 288             final String rnastruc = aa[i].getRNAStruc();
 289             final String structureLine = aa[i].label;
 290             menuItem = new JMenuItem();
 291             menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
 292             menuItem.addActionListener(new java.awt.event.ActionListener()
 293
 294             {
 295               public void actionPerformed(ActionEvent e)
 296               {
 297                         //System.out.println("1:"+structureLine);
 298                         System.out.println("1:sname"+seq.getName());
 299                         System.out.println("2:seq"+seq);
 300
 301                         //System.out.println("3:"+seq.getSequenceAsString());
 302                         System.out.println("3:strucseq"+rnastruc);
 303                         //System.out.println("4:struc"+seq.getRNA());
 304                         System.out.println("5:name"+seq.getName());
 305                         System.out.println("6:ap"+ap);
 306                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 307                             .getName(), ap);
 308                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 309                         System.out.println("end");
 310               }
 311             });
 312             viewStructureMenu.add(menuItem);
 313           }
 314         }
 315
 316         // SequenceFeatures[] test = seq.getSequenceFeatures();
 317
 318         if (seq.getAnnotation() != null)
 319         {
 320           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 321           for (int i = 0; i < seqAnno.length; i++)
 322           {
 323             if (seqAnno[i].getRNAStruc() != null)
 324             {
 325               final String rnastruc = seqAnno[i].getRNAStruc();
 326
 327               // TODO: make rnastrucF a bit more nice
 328               menuItem = new JMenuItem();
 329               menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
 330               menuItem.addActionListener(new java.awt.event.ActionListener()
 331               {
 332                 public void actionPerformed(ActionEvent e)
 333                 {
 334                   // TODO: VARNA does'nt print gaps in the sequence
 335
 336                   new AppVarna(seq.getName() + " structure", seq, seq
 337                           .getSequenceAsString(), rnastruc, seq.getName(),
 338                           ap);
 339                 }
 340               });
 341               viewStructureMenu.add(menuItem);
 342             }
 343           }
 344         }
 345
 346       }
 347
 348       menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
 349       menuItem.addActionListener(new java.awt.event.ActionListener()
 350       {
 351         public void actionPerformed(ActionEvent e)
 352         {
 353           hideSequences(false);
 354         }
 355       });
 356       add(menuItem);
 357
 358       if (ap.av.getSelectionGroup() != null
 359               && ap.av.getSelectionGroup().getSize() > 1)
 360       {
 361         menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
 362         menuItem.addActionListener(new java.awt.event.ActionListener()
 363         {
 364           public void actionPerformed(ActionEvent e)
 365           {
 366             hideSequences(true);
 367           }
 368         });
 369         sequenceMenu.add(menuItem);
 370       }
 371
 372       if (ap.av.hasHiddenRows())
 373       {
 374         final int index = ap.av.getAlignment().findIndex(seq);
 375
 376         if (ap.av.adjustForHiddenSeqs(index)
 377                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 378         {
 379           menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
 380           menuItem.addActionListener(new ActionListener()
 381           {
 382             public void actionPerformed(ActionEvent e)
 383             {
 384               ap.av.showSequence(index);
 385               if (ap.overviewPanel != null)
 386               {
 387                 ap.overviewPanel.updateOverviewImage();
 388               }
 389             }
 390           });
 391           add(menuItem);
 392         }
 393       }
 394     }
 395     // for the case when no sequences are even visible
 396     if (ap.av.hasHiddenRows())
 397     {
 398       {
 399         menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
 400         menuItem.addActionListener(new ActionListener()
 401         {
 402           public void actionPerformed(ActionEvent e)
 403           {
 404             ap.av.showAllHiddenSeqs();
 405             if (ap.overviewPanel != null)
 406             {
 407               ap.overviewPanel.updateOverviewImage();
 408             }
 409           }
 410         });
 411
 412         add(menuItem);
 413       }
 414
 415     }
 416
 417     SequenceGroup sg = ap.av.getSelectionGroup();
 418     boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
 419
 420     if (sg != null && sg.getSize() > 0)
 421     {
 422       groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
 423       groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
 424
 425       if (sg.cs instanceof ZappoColourScheme)
 426       {
 427         zappoColour.setSelected(true);
 428       }
 429       else if (sg.cs instanceof TaylorColourScheme)
 430       {
 431         taylorColour.setSelected(true);
 432       }
 433       else if (sg.cs instanceof PIDColourScheme)
 434       {
 435         PIDColour.setSelected(true);
 436       }
 437       else if (sg.cs instanceof Blosum62ColourScheme)
 438       {
 439         BLOSUM62Colour.setSelected(true);
 440       }
 441       else if (sg.cs instanceof UserColourScheme)
 442       {
 443         userDefinedColour.setSelected(true);
 444       }
 445       else if (sg.cs instanceof HydrophobicColourScheme)
 446       {
 447         hydrophobicityColour.setSelected(true);
 448       }
 449       else if (sg.cs instanceof HelixColourScheme)
 450       {
 451         helixColour.setSelected(true);
 452       }
 453       else if (sg.cs instanceof StrandColourScheme)
 454       {
 455         strandColour.setSelected(true);
 456       }
 457       else if (sg.cs instanceof TurnColourScheme)
 458       {
 459         turnColour.setSelected(true);
 460       }
 461       else if (sg.cs instanceof BuriedColourScheme)
 462       {
 463         buriedColour.setSelected(true);
 464       }
 465       else if (sg.cs instanceof ClustalxColourScheme)
 466       {
 467         clustalColour.setSelected(true);
 468       }
 469       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 470       {
 471         purinePyrimidineColour.setSelected(true);
 472       }
 473
 474
 475       /*
 476        * else if (sg.cs instanceof CovariationColourScheme) {
 477        * covariationColour.setSelected(true); }
 478        */
 479       else
 480       {
 481         noColourmenuItem.setSelected(true);
 482       }
 483
 484       if (sg.cs != null && sg.cs.conservationApplied())
 485       {
 486         conservationMenuItem.setSelected(true);
 487       }
 488       displayNonconserved.setSelected(sg.getShowNonconserved());
 489       showText.setSelected(sg.getDisplayText());
 490       showColourText.setSelected(sg.getColourText());
 491       showBoxes.setSelected(sg.getDisplayBoxes());
 492       // add any groupURLs to the groupURL submenu and make it visible
 493       if (groupLinks != null && groupLinks.size() > 0)
 494       {
 495         buildGroupURLMenu(sg, groupLinks);
 496       }
 497       // Add a 'show all structures' for the current selection
 498       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),reppdb=new Hashtable<String,PDBEntry>();
 499       SequenceI sqass = null;
 500       for (SequenceI sq : ap.av.getSequenceSelection())
 501       {
 502         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 503                 .getPDBId();
 504         if (pes != null)
 505         {
 506           reppdb.put(pes.get(0).getId(),pes.get(0));
 507           for (PDBEntry pe : pes)
 508           {
 509             pdbe.put(pe.getId(), pe);
 510             if (sqass == null)
