src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.AAFrequency;
  24 import jalview.analysis.AlignmentAnnotationUtils;
  25 import jalview.analysis.AlignmentUtils;
  26 import jalview.analysis.Conservation;
  27 import jalview.commands.ChangeCaseCommand;
  28 import jalview.commands.EditCommand;
  29 import jalview.commands.EditCommand.Action;
  30 import jalview.datamodel.AlignmentAnnotation;
  31 import jalview.datamodel.AlignmentI;
  32 import jalview.datamodel.Annotation;
  33 import jalview.datamodel.ColumnSelection;
  34 import jalview.datamodel.DBRefEntry;
  35 import jalview.datamodel.PDBEntry;
  36 import jalview.datamodel.Sequence;
  37 import jalview.datamodel.SequenceFeature;
  38 import jalview.datamodel.SequenceGroup;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.io.FormatAdapter;
  41 import jalview.io.SequenceAnnotationReport;
  42 import jalview.schemes.AnnotationColourGradient;
  43 import jalview.schemes.Blosum62ColourScheme;
  44 import jalview.schemes.BuriedColourScheme;
  45 import jalview.schemes.ClustalxColourScheme;
  46 import jalview.schemes.HelixColourScheme;
  47 import jalview.schemes.HydrophobicColourScheme;
  48 import jalview.schemes.NucleotideColourScheme;
  49 import jalview.schemes.PIDColourScheme;
  50 import jalview.schemes.PurinePyrimidineColourScheme;
  51 import jalview.schemes.ResidueProperties;
  52 import jalview.schemes.StrandColourScheme;
  53 import jalview.schemes.TaylorColourScheme;
  54 import jalview.schemes.TurnColourScheme;
  55 import jalview.schemes.UserColourScheme;
  56 import jalview.schemes.ZappoColourScheme;
  57 import jalview.util.GroupUrlLink;
  58 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  59 import jalview.util.MessageManager;
  60 import jalview.util.UrlLink;
  61
  62 import java.awt.Color;
  63 import java.awt.event.ActionEvent;
  64 import java.awt.event.ActionListener;
  65 import java.util.Arrays;
  66 import java.util.Collections;
  67 import java.util.Hashtable;
  68 import java.util.LinkedHashMap;
  69 import java.util.List;
  70 import java.util.Map;
  71 import java.util.TreeMap;
  72 import java.util.Vector;
  73
  74 import javax.swing.ButtonGroup;
  75 import javax.swing.JCheckBoxMenuItem;
  76 import javax.swing.JColorChooser;
  77 import javax.swing.JMenu;
  78 import javax.swing.JMenuItem;
  79 import javax.swing.JOptionPane;
  80 import javax.swing.JPopupMenu;
  81 import javax.swing.JRadioButtonMenuItem;
  82
  83 /**
  84  * DOCUMENT ME!
  85  *
  86  * @author $author$
  87  * @version $Revision: 1.118 $
  88  */
  89 public class PopupMenu extends JPopupMenu
  90 {
  91   private static final String ALL_ANNOTATIONS = "All";
  92
  93   private static final String COMMA = ",";
  94
  95   JMenu groupMenu = new JMenu();
  96
  97   JMenuItem groupName = new JMenuItem();
  98
  99   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 112
 113   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 114
 115   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
 116
 117   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 118
 119   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 120
 121   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 122
 123   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 124
 125   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 126
 127   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 128
 129   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 130
 131   AlignmentPanel ap;
 132
 133   JMenu sequenceMenu = new JMenu();
 134
 135   JMenuItem sequenceName = new JMenuItem();
 136
 137   JMenuItem sequenceDetails = new JMenuItem();
 138
 139   JMenuItem sequenceSelDetails = new JMenuItem();
 140
 141   JMenuItem makeReferenceSeq = new JMenuItem();
 142
 143   JMenuItem chooseAnnotations = new JMenuItem();
 144
 145   SequenceI sequence;
 146
 147   JMenuItem createGroupMenuItem = new JMenuItem();
 148
 149   JMenuItem unGroupMenuItem = new JMenuItem();
 150
 151   JMenuItem outline = new JMenuItem();
 152
 153   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 154
 155   JMenu colourMenu = new JMenu();
 156
 157   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 158
 159   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 160
 161   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 162
 163   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 164
 165   JMenu editMenu = new JMenu();
 166
 167   JMenuItem cut = new JMenuItem();
 168
 169   JMenuItem copy = new JMenuItem();
 170
 171   JMenuItem upperCase = new JMenuItem();
 172
 173   JMenuItem lowerCase = new JMenuItem();
 174
 175   JMenuItem toggle = new JMenuItem();
 176
 177   JMenu pdbMenu = new JMenu();
 178
 179   JMenuItem pdbFromFile = new JMenuItem();
 180
 181   JMenuItem enterPDB = new JMenuItem();
 182
 183   JMenuItem discoverPDB = new JMenuItem();
 184
 185   JMenu outputMenu = new JMenu();
 186
 187   JMenu seqShowAnnotationsMenu = new JMenu();
 188
 189   JMenu seqHideAnnotationsMenu = new JMenu();
 190
 191   JMenuItem seqAddReferenceAnnotations = new JMenuItem(
 192           MessageManager.getString("label.add_reference_annotations"));
 193
 194   JMenu groupShowAnnotationsMenu = new JMenu();
 195
 196   JMenu groupHideAnnotationsMenu = new JMenu();
 197
 198   JMenuItem groupAddReferenceAnnotations = new JMenuItem(
 199           MessageManager.getString("label.add_reference_annotations"));
 200
 201   JMenuItem sequenceFeature = new JMenuItem();
 202
 203   JMenuItem textColour = new JMenuItem();
 204
 205   JMenu jMenu1 = new JMenu();
 206
 207   JMenuItem proteinStructureMenu = new JMenuItem();
 208
 209   JMenu rnaStructureMenu = new JMenu();
 210
 211   JMenuItem editSequence = new JMenuItem();
 212
 213   JMenu groupLinksMenu;
 214
 215   JMenuItem hideInsertions = new JMenuItem();
 216
 217   /**
 218    * Creates a new PopupMenu object.