 511             {
 512               sqass = sq;
 513             }
 514           }
 515         }
 516       }
 517       if (pdbe.size() > 0)
 518       {
 519         final PDBEntry[] pe = pdbe.values().toArray(
 520                 new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
 521                         new PDBEntry[reppdb.size()]);
 522         final JMenuItem gpdbview,rpdbview;
 523         if (pdbe.size() == 1)
 524         {
 525           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
 526         }
 527         else
 528         {
 529           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
 530         }
 531         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
 532         gpdbview.addActionListener(new ActionListener()
 533         {
 534
 535           @Override
 536           public void actionPerformed(ActionEvent e)
 537           {
 538             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 539           }
 540         });
 541         if (reppdb.size()>1 && reppdb.size()<pdbe.size())
 542         {
 543           structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
 544           rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
 545           rpdbview.addActionListener(new ActionListener()
 546           {
 547
 548             @Override
 549             public void actionPerformed(ActionEvent e)
 550             {
 551               new AppJmol(ap, pr, ap.av.collateForPDB(pr));
 552             }
 553           });
 554         }
 555       }
 556     }
 557     else
 558     {
 559       groupMenu.setVisible(false);
 560       editMenu.setVisible(false);
 561     }
 562
 563     if (!isDefinedGroup)
 564     {
 565       createGroupMenuItem.setVisible(true);
 566       unGroupMenuItem.setVisible(false);
 567       jMenu1.setText(MessageManager.getString("action.edit_new_group"));
 568     } else {
 569       createGroupMenuItem.setVisible(false);
 570       unGroupMenuItem.setVisible(true);
 571       jMenu1.setText(MessageManager.getString("action.edit_group"));
 572     }
 573
 574     if (seq == null)
 575     {
 576       sequenceMenu.setVisible(false);
 577       structureMenu.setVisible(false);
 578     }
 579
 580     if (links != null && links.size() > 0)
 581     {
 582
 583       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
 584       Vector linkset = new Vector();
 585       for (int i = 0; i < links.size(); i++)
 586       {
 587         String link = links.elementAt(i).toString();
 588         UrlLink urlLink = null;
 589         try
 590         {
 591           urlLink = new UrlLink(link);
 592         } catch (Exception foo)
 593         {
 594           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 595                   + "'", foo);
 596           continue;
 597         }
 598         ;
 599         if (!urlLink.isValid())
 600         {
 601           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 602           continue;
 603         }
 604         final String label = urlLink.getLabel();
 605         if (seq != null && urlLink.isDynamic())
 606         {
 607
 608           // collect matching db-refs
 609           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 610                   seq.getDBRef(), new String[]
 611                   { urlLink.getTarget() });
 612           // collect id string too
 613           String id = seq.getName();
 614           String descr = seq.getDescription();
 615           if (descr != null && descr.length() < 1)
 616           {
 617             descr = null;
 618           }
 619
 620           if (dbr != null)
 621           {
 622             for (int r = 0; r < dbr.length; r++)
 623             {
 624               if (id != null && dbr[r].getAccessionId().equals(id))
 625               {
 626                 // suppress duplicate link creation for the bare sequence ID
 627                 // string with this link
 628                 id = null;
 629               }
 630               // create Bare ID link for this RUL
 631               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 632                       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],
 641                             urls[u + 1]);
 642                   }
 643                 }
 644               }
 645             }
 646           }
 647           if (id != null)
 648           {
 649             // create Bare ID link for this RUL
 650             String[] urls = urlLink.makeUrls(id, 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           // Create urls from description but only for URL links which are regex
 664           // links
 665           if (descr != null && urlLink.getRegexReplace() != null)
 666           {
 667             // create link for this URL from description where regex matches
 668             String[] urls = urlLink.makeUrls(descr, true);
 669             if (urls != null)
 670             {
 671               for (int u = 0; u < urls.length; u += 2)
 672               {
 673                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 674                 {
 675                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 676                   addshowLink(linkMenu, label, urls[u + 1]);
 677                 }
 678               }
 679             }
 680           }
 681         }
 682         else
 683         {
 684           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 685           {
 686             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 687             // Add a non-dynamic link
 688             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 689           }
 690         }
 691       }
 692       if (sequence != null)
 693       {
 694         sequenceMenu.add(linkMenu);
 695       }
 696       else
 697       {
 698         add(linkMenu);
 699       }
 700     }
 701   }
 702
 703   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 704   {
 705
 706     // TODO: usability: thread off the generation of group url content so root
 707     // menu appears asap
 708     // sequence only URLs
 709     // ID/regex match URLs
 710     groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
 711     JMenu[] linkMenus = new JMenu[]
 712     { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
 713         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
 714                                           // created.
 715     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 716     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 717     Hashtable commonDbrefs = new Hashtable();
 718     for (int sq = 0; sq < seqs.length; sq++)
 719     {
 720
 721       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 722               .findPosition(sg.getEndRes());
 723       // just collect ids from dataset sequence
 724       // TODO: check if IDs collected from selecton group intersects with the
 725       // current selection, too
 726       SequenceI sqi = seqs[sq];
 727       while (sqi.getDatasetSequence() != null)
 728       {
 729         sqi = sqi.getDatasetSequence();
 730       }
 731       DBRefEntry[] dbr = sqi.getDBRef();
 732       if (dbr != null && dbr.length > 0)
 733       {
 734         for (int d = 0; d < dbr.length; d++)
 735         {
 736           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 737           Object[] sarray = (Object[]) commonDbrefs.get(src);
 738           if (sarray == null)
 739           {
 740             sarray = new Object[2];
 741             sarray[0] = new int[]
 742             { 0 };
 743             sarray[1] = new String[seqs.length];
 744
 745             commonDbrefs.put(src, sarray);
 746           }
 747
 748           if (((String[]) sarray[1])[sq] == null)
 749           {
 750             if (!dbr[d].hasMap()
 751                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 752             {
 753               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 754               ((int[]) sarray[0])[0]++;
 755             }
 756           }
 757         }
 758       }
 759     }
 760     // now create group links for all distinct ID/sequence sets.