 219    *
 220    * @param ap
 221    *          DOCUMENT ME!
 222    * @param seq
 223    *          DOCUMENT ME!
 224    */
 225   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 226   {
 227     this(ap, seq, links, null);
 228   }
 229
 230   /**
 231    *
 232    * @param ap
 233    * @param seq
 234    * @param links
 235    * @param groupLinks
 236    */
 237   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 238           Vector links, Vector groupLinks)
 239   {
 240     // /////////////////////////////////////////////////////////
 241     // If this is activated from the sequence panel, the user may want to
 242     // edit or annotate a particular residue. Therefore display the residue menu
 243     //
 244     // If from the IDPanel, we must display the sequence menu
 245     // ////////////////////////////////////////////////////////
 246     this.ap = ap;
 247     sequence = seq;
 248
 249     ButtonGroup colours = new ButtonGroup();
 250     colours.add(noColourmenuItem);
 251     colours.add(clustalColour);
 252     colours.add(zappoColour);
 253     colours.add(taylorColour);
 254     colours.add(hydrophobicityColour);
 255     colours.add(helixColour);
 256     colours.add(strandColour);
 257     colours.add(turnColour);
 258     colours.add(buriedColour);
 259     colours.add(abovePIDColour);
 260     colours.add(userDefinedColour);
 261     colours.add(PIDColour);
 262     colours.add(BLOSUM62Colour);
 263     colours.add(purinePyrimidineColour);
 264     colours.add(RNAInteractionColour);
 265
 266     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 267     {
 268       JMenuItem item = new JMenuItem(
 269               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 270
 271       item.addActionListener(new java.awt.event.ActionListener()
 272       {
 273         @Override
 274         public void actionPerformed(ActionEvent e)
 275         {
 276           outputText_actionPerformed(e);
 277         }
 278       });
 279
 280       outputMenu.add(item);
 281     }
 282
 283     /*
 284      * Build menus for annotation types that may be shown or hidden, and for
 285      * 'reference annotations' that may be added to the alignment. First for the
 286      * currently selected sequence (if there is one):
 287      */
 288     final List<SequenceI> selectedSequence = (seq == null ? Collections
 289             .<SequenceI> emptyList() : Arrays.asList(seq));
 290     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
 291             seqHideAnnotationsMenu, selectedSequence);
 292     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
 293             selectedSequence);
 294
 295     /*
 296      * And repeat for the current selection group (if there is one):
 297      */
 298     final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
 299             .<SequenceI> emptyList() : ap.av.getSelectionGroup()
 300             .getSequences());
 301     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
 302             groupHideAnnotationsMenu, selectedGroup);
 303     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
 304             selectedGroup);
 305
 306     try
 307     {
 308       jbInit();
 309     } catch (Exception e)
 310     {
 311       e.printStackTrace();
 312     }
 313
 314     JMenuItem menuItem;
 315     if (seq != null)
 316     {
 317       sequenceMenu.setText(sequence.getName());
 318       if (seq == ap.av.getAlignment().getSeqrep())
 319       {
 320         makeReferenceSeq.setText("Unmark representative");
 321       } else {
 322         makeReferenceSeq.setText("Mark as representative");
 323       }
 324
 325       if (ap.av.getAlignment().isNucleotide() == false)
 326       {
 327         remove(rnaStructureMenu);
 328       }
 329
 330       if (ap.av.getAlignment().isNucleotide() == true)
 331       {
 332         AlignmentAnnotation[] aa = ap.av.getAlignment()
 333                 .getAlignmentAnnotation();
 334         for (int i = 0; aa != null && i < aa.length; i++)
 335         {
 336           if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
 337           {
 338             final String rnastruc = aa[i].getRNAStruc();
 339             final String structureLine = aa[i].label + " (alignment)";
 340             menuItem = new JMenuItem();
 341             menuItem.setText(MessageManager.formatMessage(
 342                     "label.2d_rna_structure_line", new Object[]
 343                     { structureLine }));
 344             menuItem.addActionListener(new java.awt.event.ActionListener()
 345             {
 346               @Override
 347               public void actionPerformed(ActionEvent e)
 348               {
 349                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
 350                         rnastruc, seq.getName(), ap);
 351                 System.out.println("end");
 352               }
 353             });
 354             rnaStructureMenu.add(menuItem);
 355           }
 356         }
 357
 358
 359         if (seq.getAnnotation() != null)
 360         {
 361           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 362           for (int i = 0; i < seqAnno.length; i++)
 363           {
 364             if (seqAnno[i].isValidStruc())
 365             {
 366               final String rnastruc = seqAnno[i].getRNAStruc();
 367
 368               // TODO: make rnastrucF a bit more nice
 369               menuItem = new JMenuItem();
 370               menuItem.setText(MessageManager.formatMessage(
 371                       "label.2d_rna_sequence_name", new Object[]
 372                       { seq.getName() }));
 373               menuItem.addActionListener(new java.awt.event.ActionListener()
 374               {
 375                 @Override
 376                 public void actionPerformed(ActionEvent e)
 377                 {
 378                   // TODO: VARNA does'nt print gaps in the sequence
 379
 380                   new AppVarna(seq.getName() + " structure", seq, seq
 381                           .getSequenceAsString(), rnastruc, seq.getName(),
 382                           ap);
 383                 }
 384               });
 385               rnaStructureMenu.add(menuItem);
 386             }
 387           }
 388         }
 389       }
 390
 391       menuItem = new JMenuItem(
 392               MessageManager.getString("action.hide_sequences"));
 393       menuItem.addActionListener(new java.awt.event.ActionListener()
 394       {
 395         @Override
 396         public void actionPerformed(ActionEvent e)
 397         {
 398           hideSequences(false);
 399         }
 400       });
 401       add(menuItem);
 402
 403       if (ap.av.getSelectionGroup() != null
 404               && ap.av.getSelectionGroup().getSize() > 1)
 405       {
 406         menuItem = new JMenuItem(MessageManager.formatMessage(
 407                 "label.represent_group_with", new Object[]
 408                 { seq.getName() }));
 409         menuItem.addActionListener(new java.awt.event.ActionListener()
 410         {
 411           @Override
 412           public void actionPerformed(ActionEvent e)
 413           {
 414             hideSequences(true);
 415           }
 416         });
 417         sequenceMenu.add(menuItem);
 418       }
 419
 420       if (ap.av.hasHiddenRows())
 421       {
 422         final int index = ap.av.getAlignment().findIndex(seq);
 423
 424         if (ap.av.adjustForHiddenSeqs(index)
 425                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 426         {
 427           menuItem = new JMenuItem(
 428                   MessageManager.getString("action.reveal_sequences"));
 429           menuItem.addActionListener(new ActionListener()
 430           {
 431             @Override
 432             public void actionPerformed(ActionEvent e)
 433             {
 434               ap.av.showSequence(index);
 435               if (ap.overviewPanel != null)
 436               {
 437                 ap.overviewPanel.updateOverviewImage();
 438               }
 439             }
 440           });
 441           add(menuItem);
 442         }
 443       }
 444     }
 445     // for the case when no sequences are even visible
 446     if (ap.av.hasHiddenRows())
 447     {
 448       {
 449         menuItem = new JMenuItem(
 450                 MessageManager.getString("action.reveal_all"));
 451         menuItem.addActionListener(new ActionListener()
 452         {
 453           @Override
 454           public void actionPerformed(ActionEvent e)
 455           {
 456             ap.av.showAllHiddenSeqs();
 457             if (ap.overviewPanel != null)
 458             {
 459               ap.overviewPanel.updateOverviewImage();
 460             }
 461           }
 462         });
 463
 464         add(menuItem);
 465       }
 466
 467     }
 468
 469     SequenceGroup sg = ap.av.getSelectionGroup();
 470     boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
 471             .getGroups().contains(sg) : false;
 472
 473     if (sg != null && sg.getSize() > 0)
 474     {
 475       groupName.setText(MessageManager.formatMessage("label.name_param",
 476               new Object[]
 477               { sg.getName() }));
 478       groupName.setText(MessageManager
 479               .getString("label.edit_name_and_description_current_group"));
 480
 481       if (sg.cs instanceof ZappoColourScheme)
 482       {
 483         zappoColour.setSelected(true);
 484       }
 485       else if (sg.cs instanceof TaylorColourScheme)
 486       {
 487         taylorColour.setSelected(true);
 488       }
 489       else if (sg.cs instanceof PIDColourScheme)
 490       {
 491         PIDColour.setSelected(true);
 492       }
 493       else if (sg.cs instanceof Blosum62ColourScheme)
 494       {
 495         BLOSUM62Colour.setSelected(true);
 496       }
 497       else if (sg.cs instanceof UserColourScheme)
 498       {
 499         userDefinedColour.setSelected(true);
 500       }
 501       else if (sg.cs instanceof HydrophobicColourScheme)
 502       {
 503         hydrophobicityColour.setSelected(true);
 504       }
 505       else if (sg.cs instanceof HelixColourScheme)
 506       {
 507         helixColour.setSelected(true);
 508       }
 509       else if (sg.cs instanceof StrandColourScheme)
 510       {
 511         strandColour.setSelected(true);
 512       }
 513       else if (sg.cs instanceof TurnColourScheme)
 514       {
 515         turnColour.setSelected(true);
 516       }
 517       else if (sg.cs instanceof BuriedColourScheme)
 518       {
 519         buriedColour.setSelected(true);
 520       }
 521       else if (sg.cs instanceof ClustalxColourScheme)
 522       {
 523         clustalColour.setSelected(true);
 524       }
 525       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 526       {
 527         purinePyrimidineColour.setSelected(true);
 528       }
 529
 530       /*
 531        * else if (sg.cs instanceof CovariationColourScheme) {
 532        * covariationColour.setSelected(true); }
 533        */
 534       else
 535       {
 536         noColourmenuItem.setSelected(true);
 537       }
 538
 539       if (sg.cs != null && sg.cs.conservationApplied())
 540       {
 541         conservationMenuItem.setSelected(true);
 542       }
 543       displayNonconserved.setSelected(sg.getShowNonconserved());
 544       showText.setSelected(sg.getDisplayText());
 545       showColourText.setSelected(sg.getColourText());
 546       showBoxes.setSelected(sg.getDisplayBoxes());
 547       // add any groupURLs to the groupURL submenu and make it visible
 548       if (groupLinks != null && groupLinks.size() > 0)
 549       {
 550         buildGroupURLMenu(sg, groupLinks);
 551       }
 552       // Add a 'show all structures' for the current selection
 553       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
 554       SequenceI sqass = null;
 555       for (SequenceI sq : ap.av.getSequenceSelection())
 556       {
 557         Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
 558         if (pes != null && pes.size() > 0)
 559         {
 560           reppdb.put(pes.get(0).getId(), pes.get(0));
 561           for (PDBEntry pe : pes)
 562           {
 563             pdbe.put(pe.getId(), pe);
 564             if (sqass == null)
 565             {
 566               sqass = sq;
 567             }
 568           }
 569         }
 570       }
 571       if (pdbe.size() > 0)
 572       {
 573         final PDBEntry[] pe = pdbe.values().toArray(
 574                 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
 575                 new PDBEntry[reppdb.size()]);
 576         final JMenuItem gpdbview, rpdbview;
 577       }
 578     }
 579     else
 580     {
 581       groupMenu.setVisible(false);
 582       editMenu.setVisible(false);
 583     }
 584
 585     if (!isDefinedGroup)
 586     {
 587       createGroupMenuItem.setVisible(true);
 588       unGroupMenuItem.setVisible(false);
 589       jMenu1.setText(MessageManager.getString("action.edit_new_group"));
 590     }
 591     else
 592     {
 593       createGroupMenuItem.setVisible(false);
 594       unGroupMenuItem.setVisible(true);
 595       jMenu1.setText(MessageManager.getString("action.edit_group"));
 596     }
 597
 598     if (seq == null)
 599     {
 600       sequenceMenu.setVisible(false);
 601       proteinStructureMenu.setVisible(false);
 602       rnaStructureMenu.setVisible(false);
 603     }
 604
 605     if (links != null && links.size() > 0)
 606     {
 607
 608       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
 609       Vector linkset = new Vector();
 610       for (int i = 0; i < links.size(); i++)
 611       {
 612         String link = links.elementAt(i).toString();
 613         UrlLink urlLink = null;
 614         try