 761     boolean addMenu = false; // indicates if there are any group links to give
 762                              // to user
 763     for (int i = 0; i < groupLinks.size(); i++)
 764     {
 765       String link = groupLinks.elementAt(i).toString();
 766       GroupUrlLink urlLink = null;
 767       try
 768       {
 769         urlLink = new GroupUrlLink(link);
 770       } catch (Exception foo)
 771       {
 772         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 773                 + "'", foo);
 774         continue;
 775       }
 776       ;
 777       if (!urlLink.isValid())
 778       {
 779         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 780         continue;
 781       }
 782       final String label = urlLink.getLabel();
 783       boolean usingNames = false;
 784       // Now see which parts of the group apply for this URL
 785       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 786       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 787       String[] seqstr, ids; // input to makeUrl
 788       if (idset != null)
 789       {
 790         int numinput = ((int[]) idset[0])[0];
 791         String[] allids = ((String[]) idset[1]);
 792         seqstr = new String[numinput];
 793         ids = new String[numinput];
 794         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 795         {
 796           if (allids[sq] != null)
 797           {
 798             ids[idcount] = allids[sq];
 799             seqstr[idcount++] = idandseqs[1][sq];
 800           }
 801         }
 802       }
 803       else
 804       {
 805         // just use the id/seq set
 806         seqstr = idandseqs[1];
 807         ids = idandseqs[0];
 808         usingNames = true;
 809       }
 810       // and try and make the groupURL!
 811
 812       Object[] urlset = null;
 813       try
 814       {
 815         urlset = urlLink.makeUrlStubs(ids, seqstr,
 816                 "FromJalview" + System.currentTimeMillis(), false);
 817       } catch (UrlStringTooLongException e)
 818       {
 819       }
 820       if (urlset != null)
 821       {
 822         int type = urlLink.getGroupURLType() & 3;
 823         // System.out.println(urlLink.getGroupURLType()
 824         // +" "+((String[])urlset[3])[0]);
 825         // first two bits ofurlLink type bitfield are sequenceids and sequences
 826         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 827         addshowLink(linkMenus[type], label
 828                 + (((type & 1) == 1) ? ("("
 829                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 830                 urlLink, urlset);
 831         addMenu = true;
 832       }
 833     }
 834     if (addMenu)
 835     {
 836       groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
 837       for (int m = 0; m < linkMenus.length; m++)
 838       {
 839         if (linkMenus[m] != null
 840                 && linkMenus[m].getMenuComponentCount() > 0)
 841         {
 842           groupLinksMenu.add(linkMenus[m]);
 843         }
 844       }
 845
 846       groupMenu.add(groupLinksMenu);
 847     }
 848   }
 849
 850   /**
 851    * add a show URL menu item to the given linkMenu
 852    *
 853    * @param linkMenu
 854    * @param label
 855    *          - menu label string
 856    * @param url
 857    *          - url to open
 858    */
 859   private void addshowLink(JMenu linkMenu, String label, final String url)
 860   {
 861     JMenuItem item = new JMenuItem(label);
 862     item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
 863     item.addActionListener(new java.awt.event.ActionListener()
 864     {
 865       public void actionPerformed(ActionEvent e)
 866       {
 867         new Thread(new Runnable()
 868         {
 869
 870           public void run()
 871           {
 872             showLink(url);
 873           }
 874
 875         }).start();
 876       }
 877     });
 878
 879     linkMenu.add(item);
 880   }
 881
 882   /**
 883    * add a late bound groupURL item to the given linkMenu
 884    *
 885    * @param linkMenu
 886    * @param label
 887    *          - menu label string
 888    * @param urlgenerator
 889    *          GroupURLLink used to generate URL
 890    * @param urlstub
 891    *          Object array returned from the makeUrlStubs function.
 892    */
 893   private void addshowLink(JMenu linkMenu, String label,
 894           final GroupUrlLink urlgenerator, final Object[] urlstub)
 895   {
 896     JMenuItem item = new JMenuItem(label);
 897     item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
 898     // TODO: put in info about what is being sent.
 899     item.addActionListener(new java.awt.event.ActionListener()
 900     {
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         new Thread(new Runnable()
 904         {
 905
 906           public void run()
 907           {
 908             try
 909             {
 910               showLink(urlgenerator.constructFrom(urlstub));
 911             } catch (UrlStringTooLongException e)
 912             {
 913             }
 914           }
 915
 916         }).start();
 917       }
 918     });
 919
 920     linkMenu.add(item);
 921   }
 922
 923   /**
 924    * DOCUMENT ME!
 925    *
 926    * @throws Exception
 927    *           DOCUMENT ME!