 615         {
 616           urlLink = new UrlLink(link);
 617         } catch (Exception foo)
 618         {
 619           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 620                   + "'", foo);
 621           continue;
 622         }
 623         ;
 624         if (!urlLink.isValid())
 625         {
 626           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 627           continue;
 628         }
 629         final String label = urlLink.getLabel();
 630         if (seq != null && urlLink.isDynamic())
 631         {
 632
 633           // collect matching db-refs
 634           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 635                   seq.getDBRef(), new String[]
 636                   { urlLink.getTarget() });
 637           // collect id string too
 638           String id = seq.getName();
 639           String descr = seq.getDescription();
 640           if (descr != null && descr.length() < 1)
 641           {
 642             descr = null;
 643           }
 644
 645           if (dbr != null)
 646           {
 647             for (int r = 0; r < dbr.length; r++)
 648             {
 649               if (id != null && dbr[r].getAccessionId().equals(id))
 650               {
 651                 // suppress duplicate link creation for the bare sequence ID
 652                 // string with this link
 653                 id = null;
 654               }
 655               // create Bare ID link for this RUL
 656               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 657                       true);
 658               if (urls != null)
 659               {
 660                 for (int u = 0; u < urls.length; u += 2)
 661                 {
 662                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 663                   {
 664                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 665                     addshowLink(linkMenu, label + "|" + urls[u],
 666                             urls[u + 1]);
 667                   }
 668                 }
 669               }
 670             }
 671           }
 672           if (id != null)
 673           {
 674             // create Bare ID link for this RUL
 675             String[] urls = urlLink.makeUrls(id, true);
 676             if (urls != null)
 677             {
 678               for (int u = 0; u < urls.length; u += 2)
 679               {
 680                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 681                 {
 682                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 683                   addshowLink(linkMenu, label, urls[u + 1]);
 684                 }
 685               }
 686             }
 687           }
 688           // Create urls from description but only for URL links which are regex
 689           // links
 690           if (descr != null && urlLink.getRegexReplace() != null)
 691           {
 692             // create link for this URL from description where regex matches
 693             String[] urls = urlLink.makeUrls(descr, true);
 694             if (urls != null)
 695             {
 696               for (int u = 0; u < urls.length; u += 2)
 697               {
 698                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 699                 {
 700                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 701                   addshowLink(linkMenu, label, urls[u + 1]);
 702                 }
 703               }
 704             }
 705           }
 706         }
 707         else
 708         {
 709           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 710           {
 711             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 712             // Add a non-dynamic link
 713             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 714           }
 715         }
 716       }
 717       if (sequence != null)
 718       {
 719         sequenceMenu.add(linkMenu);
 720       }
 721       else
 722       {
 723         add(linkMenu);
 724       }
 725     }
 726   }
 727
 728   /**
 729    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
 730    * "All" is added first, followed by a separator. Then add any annotation
 731    * types associated with the current selection. Separate menus are built for
 732    * the selected sequence group (if any), and the selected sequence.
 733    * <p>
 734    * Some annotation rows are always rendered together - these can be identified
 735    * by a common graphGroup property > -1. Only one of each group will be marked
 736    * as visible (to avoid duplication of the display). For such groups we add a
 737    * composite type name, e.g.
 738    * <p>
 739    * IUPredWS (Long), IUPredWS (Short)
 740    *
 741    * @param seq
 742    */
 743   protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
 744           List<SequenceI> forSequences)
 745   {
 746     showMenu.removeAll();
 747     hideMenu.removeAll();
 748
 749     final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
 750     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
 751     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
 752             false);
 753     showMenu.addSeparator();
 754     hideMenu.addSeparator();
 755
 756     final AlignmentAnnotation[] annotations = ap.getAlignment()
 757             .getAlignmentAnnotation();
 758
 759     /*
 760      * Find shown/hidden annotations types, distinguished by source (calcId),
 761      * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
 762      * the insertion order, which is the order of the annotations on the
 763      * alignment.
 764      */
 765     Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
 766     Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
 767     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
 768             hiddenTypes,
 769             AlignmentAnnotationUtils.asList(annotations),
 770             forSequences);
 771
 772     for (String calcId : hiddenTypes.keySet())
 773     {
 774       for (List<String> type : hiddenTypes.get(calcId))
 775       {
 776         addAnnotationTypeToShowHide(showMenu, forSequences,
 777                 calcId, type, false, true);
 778       }
 779     }
 780     // grey out 'show annotations' if none are hidden
 781     showMenu.setEnabled(!hiddenTypes.isEmpty());
 782
 783     for (String calcId : shownTypes.keySet())
 784     {
 785       for (List<String> type : shownTypes.get(calcId))
 786       {
 787         addAnnotationTypeToShowHide(hideMenu, forSequences,
 788                 calcId, type, false, false);
 789       }
 790     }
 791     // grey out 'hide annotations' if none are shown
 792     hideMenu.setEnabled(!shownTypes.isEmpty());
 793   }
 794
 795   /**
 796    * Returns a list of sequences - either the current selection group (if there
 797    * is one), else the specified single sequence.
 798    *
 799    * @param seq
 800    * @return
 801    */
 802   protected List<SequenceI> getSequenceScope(SequenceI seq)
 803   {
 804     List<SequenceI> forSequences = null;
 805     final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
 806     if (selectionGroup != null && selectionGroup.getSize() > 0)
 807     {
 808       forSequences = selectionGroup.getSequences();
 809     }
 810     else
 811     {
 812       forSequences = seq == null ? Collections.<SequenceI> emptyList()
 813               : Arrays.asList(seq);
 814     }
 815     return forSequences;
 816   }
 817
 818   /**
 819    * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
 820    * menus.
 821    *
 822    * @param showOrHideMenu
 823    *          the menu to add to
 824    * @param forSequences
 825    *          the sequences whose annotations may be shown or hidden
 826    * @param calcId
 827    * @param types
 828    *          the label to add
 829    * @param allTypes
 830    *          if true this is a special label meaning 'All'
 831    * @param actionIsShow
 832    *          if true, the select menu item action is to show the annotation
 833    *          type, else hide
 834    */
 835   protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
 836           final List<SequenceI> forSequences, String calcId,
 837           final List<String> types, final boolean allTypes,
 838           final boolean actionIsShow)
 839   {
 840     String label = types.toString(); // [a, b, c]
 841     label = label.substring(1, label.length() - 1); // a, b, c
 842     final JMenuItem item = new JMenuItem(label);
 843     item.setToolTipText(calcId);
 844     item.addActionListener(new java.awt.event.ActionListener()
 845     {
 846       @Override
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
 850                 forSequences, allTypes, actionIsShow);
 851         refresh();
 852       }
 853     });
 854     showOrHideMenu.add(item);
 855   }
 856
 857   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 858   {
 859
 860     // TODO: usability: thread off the generation of group url content so root
 861     // menu appears asap
 862     // sequence only URLs
 863     // ID/regex match URLs
 864     groupLinksMenu = new JMenu(
 865             MessageManager.getString("action.group_link"));
 866     JMenu[] linkMenus = new JMenu[]
 867     { null, new JMenu(MessageManager.getString("action.ids")),
 868         new JMenu(MessageManager.getString("action.sequences")),
 869         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
 870                                                                        // types
 871                                                                        // of url
 872                                                                        // that
 873                                                                        // might
 874                                                                        // be
 875     // created.
 876     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 877     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 878     Hashtable commonDbrefs = new Hashtable();
 879     for (int sq = 0; sq < seqs.length; sq++)
 880     {
 881
 882       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 883               .findPosition(sg.getEndRes());
 884       // just collect ids from dataset sequence
 885       // TODO: check if IDs collected from selecton group intersects with the
 886       // current selection, too
 887       SequenceI sqi = seqs[sq];
 888       while (sqi.getDatasetSequence() != null)
 889       {
 890         sqi = sqi.getDatasetSequence();
 891       }
 892       DBRefEntry[] dbr = sqi.getDBRef();
 893       if (dbr != null && dbr.length > 0)
 894       {
 895         for (int d = 0; d < dbr.length; d++)
 896         {
 897           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 898           Object[] sarray = (Object[]) commonDbrefs.get(src);
 899           if (sarray == null)
 900           {
 901             sarray = new Object[2];
 902             sarray[0] = new int[]
 903             { 0 };
 904             sarray[1] = new String[seqs.length];
 905
 906             commonDbrefs.put(src, sarray);
 907           }
 908
 909           if (((String[]) sarray[1])[sq] == null)
 910           {
 911             if (!dbr[d].hasMap()
 912                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 913             {
 914               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 915               ((int[]) sarray[0])[0]++;
 916             }
 917           }
 918         }
 919       }
 920     }
 921     // now create group links for all distinct ID/sequence sets.
 922     boolean addMenu = false; // indicates if there are any group links to give
 923                              // to user
 924     for (int i = 0; i < groupLinks.size(); i++)
 925     {
 926       String link = groupLinks.elementAt(i).toString();
 927       GroupUrlLink urlLink = null;
 928       try
 929       {
 930         urlLink = new GroupUrlLink(link);
 931       } catch (Exception foo)
 932       {
 933         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 934                 + "'", foo);
 935         continue;
 936       }
 937       ;
 938       if (!urlLink.isValid())
 939       {
 940         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 941         continue;
 942       }
 943       final String label = urlLink.getLabel();
 944       boolean usingNames = false;
 945       // Now see which parts of the group apply for this URL
 946       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 947       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 948       String[] seqstr, ids; // input to makeUrl
 949       if (idset != null)
 950       {
 951         int numinput = ((int[]) idset[0])[0];
 952         String[] allids = ((String[]) idset[1]);
 953         seqstr = new String[numinput];
 954         ids = new String[numinput];
 955         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 956         {
 957           if (allids[sq] != null)
 958           {
 959             ids[idcount] = allids[sq];
 960             seqstr[idcount++] = idandseqs[1][sq];
 961           }
 962         }
 963       }
 964       else
 965       {
 966         // just use the id/seq set
 967         seqstr = idandseqs[1];
 968         ids = idandseqs[0];
 969         usingNames = true;
 970       }
 971       // and try and make the groupURL!