 928    */
 929   private void jbInit() throws Exception
 930   {
 931     groupMenu.setText(MessageManager.getString("label.group"));
 932     groupMenu.setText(MessageManager.getString("label.selection"));
 933     groupName.setText(MessageManager.getString("label.name"));
 934     groupName.addActionListener(new java.awt.event.ActionListener()
 935     {
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         groupName_actionPerformed();
 939       }
 940     });
 941     sequenceMenu.setText(MessageManager.getString("label.sequence"));
 942     sequenceName.setText(MessageManager.getString("label.edit_name_description"));
 943     sequenceName.addActionListener(new java.awt.event.ActionListener()
 944     {
 945       public void actionPerformed(ActionEvent e)
 946       {
 947         sequenceName_actionPerformed();
 948       }
 949     });
 950     sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
 951     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 952     {
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         sequenceDetails_actionPerformed();
 956       }
 957     });
 958     sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
 959     sequenceSelDetails
 960             .addActionListener(new java.awt.event.ActionListener()
 961             {
 962               public void actionPerformed(ActionEvent e)
 963               {
 964                 sequenceSelectionDetails_actionPerformed();
 965               }
 966             });
 967     PIDColour.setFocusPainted(false);
 968     unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
 969     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 970     {
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         unGroupMenuItem_actionPerformed();
 974       }
 975     });
 976     createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
 977     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 978     {
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         createGroupMenuItem_actionPerformed();
 982       }
 983     });
 984
 985     outline.setText(MessageManager.getString("action.border_colour"));
 986     outline.addActionListener(new java.awt.event.ActionListener()
 987     {
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         outline_actionPerformed();
 991       }
 992     });
 993     nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
 994     nucleotideMenuItem.addActionListener(new ActionListener()
 995     {
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         nucleotideMenuItem_actionPerformed();
 999       }
1000     });
1001     colourMenu.setText(MessageManager.getString("label.group_colour"));
1002     showBoxes.setText(MessageManager.getString("action.boxes"));
1003     showBoxes.setState(true);
1004     showBoxes.addActionListener(new ActionListener()
1005     {
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         showBoxes_actionPerformed();
1009       }
1010     });
1011     showText.setText(MessageManager.getString("action.text"));
1012     showText.setState(true);
1013     showText.addActionListener(new ActionListener()
1014     {
1015       public void actionPerformed(ActionEvent e)
1016       {
1017         showText_actionPerformed();
1018       }
1019     });
1020     showColourText.setText(MessageManager.getString("label.colour_text"));
1021     showColourText.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         showColourText_actionPerformed();
1026       }
1027     });
1028     displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
1029     displayNonconserved.setState(true);
1030     displayNonconserved.addActionListener(new ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         showNonconserved_actionPerformed();
1035       }
1036     });
1037     editMenu.setText(MessageManager.getString("action.edit"));
1038     cut.setText(MessageManager.getString("action.cut"));
1039     cut.addActionListener(new ActionListener()
1040     {
1041       public void actionPerformed(ActionEvent e)
1042       {
1043         cut_actionPerformed();
1044       }
1045     });
1046     upperCase.setText(MessageManager.getString("label.to_upper_case"));
1047     upperCase.addActionListener(new ActionListener()
1048     {
1049       public void actionPerformed(ActionEvent e)
1050       {
1051         changeCase(e);
1052       }
1053     });
1054     copy.setText(MessageManager.getString("action.copy"));
1055     copy.addActionListener(new ActionListener()
1056     {
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         copy_actionPerformed();
1060       }
1061     });
1062     lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1063     lowerCase.addActionListener(new ActionListener()
1064     {
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         changeCase(e);
1068       }
1069     });
1070     toggle.setText(MessageManager.getString("label.toggle_case"));
1071     toggle.addActionListener(new ActionListener()
1072     {
1073       public void actionPerformed(ActionEvent e)
1074       {
1075         changeCase(e);
1076       }
1077     });
1078     pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
1079     pdbFromFile.setText(MessageManager.getString("label.from_file"));
1080     pdbFromFile.addActionListener(new ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         pdbFromFile_actionPerformed();
1085       }
1086     });
1087 //    RNAFold.setText("From RNA Fold with predict2D");
1088 //    RNAFold.addActionListener(new ActionListener()
1089 //    {
1090 //      public void actionPerformed(ActionEvent e)
1091 //      {
1092 //        try {
1093 //                      RNAFold_actionPerformed();
1094 //              } catch (Exception e1) {
1095 //                      // TODO Auto-generated catch block
1096 //                      e1.printStackTrace();
1097 //              }
1098 //      }
1099 //    });
1100 //    ContraFold.setText("From Contra Fold with predict2D");
1101 //    ContraFold.addActionListener(new ActionListener()
1102 //    {
1103 //      public void actionPerformed(ActionEvent e)
1104 //      {
1105 //        try {
1106 //                      ContraFold_actionPerformed();
1107 //              } catch (Exception e1) {
1108 //                      // TODO Auto-generated catch block
1109 //                      e1.printStackTrace();
1110 //              }
1111 //      }
1112 //    });
1113     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1114     enterPDB.addActionListener(new ActionListener()
1115     {
1116       public void actionPerformed(ActionEvent e)
1117       {
1118         enterPDB_actionPerformed();
1119       }
1120     });
1121     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1122     discoverPDB.addActionListener(new ActionListener()
1123     {
1124       public void actionPerformed(ActionEvent e)
1125       {
1126         discoverPDB_actionPerformed();
1127       }
1128     });
1129     outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
1130     sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
1131     sequenceFeature.addActionListener(new ActionListener()
1132     {
1133       public void actionPerformed(ActionEvent e)
1134       {
1135         sequenceFeature_actionPerformed();
1136       }
1137     });
1138     textColour.setText(MessageManager.getString("label.text_colour"));
1139     textColour.addActionListener(new ActionListener()
1140     {
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         textColour_actionPerformed();
1144       }
1145     });
1146     jMenu1.setText(MessageManager.getString("label.group"));
1147     structureMenu.setText(MessageManager.getString("label.structure"));
1148     viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
1149     // colStructureMenu.setText("Colour By Structure");
1150     editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
1151     editSequence.addActionListener(new ActionListener()
1152     {
1153       public void actionPerformed(ActionEvent actionEvent)
1154       {
1155         editSequence_actionPerformed(actionEvent);
1156       }
1157     });
1158
1159     /*
1160      * annotationMenuItem.setText("By Annotation");
1161      * annotationMenuItem.addActionListener(new ActionListener() { public void
1162      * actionPerformed(ActionEvent actionEvent) {
1163      * annotationMenuItem_actionPerformed(actionEvent); } });
1164      */
1165     groupMenu.add(sequenceSelDetails);
1166     add(groupMenu);
1167     add(sequenceMenu);
1168     this.add(structureMenu);
1169     groupMenu.add(editMenu);
1170     groupMenu.add(outputMenu);
1171     groupMenu.add(sequenceFeature);
1172     groupMenu.add(createGroupMenuItem);
1173     groupMenu.add(unGroupMenuItem);
1174     groupMenu.add(jMenu1);
1175     sequenceMenu.add(sequenceName);
1176     sequenceMenu.add(sequenceDetails);
1177     colourMenu.add(textColour);
1178     colourMenu.add(noColourmenuItem);
1179     colourMenu.add(clustalColour);
1180     colourMenu.add(BLOSUM62Colour);
1181     colourMenu.add(PIDColour);
1182     colourMenu.add(zappoColour);
1183     colourMenu.add(taylorColour);
1184     colourMenu.add(hydrophobicityColour);
1185     colourMenu.add(helixColour);
1186     colourMenu.add(strandColour);
1187     colourMenu.add(turnColour);
1188     colourMenu.add(buriedColour);
1189     colourMenu.add(nucleotideMenuItem);
1190     if (ap.getAlignment().isNucleotide()) {
1191         // JBPNote - commented since the colourscheme isn't functional
1192         //  colourMenu.add(RNAInteractionColour);
1193         colourMenu.add(purinePyrimidineColour);
1194     }
1195     // colourMenu.add(covariationColour);
1196     colourMenu.add(userDefinedColour);
1197
1198     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1199     {
1200       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1201               .getUserColourSchemes().keys();
1202
1203       while (userColours.hasMoreElements())
1204       {
1205         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1206         item.addActionListener(new ActionListener()
1207         {
1208           public void actionPerformed(ActionEvent evt)
1209           {
1210             userDefinedColour_actionPerformed(evt);
1211           }
1212         });
1213         colourMenu.add(item);
1214       }
1215     }
1216
1217     colourMenu.addSeparator();
1218     colourMenu.add(abovePIDColour);
1219     colourMenu.add(conservationMenuItem);
1220     // colourMenu.add(annotationMenuItem);
1221     editMenu.add(copy);
1222     editMenu.add(cut);
1223     editMenu.add(editSequence);
1224     editMenu.add(upperCase);
1225     editMenu.add(lowerCase);
1226     editMenu.add(toggle);
1227     pdbMenu.add(pdbFromFile);
1228     // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1229     //    pdbMenu.add(RNAFold);
1230     //    pdbMenu.add(ContraFold);
1231     pdbMenu.add(enterPDB);
1232     pdbMenu.add(discoverPDB);
1233     jMenu1.add(groupName);
1234     jMenu1.add(colourMenu);
1235     jMenu1.add(showBoxes);
1236     jMenu1.add(showText);
1237     jMenu1.add(showColourText);
1238     jMenu1.add(outline);
1239     jMenu1.add(displayNonconserved);
1240     structureMenu.add(pdbMenu);
1241     structureMenu.add(viewStructureMenu);
1242     // structureMenu.add(colStructureMenu);
1243     noColourmenuItem.setText(MessageManager.getString("label.none"));
1244     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1245     {
1246       public void actionPerformed(ActionEvent e)
1247       {
1248         noColourmenuItem_actionPerformed();
1249       }
1250     });
1251
1252     clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
1253     clustalColour.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         clustalColour_actionPerformed();
1258       }
1259     });
1260     zappoColour.setText(MessageManager.getString("label.zappo"));
1261     zappoColour.addActionListener(new java.awt.event.ActionListener()
1262     {
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         zappoColour_actionPerformed();
1266       }
1267     });
1268     taylorColour.setText(MessageManager.getString("label.taylor"));
1269     taylorColour.addActionListener(new java.awt.event.ActionListener()
1270     {
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         taylorColour_actionPerformed();
1274       }
1275     });
1276     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
1277     hydrophobicityColour
1278             .addActionListener(new java.awt.event.ActionListener()
1279             {
1280               public void actionPerformed(ActionEvent e)
1281               {
1282                 hydrophobicityColour_actionPerformed();
1283               }
1284             });
1285     helixColour.setText(MessageManager.getString("label.helix_propensity"));
1286     helixColour.addActionListener(new java.awt.event.ActionListener()
1287     {
1288       public void actionPerformed(ActionEvent e)
1289       {
1290         helixColour_actionPerformed();
1291       }
1292     });
1293     strandColour.setText(MessageManager.getString("label.strand_propensity"));
1294     strandColour.addActionListener(new java.awt.event.ActionListener()
1295     {
1296       public void actionPerformed(ActionEvent e)
1297       {
1298         strandColour_actionPerformed();
1299       }
1300     });
1301     turnColour.setText(MessageManager.getString("label.turn_propensity"));
1302     turnColour.addActionListener(new java.awt.event.ActionListener()
1303     {
1304       public void actionPerformed(ActionEvent e)
1305       {
1306         turnColour_actionPerformed();
1307       }
1308     });
1309     buriedColour.setText(MessageManager.getString("label.buried_index"));
1310     buriedColour.addActionListener(new java.awt.event.ActionListener()
1311     {
1312       public void actionPerformed(ActionEvent e)
1313       {
1314         buriedColour_actionPerformed();
1315       }
1316     });
1317     abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
1318     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1319     {
1320       public void actionPerformed(ActionEvent e)
1321       {
1322         abovePIDColour_actionPerformed();
1323       }
1324     });
1325     userDefinedColour.setText(MessageManager.getString("action.user_defined"));
1326     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1327     {
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         userDefinedColour_actionPerformed(e);
1331       }
1332     });
1333     PIDColour.setText(MessageManager.getString("label.percentage_identity"));
1334     PIDColour.addActionListener(new java.awt.event.ActionListener()
1335     {
1336       public void actionPerformed(ActionEvent e)
1337       {
1338         PIDColour_actionPerformed();
1339       }
1340     });
1341     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1342     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1343     {
1344       public void actionPerformed(ActionEvent e)
1345       {
1346         BLOSUM62Colour_actionPerformed();
1347       }
1348     });
1349     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
1350     purinePyrimidineColour
1351             .addActionListener(new java.awt.event.ActionListener()
1352             {
1353               public void actionPerformed(ActionEvent e)
1354               {
1355                 purinePyrimidineColour_actionPerformed();
1356               }
1357             });
1358
1359
1360     /*
1361      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1362      * public void actionPerformed(ActionEvent e) {
1363      * covariationColour_actionPerformed(); } });
1364      */
1365
1366     conservationMenuItem.setText(MessageManager.getString("label.conservation"));
1367     conservationMenuItem
1368             .addActionListener(new java.awt.event.ActionListener()
1369             {
1370               public void actionPerformed(ActionEvent e)
1371               {
1372                 conservationMenuItem_actionPerformed();
1373               }
1374             });
1375   }
1376
1377   protected void sequenceSelectionDetails_actionPerformed()
1378   {
1379     createSequenceDetailsReport(ap.av.getSequenceSelection());
1380   }
1381
1382   protected void sequenceDetails_actionPerformed()
1383   {
1384     createSequenceDetailsReport(new SequenceI[]
1385     { sequence });
1386   }
1387
1388   public void createSequenceDetailsReport(SequenceI[] sequences)
1389   {
1390     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1391     StringBuffer contents = new StringBuffer();
1392     for (SequenceI seq : sequences)
1393     {
1394       contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
1395               + "</h2></p><p>");
1396       new SequenceAnnotationReport(null)
1397               .createSequenceAnnotationReport(
1398                       contents,
1399                       seq,
1400                       true,
1401                       true,
1402                       false,
1403                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1404                               : null);
1405       contents.append("</p>");
1406     }
1407     cap.setText("<html>" + contents.toString() + "</html>");
1408
1409     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")}))
1410                 ,500, 400);
1411
1412   }
1413
1414   protected void showNonconserved_actionPerformed()
1415   {
1416     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1417     refresh();
1418   }
1419
1420   /**
1421    * call to refresh view after settings change
1422    */
1423   void refresh()
1424   {
1425     ap.updateAnnotation();
1426     ap.paintAlignment(true);
1427
1428     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1429   }
1430
1431   /**
1432    * DOCUMENT ME!