 972
 973       Object[] urlset = null;
 974       try
 975       {
 976         urlset = urlLink.makeUrlStubs(ids, seqstr,
 977                 "FromJalview" + System.currentTimeMillis(), false);
 978       } catch (UrlStringTooLongException e)
 979       {
 980       }
 981       if (urlset != null)
 982       {
 983         int type = urlLink.getGroupURLType() & 3;
 984         // first two bits ofurlLink type bitfield are sequenceids and sequences
 985         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 986         addshowLink(linkMenus[type], label
 987                 + (((type & 1) == 1) ? ("("
 988                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 989                 urlLink, urlset);
 990         addMenu = true;
 991       }
 992     }
 993     if (addMenu)
 994     {
 995       groupLinksMenu = new JMenu(
 996               MessageManager.getString("action.group_link"));
 997       for (int m = 0; m < linkMenus.length; m++)
 998       {
 999         if (linkMenus[m] != null
1000                 && linkMenus[m].getMenuComponentCount() > 0)
1001         {
1002           groupLinksMenu.add(linkMenus[m]);
1003         }
1004       }
1005
1006       groupMenu.add(groupLinksMenu);
1007     }
1008   }
1009
1010   /**
1011    * add a show URL menu item to the given linkMenu
1012    *
1013    * @param linkMenu
1014    * @param label
1015    *          - menu label string
1016    * @param url
1017    *          - url to open
1018    */
1019   private void addshowLink(JMenu linkMenu, String label, final String url)
1020   {
1021     JMenuItem item = new JMenuItem(label);
1022     item.setToolTipText(MessageManager.formatMessage(
1023             "label.open_url_param", new Object[]
1024             { url }));
1025     item.addActionListener(new java.awt.event.ActionListener()
1026     {
1027       @Override
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         new Thread(new Runnable()
1031         {
1032
1033           @Override
1034           public void run()
1035           {
1036             showLink(url);
1037           }
1038
1039         }).start();
1040       }
1041     });
1042
1043     linkMenu.add(item);
1044   }
1045
1046   /**
1047    * add a late bound groupURL item to the given linkMenu
1048    *
1049    * @param linkMenu
1050    * @param label
1051    *          - menu label string
1052    * @param urlgenerator
1053    *          GroupURLLink used to generate URL
1054    * @param urlstub
1055    *          Object array returned from the makeUrlStubs function.
1056    */
1057   private void addshowLink(JMenu linkMenu, String label,
1058           final GroupUrlLink urlgenerator, final Object[] urlstub)
1059   {
1060     JMenuItem item = new JMenuItem(label);
1061     item.setToolTipText(MessageManager.formatMessage(
1062             "label.open_url_seqs_param",
1063             new Object[]
1064             { urlgenerator.getUrl_prefix(),
1065                 urlgenerator.getNumberInvolved(urlstub) }));
1066     // TODO: put in info about what is being sent.
1067     item.addActionListener(new java.awt.event.ActionListener()
1068     {
1069       @Override
1070       public void actionPerformed(ActionEvent e)
1071       {
1072         new Thread(new Runnable()
1073         {
1074
1075           @Override
1076           public void run()
1077           {
1078             try
1079             {
1080               showLink(urlgenerator.constructFrom(urlstub));
1081             } catch (UrlStringTooLongException e)
1082             {
1083             }
1084           }
1085
1086         }).start();
1087       }
1088     });
1089
1090     linkMenu.add(item);
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @throws Exception
1097    *           DOCUMENT ME!
1098    */
1099   private void jbInit() throws Exception
1100   {
1101     groupMenu.setText(MessageManager.getString("label.group"));
1102     groupMenu.setText(MessageManager.getString("label.selection"));
1103     groupName.setText(MessageManager.getString("label.name"));
1104     groupName.addActionListener(new java.awt.event.ActionListener()
1105     {
1106       @Override
1107       public void actionPerformed(ActionEvent e)
1108       {
1109         groupName_actionPerformed();
1110       }
1111     });
1112     sequenceMenu.setText(MessageManager.getString("label.sequence"));
1113     sequenceName.setText(MessageManager
1114             .getString("label.edit_name_description"));
1115     sequenceName.addActionListener(new java.awt.event.ActionListener()
1116     {
1117       @Override
1118       public void actionPerformed(ActionEvent e)
1119       {
1120         sequenceName_actionPerformed();
1121       }
1122     });
1123     chooseAnnotations.setText(MessageManager
1124             .getString("label.choose_annotations") + "...");
1125     chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1126     {
1127       @Override
1128       public void actionPerformed(ActionEvent e)
1129       {
1130         chooseAnnotations_actionPerformed(e);
1131       }
1132     });
1133     sequenceDetails.setText(MessageManager
1134             .getString("label.sequence_details") + "...");
1135     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1136     {
1137       @Override
1138       public void actionPerformed(ActionEvent e)
1139       {
1140         sequenceDetails_actionPerformed();
1141       }
1142     });
1143     sequenceSelDetails.setText(MessageManager
1144             .getString("label.sequence_details") + "...");
1145     sequenceSelDetails
1146             .addActionListener(new java.awt.event.ActionListener()
1147             {
1148               @Override
1149               public void actionPerformed(ActionEvent e)
1150               {
1151                 sequenceSelectionDetails_actionPerformed();
1152               }
1153             });
1154     PIDColour.setFocusPainted(false);
1155     unGroupMenuItem
1156             .setText(MessageManager.getString("action.remove_group"));
1157     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1158     {
1159       @Override
1160       public void actionPerformed(ActionEvent e)
1161       {
1162         unGroupMenuItem_actionPerformed();
1163       }
1164     });
1165     createGroupMenuItem.setText(MessageManager
1166             .getString("action.create_group"));
1167     createGroupMenuItem
1168             .addActionListener(new java.awt.event.ActionListener()
1169             {
1170               @Override
1171               public void actionPerformed(ActionEvent e)
1172               {
1173                 createGroupMenuItem_actionPerformed();
1174               }
1175             });
1176
1177     outline.setText(MessageManager.getString("action.border_colour"));
1178     outline.addActionListener(new java.awt.event.ActionListener()
1179     {
1180       @Override
1181       public void actionPerformed(ActionEvent e)
1182       {
1183         outline_actionPerformed();
1184       }
1185     });
1186     nucleotideMenuItem
1187             .setText(MessageManager.getString("label.nucleotide"));
1188     nucleotideMenuItem.addActionListener(new ActionListener()
1189     {
1190       @Override
1191       public void actionPerformed(ActionEvent e)
1192       {
1193         nucleotideMenuItem_actionPerformed();
1194       }
1195     });
1196     colourMenu.setText(MessageManager.getString("label.group_colour"));
1197     showBoxes.setText(MessageManager.getString("action.boxes"));