1433    *
1434    * @param e
1435    *          DOCUMENT ME!
1436    */
1437   protected void clustalColour_actionPerformed()
1438   {
1439     SequenceGroup sg = getGroup();
1440     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1441     refresh();
1442   }
1443
1444   /**
1445    * DOCUMENT ME!
1446    *
1447    * @param e
1448    *          DOCUMENT ME!
1449    */
1450   protected void zappoColour_actionPerformed()
1451   {
1452     getGroup().cs = new ZappoColourScheme();
1453     refresh();
1454   }
1455
1456   /**
1457    * DOCUMENT ME!
1458    *
1459    * @param e
1460    *          DOCUMENT ME!
1461    */
1462   protected void taylorColour_actionPerformed()
1463   {
1464     getGroup().cs = new TaylorColourScheme();
1465     refresh();
1466   }
1467
1468   /**
1469    * DOCUMENT ME!
1470    *
1471    * @param e
1472    *          DOCUMENT ME!
1473    */
1474   protected void hydrophobicityColour_actionPerformed()
1475   {
1476     getGroup().cs = new HydrophobicColourScheme();
1477     refresh();
1478   }
1479
1480   /**
1481    * DOCUMENT ME!
1482    *
1483    * @param e
1484    *          DOCUMENT ME!
1485    */
1486   protected void helixColour_actionPerformed()
1487   {
1488     getGroup().cs = new HelixColourScheme();
1489     refresh();
1490   }
1491
1492   /**
1493    * DOCUMENT ME!
1494    *
1495    * @param e
1496    *          DOCUMENT ME!
1497    */
1498   protected void strandColour_actionPerformed()
1499   {
1500     getGroup().cs = new StrandColourScheme();
1501     refresh();
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    *
1507    * @param e
1508    *          DOCUMENT ME!
1509    */
1510   protected void turnColour_actionPerformed()
1511   {
1512     getGroup().cs = new TurnColourScheme();
1513     refresh();
1514   }
1515
1516   /**
1517    * DOCUMENT ME!
1518    *
1519    * @param e
1520    *          DOCUMENT ME!
1521    */
1522   protected void buriedColour_actionPerformed()
1523   {
1524     getGroup().cs = new BuriedColourScheme();
1525     refresh();
1526   }
1527
1528   /**
1529    * DOCUMENT ME!
1530    *
1531    * @param e
1532    *          DOCUMENT ME!
1533    */
1534   public void nucleotideMenuItem_actionPerformed()
1535   {
1536     getGroup().cs = new NucleotideColourScheme();
1537     refresh();
1538   }
1539
1540   protected void purinePyrimidineColour_actionPerformed()
1541   {
1542     getGroup().cs = new PurinePyrimidineColourScheme();
1543     refresh();
1544   }
1545
1546
1547   /*
1548    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1549    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1550    */
1551   /**
1552    * DOCUMENT ME!
1553    *
1554    * @param e
1555    *          DOCUMENT ME!
1556    */
1557   protected void abovePIDColour_actionPerformed()
1558   {
1559     SequenceGroup sg = getGroup();
1560     if (sg.cs == null)
1561     {
1562       return;
1563     }
1564
1565     if (abovePIDColour.isSelected())
1566     {
1567       sg.cs.setConsensus(AAFrequency.calculate(
1568               sg.getSequences(ap.av.getHiddenRepSequences()),
1569               sg.getStartRes(), sg.getEndRes() + 1));
1570
1571       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1572               .getName());
1573
1574       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1575
1576       SliderPanel.showPIDSlider();
1577     }
1578     else
1579     // remove PIDColouring
1580     {
1581       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1582     }
1583
1584     refresh();
1585   }
1586
1587   /**
1588    * DOCUMENT ME!
1589    *
1590    * @param e
1591    *          DOCUMENT ME!
1592    */
1593   protected void userDefinedColour_actionPerformed(ActionEvent e)
1594   {
1595     SequenceGroup sg = getGroup();
1596
1597     if (e.getSource().equals(userDefinedColour))
1598     {
1599       new UserDefinedColours(ap, sg);
1600     }
1601     else
1602     {
1603       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1604               .getUserColourSchemes().get(e.getActionCommand());
1605
1606       sg.cs = udc;
1607     }
1608     refresh();
1609   }
1610
1611   /**
1612    * DOCUMENT ME!
1613    *
1614    * @param e
1615    *          DOCUMENT ME!
1616    */
1617   protected void PIDColour_actionPerformed()
1618   {
1619     SequenceGroup sg = getGroup();
1620     sg.cs = new PIDColourScheme();
1621     sg.cs.setConsensus(AAFrequency.calculate(
1622             sg.getSequences(ap.av.getHiddenRepSequences()),
1623             sg.getStartRes(), sg.getEndRes() + 1));
1624     refresh();
1625   }
1626
1627   /**
1628    * DOCUMENT ME!
1629    *
1630    * @param e
1631    *          DOCUMENT ME!
1632    */
1633   protected void BLOSUM62Colour_actionPerformed()
1634   {
1635     SequenceGroup sg = getGroup();
1636
1637     sg.cs = new Blosum62ColourScheme();
1638
1639     sg.cs.setConsensus(AAFrequency.calculate(
1640             sg.getSequences(ap.av.getHiddenRepSequences()),
1641             sg.getStartRes(), sg.getEndRes() + 1));
1642
1643     refresh();
1644   }
1645
1646   /**
1647    * DOCUMENT ME!
1648    *
1649    * @param e
1650    *          DOCUMENT ME!
1651    */
1652   protected void noColourmenuItem_actionPerformed()
1653   {
1654     getGroup().cs = null;
1655     refresh();
1656   }
1657
1658   /**
1659    * DOCUMENT ME!
1660    *
1661    * @param e
1662    *          DOCUMENT ME!