1198     showBoxes.setState(true);
1199     showBoxes.addActionListener(new ActionListener()
1200     {
1201       @Override
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         showBoxes_actionPerformed();
1205       }
1206     });
1207     showText.setText(MessageManager.getString("action.text"));
1208     showText.setState(true);
1209     showText.addActionListener(new ActionListener()
1210     {
1211       @Override
1212       public void actionPerformed(ActionEvent e)
1213       {
1214         showText_actionPerformed();
1215       }
1216     });
1217     showColourText.setText(MessageManager.getString("label.colour_text"));
1218     showColourText.addActionListener(new ActionListener()
1219     {
1220       @Override
1221       public void actionPerformed(ActionEvent e)
1222       {
1223         showColourText_actionPerformed();
1224       }
1225     });
1226     displayNonconserved.setText(MessageManager
1227             .getString("label.show_non_conversed"));
1228     displayNonconserved.setState(true);
1229     displayNonconserved.addActionListener(new ActionListener()
1230     {
1231       @Override
1232       public void actionPerformed(ActionEvent e)
1233       {
1234         showNonconserved_actionPerformed();
1235       }
1236     });
1237     editMenu.setText(MessageManager.getString("action.edit"));
1238     cut.setText(MessageManager.getString("action.cut"));
1239     cut.addActionListener(new ActionListener()
1240     {
1241       @Override
1242       public void actionPerformed(ActionEvent e)
1243       {
1244         cut_actionPerformed();
1245       }
1246     });
1247     upperCase.setText(MessageManager.getString("label.to_upper_case"));
1248     upperCase.addActionListener(new ActionListener()
1249     {
1250       @Override
1251       public void actionPerformed(ActionEvent e)
1252       {
1253         changeCase(e);
1254       }
1255     });
1256     copy.setText(MessageManager.getString("action.copy"));
1257     copy.addActionListener(new ActionListener()
1258     {
1259       @Override
1260       public void actionPerformed(ActionEvent e)
1261       {
1262         copy_actionPerformed();
1263       }
1264     });
1265     lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1266     lowerCase.addActionListener(new ActionListener()
1267     {
1268       @Override
1269       public void actionPerformed(ActionEvent e)
1270       {
1271         changeCase(e);
1272       }
1273     });
1274     toggle.setText(MessageManager.getString("label.toggle_case"));
1275     toggle.addActionListener(new ActionListener()
1276     {
1277       @Override
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         changeCase(e);
1281       }
1282     });
1283     pdbMenu.setText(MessageManager
1284             .getString("label.associate_structure_with_sequence"));
1285     pdbFromFile.setText(MessageManager.getString("label.from_file"));
1286     pdbFromFile.addActionListener(new ActionListener()
1287     {
1288       @Override
1289       public void actionPerformed(ActionEvent e)
1290       {
1291         pdbFromFile_actionPerformed();
1292       }
1293     });
1294
1295     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1296     enterPDB.addActionListener(new ActionListener()
1297     {
1298       @Override
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         enterPDB_actionPerformed();
1302       }
1303     });
1304     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1305     discoverPDB.addActionListener(new ActionListener()
1306     {
1307       @Override
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         discoverPDB_actionPerformed();
1311       }
1312     });
1313     outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1314             + "...");
1315     seqShowAnnotationsMenu.setText(MessageManager
1316             .getString("label.show_annotations"));
1317     seqHideAnnotationsMenu.setText(MessageManager
1318             .getString("label.hide_annotations"));
1319     groupShowAnnotationsMenu.setText(MessageManager
1320             .getString("label.show_annotations"));
1321     groupHideAnnotationsMenu.setText(MessageManager
1322             .getString("label.hide_annotations"));
1323     sequenceFeature.setText(MessageManager
1324             .getString("label.create_sequence_feature"));
1325     sequenceFeature.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         sequenceFeature_actionPerformed();
1331       }
1332     });
1333     textColour.setText(MessageManager.getString("label.text_colour"));
1334     textColour.addActionListener(new ActionListener()
1335     {
1336       @Override
1337       public void actionPerformed(ActionEvent e)
1338       {
1339         textColour_actionPerformed();
1340       }
1341     });
1342     jMenu1.setText(MessageManager.getString("label.group"));
1343     proteinStructureMenu.setText(MessageManager
1344             .getString("label.view_protein_structure"));
1345     proteinStructureMenu.addActionListener(new ActionListener()
1346     {
1347       @Override
1348       public void actionPerformed(ActionEvent actionEvent)
1349       {
1350         SequenceI[] selectedSeqs = new SequenceI[]
1351         { sequence };
1352         if (ap.av.getSelectionGroup() != null)
1353         {
1354           selectedSeqs = ap.av.getSequenceSelection();
1355         }
1356         new StructureChooser(selectedSeqs, sequence, ap);
1357       }
1358     });
1359
1360     rnaStructureMenu.setText(MessageManager
1361             .getString("label.view_rna_structure"));
1362
1363     // colStructureMenu.setText("Colour By Structure");
1364     editSequence.setText(MessageManager.getString("label.edit_sequence")
1365             + "...");
1366     editSequence.addActionListener(new ActionListener()
1367     {
1368       @Override
1369       public void actionPerformed(ActionEvent actionEvent)
1370       {
1371         editSequence_actionPerformed(actionEvent);
1372       }
1373     });
1374     makeReferenceSeq.setText(MessageManager
1375             .getString("label.mark_as_representative"));
1376     makeReferenceSeq.addActionListener(new ActionListener()
1377     {
1378
1379       @Override
1380       public void actionPerformed(ActionEvent actionEvent)
1381       {
1382         makeReferenceSeq_actionPerformed(actionEvent);
1383
1384       }
1385     });
1386     hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
1387     hideInsertions.addActionListener(new ActionListener()
1388     {
1389
1390       @Override
1391       public void actionPerformed(ActionEvent e)
1392       {
1393         hideInsertions_actionPerformed(e);
1394       }
1395     });
1396     /*
1397      * annotationMenuItem.setText("By Annotation");
1398      * annotationMenuItem.addActionListener(new ActionListener() { public void
1399      * actionPerformed(ActionEvent actionEvent) {
1400      * annotationMenuItem_actionPerformed(actionEvent); } });
1401      */
1402     groupMenu.add(sequenceSelDetails);
1403     add(groupMenu);
1404     add(sequenceMenu);
1405     add(rnaStructureMenu);
1406     add(proteinStructureMenu);
1407     if (sequence!=null)
1408     {
1409       add(hideInsertions);
1410     }
1411     // annotations configuration panel suppressed for now
1412     // groupMenu.add(chooseAnnotations);
1413
1414     /*
1415      * Add show/hide annotations to the Sequence menu, and to the Selection menu
1416      * (if a selection group is in force).