1663    */
1664   protected void conservationMenuItem_actionPerformed()
1665   {
1666     SequenceGroup sg = getGroup();
1667     if (sg.cs == null)
1668     {
1669       return;
1670     }
1671
1672     if (conservationMenuItem.isSelected())
1673     {
1674     // JBPNote: Conservation name shouldn't be i18n translated
1675       Conservation c = new Conservation("Group",
1676               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1677                       .getHiddenRepSequences()), sg.getStartRes(),
1678               sg.getEndRes() + 1);
1679
1680       c.calculate();
1681       c.verdict(false, ap.av.getConsPercGaps());
1682
1683       sg.cs.setConservation(c);
1684
1685       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1686       SliderPanel.showConservationSlider();
1687     }
1688     else
1689     // remove ConservationColouring
1690     {
1691       sg.cs.setConservation(null);
1692     }
1693
1694     refresh();
1695   }
1696
1697   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1698   {
1699     SequenceGroup sg = getGroup();
1700     if (sg == null)
1701     {
1702       return;
1703     }
1704
1705     AnnotationColourGradient acg = new AnnotationColourGradient(
1706             sequence.getAnnotation()[0], null,
1707             AnnotationColourGradient.NO_THRESHOLD);
1708
1709     acg.setPredefinedColours(true);
1710     sg.cs = acg;
1711
1712     refresh();
1713   }
1714
1715   /**
1716    * DOCUMENT ME!
1717    *
1718    * @param e
1719    *          DOCUMENT ME!
1720    */
1721   protected void groupName_actionPerformed()
1722   {
1723
1724     SequenceGroup sg = getGroup();
1725     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1726             sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",
1727             MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
1728             ap.alignFrame);
1729
1730     if (!dialog.accept)
1731     {
1732       return;
1733     }
1734
1735     sg.setName(dialog.getName());
1736     sg.setDescription(dialog.getDescription());
1737     refresh();
1738   }
1739
1740   /**
1741    * Get selection group - adding it to the alignment if necessary.
1742    *
1743    * @return sequence group to operate on
1744    */
1745   SequenceGroup getGroup()
1746   {
1747     SequenceGroup sg = ap.av.getSelectionGroup();
1748     // this method won't add a new group if it already exists
1749     if (sg != null)
1750     {
1751       ap.av.getAlignment().addGroup(sg);
1752     }
1753
1754     return sg;
1755   }
1756
1757   /**
1758    * DOCUMENT ME!
1759    *
1760    * @param e
1761    *          DOCUMENT ME!
1762    */
1763   void sequenceName_actionPerformed()
1764   {
1765     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1766             sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",
1767             MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
1768             ap.alignFrame);
1769
1770     if (!dialog.accept)
1771     {
1772       return;
1773     }
1774
1775     if (dialog.getName() != null)
1776     {
1777       if (dialog.getName().indexOf(" ") > -1)
1778       {
1779         JOptionPane.showMessageDialog(ap,
1780                 MessageManager.getString("label.spaces_converted_to_backslashes"),
1781                 MessageManager.getString("label.no_spaces_allowed_sequence_name"),
1782                 JOptionPane.WARNING_MESSAGE);
1783       }
1784
1785       sequence.setName(dialog.getName().replace(' ', '_'));
1786       ap.paintAlignment(false);
1787     }
1788
1789     sequence.setDescription(dialog.getDescription());
1790
1791     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1792             .getSequences());
1793
1794   }
1795
1796   /**
1797    * DOCUMENT ME!
1798    *
1799    * @param e
1800    *          DOCUMENT ME!
1801    */
1802   void unGroupMenuItem_actionPerformed()
1803   {
1804     SequenceGroup sg = ap.av.getSelectionGroup();
1805     ap.av.getAlignment().deleteGroup(sg);
1806     ap.av.setSelectionGroup(null);
1807     refresh();
1808   }
1809   void createGroupMenuItem_actionPerformed()
1810   {
1811     getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
1812     refresh();
1813   }
1814
1815   /**
1816    * DOCUMENT ME!
1817    *
1818    * @param e
1819    *          DOCUMENT ME!
1820    */
1821   protected void outline_actionPerformed()
1822   {
1823     SequenceGroup sg = getGroup();
1824     Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
1825             Color.BLUE);
1826
1827     if (col != null)
1828     {
1829       sg.setOutlineColour(col);
1830     }
1831
1832     refresh();
1833   }
1834
1835   /**
1836    * DOCUMENT ME!
1837    *
1838    * @param e
1839    *          DOCUMENT ME!
1840    */
1841   public void showBoxes_actionPerformed()
1842   {
1843     getGroup().setDisplayBoxes(showBoxes.isSelected());
1844     refresh();
1845   }
1846
1847   /**
1848    * DOCUMENT ME!
1849    *
1850    * @param e
1851    *          DOCUMENT ME!
1852    */
1853   public void showText_actionPerformed()
1854   {
1855     getGroup().setDisplayText(showText.isSelected());
1856     refresh();
1857   }
1858
1859   /**
1860    * DOCUMENT ME!
1861    *
1862    * @param e
1863    *          DOCUMENT ME!
1864    */
1865   public void showColourText_actionPerformed()
1866   {
1867     getGroup().setColourText(showColourText.isSelected());
1868     refresh();
1869   }
1870
1871   public void showLink(String url)
1872   {
1873     try
1874     {
1875       jalview.util.BrowserLauncher.openURL(url);
1876     } catch (Exception ex)
1877     {
1878       JOptionPane
1879               .showInternalMessageDialog(
1880                       Desktop.desktop,
1881                       MessageManager.getString("label.web_browser_not_found_unix"),
1882                       MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
1883
1884       ex.printStackTrace();
1885     }
1886   }
1887
1888   void hideSequences(boolean representGroup)
1889   {
1890     SequenceGroup sg = ap.av.getSelectionGroup();
1891     if (sg == null || sg.getSize() < 1)
1892     {
1893       ap.av.hideSequence(new SequenceI[]
1894       { sequence });
1895       return;
1896     }
1897
1898     ap.av.setSelectionGroup(null);
1899
1900     if (representGroup)
1901     {
1902       ap.av.hideRepSequences(sequence, sg);
1903
1904       return;
1905     }
1906
1907     int gsize = sg.getSize();
1908     SequenceI[] hseqs;
1909
1910     hseqs = new SequenceI[gsize];
1911
1912     int index = 0;
1913     for (int i = 0; i < gsize; i++)
1914     {
1915       hseqs[index++] = sg.getSequenceAt(i);
1916     }
1917
1918     ap.av.hideSequence(hseqs);
1919     // refresh(); TODO: ? needed ?
1920     ap.av.sendSelection();
1921   }
1922
1923   public void copy_actionPerformed()
1924   {
1925     ap.alignFrame.copy_actionPerformed(null);
1926   }
1927
1928   public void cut_actionPerformed()
1929   {
1930     ap.alignFrame.cut_actionPerformed(null);
1931   }
1932
1933   void changeCase(ActionEvent e)
1934   {
1935     Object source = e.getSource();
1936     SequenceGroup sg = ap.av.getSelectionGroup();
1937
1938     if (sg != null)
1939     {
1940       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1941               sg.getEndRes() + 1);
1942
1943       String description;
1944       int caseChange;
1945
1946       if (source == toggle)
1947       {
1948         description = MessageManager.getString("label.toggle_case");
1949         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1950       }
1951       else if (source == upperCase)
1952       {
1953         description = MessageManager.getString("label.to_upper_case");
1954         caseChange = ChangeCaseCommand.TO_UPPER;
1955       }
1956       else
1957       {
1958         description = MessageManager.getString("label.to_lower_case");
1959         caseChange = ChangeCaseCommand.TO_LOWER;
1960       }
1961
1962       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1963               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1964               startEnd, caseChange);
1965
1966       ap.alignFrame.addHistoryItem(caseCommand);
1967
1968       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1969               .getSequences());
1970
1971     }
1972   }
1973
1974   public void outputText_actionPerformed(ActionEvent e)
1975   {
1976     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1977     cap.setForInput(null);
1978     Desktop.addInternalFrame(cap,
1979             MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
1980
1981     String[] omitHidden = null;
1982
1983     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1984     // or we simply trust the user wants
1985     // wysiwig behaviour
1986     SequenceGroup sg = ap.av.getSelectionGroup();
1987     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1988     omitHidden = ap.av.getViewAsString(true);
1989     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1990     AlignmentAnnotation[] nala = ap.av.getAlignment()
1991             .getAlignmentAnnotation();
1992     if (nala != null)
1993     {
1994       for (int i = 0; i < nala.length; i++)
1995       {
1996         AlignmentAnnotation na = nala[i];
1997         oal.addAnnotation(na);
1998       }
1999     }
2000     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2001             oal, omitHidden, csel, sg));
2002     oal = null;
2003   }
2004
2005   public void pdbFromFile_actionPerformed()
2006   {
2007     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2008             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2009     chooser.setFileView(new jalview.io.JalviewFileView());
2010     chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
2011     chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
2012
2013     int value = chooser.showOpenDialog(null);
2014
2015     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2016     {
2017       String choice = chooser.getSelectedFile().getPath();
2018       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2019       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2020               jalview.io.AppletFormatAdapter.FILE, sequence, true);
2021     }
2022
2023   }
2024     // JBNote: commented out - these won't be instantiated here...!
2025 //  public void RNAFold_actionPerformed() throws Exception
2026 //  {
2027 //        Predict2D P2D = new Predict2D();
2028 //        P2D.getStructure2DFromRNAFold("toto");
2029 //  }
2030 //
2031 //  public void ContraFold_actionPerformed() throws Exception
2032 //  {
2033 //        Predict2D P2D = new Predict2D();
2034 //        P2D.getStructure2DFromContraFold("toto");
2035 //  }
2036   public void enterPDB_actionPerformed()
2037   {
2038     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2039             MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
2040
2041     if (id != null && id.length() > 0)
2042     {
2043       PDBEntry entry = new PDBEntry();
2044       entry.setId(id.toUpperCase());
2045       sequence.getDatasetSequence().addPDBId(entry);
2046     }
2047   }
2048
2049   public void discoverPDB_actionPerformed()
2050   {
2051
2052     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2053     { sequence }
2054             : ap.av.getSequenceSelection());
2055     Thread discpdb = new Thread(new Runnable()
2056     {
2057       public void run()
2058       {
2059
2060         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2061                 .fetchDBRefs(false);
2062       }
2063
2064     });
2065     discpdb.start();
2066   }
2067
2068   public void sequenceFeature_actionPerformed()
2069   {
2070     SequenceGroup sg = ap.av.getSelectionGroup();
2071     if (sg == null)
2072     {
2073       return;
2074     }
2075
2076     int rsize = 0, gSize = sg.getSize();
2077     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2078     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2079
2080     for (int i = 0; i < gSize; i++)
2081     {
2082       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2083       int end = sg.findEndRes(sg.getSequenceAt(i));
2084       if (start <= end)
2085       {
2086         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2087         features[rsize] = new SequenceFeature(null, null, null, start, end,
2088                 "Jalview");
2089         rsize++;
2090       }
2091     }
2092     rseqs = new SequenceI[rsize];
2093     tfeatures = new SequenceFeature[rsize];
2094     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2095     System.arraycopy(features, 0, tfeatures, 0, rsize);
2096     features = tfeatures;
2097     seqs = rseqs;
2098     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2099             features, true, ap))
2100     {
2101       ap.alignFrame.setShowSeqFeatures(true);
2102       ap.highlightSearchResults(null);
2103     }
2104   }
2105
2106   public void textColour_actionPerformed()
2107   {
2108     SequenceGroup sg = getGroup();
2109     if (sg != null)
2110     {
2111       new TextColourChooser().chooseColour(ap, sg);
2112     }
2113   }
2114
2115   public void colourByStructure(String pdbid)
2116   {
2117     Annotation[] anots = ap.av.getStructureSelectionManager()
2118             .colourSequenceFromStructure(sequence, pdbid);
2119
2120     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2121             "Coloured by " + pdbid, anots);
2122
2123     ap.av.getAlignment().addAnnotation(an);
2124     an.createSequenceMapping(sequence, 0, true);
2125     // an.adjustForAlignment();
2126     ap.av.getAlignment().setAnnotationIndex(an, 0);
2127
2128     ap.adjustAnnotationHeight();
2129
2130     sequence.addAlignmentAnnotation(an);
2131
2132   }
2133
2134   public void editSequence_actionPerformed(ActionEvent actionEvent)
2135   {
2136     SequenceGroup sg = ap.av.getSelectionGroup();
2137
2138     if (sg != null)
2139     {
2140       if (sequence == null)
2141         sequence = (Sequence) sg.getSequenceAt(0);
2142
2143       EditNameDialog dialog = new EditNameDialog(
2144               sequence.getSequenceAsString(sg.getStartRes(),
2145                       sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
2146                       MessageManager.getString("label.edit_sequence"), ap.alignFrame);
2147
2148       if (dialog.accept)
2149       {
2150         EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
2151                 EditCommand.REPLACE, dialog.getName().replace(' ',
2152                         ap.av.getGapCharacter()),
2153                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2154                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2155
2156         ap.alignFrame.addHistoryItem(editCommand);
2157
2158         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2159                 .getSequences());
2160       }
2161     }
2162   }
2163
2164 }