1417      */
1418     sequenceMenu.add(seqShowAnnotationsMenu);
1419     sequenceMenu.add(seqHideAnnotationsMenu);
1420     sequenceMenu.add(seqAddReferenceAnnotations);
1421     groupMenu.add(groupShowAnnotationsMenu);
1422     groupMenu.add(groupHideAnnotationsMenu);
1423     groupMenu.add(groupAddReferenceAnnotations);
1424     groupMenu.add(editMenu);
1425     groupMenu.add(outputMenu);
1426     groupMenu.add(sequenceFeature);
1427     groupMenu.add(createGroupMenuItem);
1428     groupMenu.add(unGroupMenuItem);
1429     groupMenu.add(jMenu1);
1430     sequenceMenu.add(sequenceName);
1431     sequenceMenu.add(sequenceDetails);
1432     sequenceMenu.add(makeReferenceSeq);
1433     colourMenu.add(textColour);
1434     colourMenu.add(noColourmenuItem);
1435     colourMenu.add(clustalColour);
1436     colourMenu.add(BLOSUM62Colour);
1437     colourMenu.add(PIDColour);
1438     colourMenu.add(zappoColour);
1439     colourMenu.add(taylorColour);
1440     colourMenu.add(hydrophobicityColour);
1441     colourMenu.add(helixColour);
1442     colourMenu.add(strandColour);
1443     colourMenu.add(turnColour);
1444     colourMenu.add(buriedColour);
1445     colourMenu.add(nucleotideMenuItem);
1446     if (ap.getAlignment().isNucleotide())
1447     {
1448       // JBPNote - commented since the colourscheme isn't functional
1449       colourMenu.add(purinePyrimidineColour);
1450     }
1451     colourMenu.add(userDefinedColour);
1452
1453     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1454     {
1455       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1456               .getUserColourSchemes().keys();
1457
1458       while (userColours.hasMoreElements())
1459       {
1460         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1461         item.addActionListener(new ActionListener()
1462         {
1463           @Override
1464           public void actionPerformed(ActionEvent evt)
1465           {
1466             userDefinedColour_actionPerformed(evt);
1467           }
1468         });
1469         colourMenu.add(item);
1470       }
1471     }
1472
1473     colourMenu.addSeparator();
1474     colourMenu.add(abovePIDColour);
1475     colourMenu.add(conservationMenuItem);
1476     editMenu.add(copy);
1477     editMenu.add(cut);
1478     editMenu.add(editSequence);
1479     editMenu.add(upperCase);
1480     editMenu.add(lowerCase);
1481     editMenu.add(toggle);
1482     pdbMenu.add(pdbFromFile);
1483     // JBPNote: These shouldn't be added here - should appear in a generic
1484     // 'apply web service to this sequence menu'
1485     // pdbMenu.add(RNAFold);
1486     // pdbMenu.add(ContraFold);
1487     pdbMenu.add(enterPDB);
1488     pdbMenu.add(discoverPDB);
1489     jMenu1.add(groupName);
1490     jMenu1.add(colourMenu);
1491     jMenu1.add(showBoxes);
1492     jMenu1.add(showText);
1493     jMenu1.add(showColourText);
1494     jMenu1.add(outline);
1495     jMenu1.add(displayNonconserved);
1496     noColourmenuItem.setText(MessageManager.getString("label.none"));
1497     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1498     {
1499       @Override
1500       public void actionPerformed(ActionEvent e)
1501       {
1502         noColourmenuItem_actionPerformed();
1503       }
1504     });
1505
1506     clustalColour.setText(MessageManager
1507             .getString("label.clustalx_colours"));
1508     clustalColour.addActionListener(new java.awt.event.ActionListener()
1509     {
1510       @Override
1511       public void actionPerformed(ActionEvent e)
1512       {
1513         clustalColour_actionPerformed();
1514       }
1515     });
1516     zappoColour.setText(MessageManager.getString("label.zappo"));
1517     zappoColour.addActionListener(new java.awt.event.ActionListener()
1518     {
1519       @Override
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         zappoColour_actionPerformed();
1523       }
1524     });
1525     taylorColour.setText(MessageManager.getString("label.taylor"));
1526     taylorColour.addActionListener(new java.awt.event.ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         taylorColour_actionPerformed();
1532       }
1533     });
1534     hydrophobicityColour.setText(MessageManager
1535             .getString("label.hydrophobicity"));
1536     hydrophobicityColour
1537             .addActionListener(new java.awt.event.ActionListener()
1538             {
1539               @Override
1540               public void actionPerformed(ActionEvent e)
1541               {
1542                 hydrophobicityColour_actionPerformed();
1543               }
1544             });
1545     helixColour.setText(MessageManager.getString("label.helix_propensity"));
1546     helixColour.addActionListener(new java.awt.event.ActionListener()
1547     {
1548       @Override
1549       public void actionPerformed(ActionEvent e)
1550       {
1551         helixColour_actionPerformed();
1552       }
1553     });
1554     strandColour.setText(MessageManager
1555             .getString("label.strand_propensity"));
1556     strandColour.addActionListener(new java.awt.event.ActionListener()
1557     {
1558       @Override
1559       public void actionPerformed(ActionEvent e)
1560       {
1561         strandColour_actionPerformed();
1562       }
1563     });
1564     turnColour.setText(MessageManager.getString("label.turn_propensity"));
1565     turnColour.addActionListener(new java.awt.event.ActionListener()
1566     {
1567       @Override
1568       public void actionPerformed(ActionEvent e)
1569       {
1570         turnColour_actionPerformed();
1571       }
1572     });
1573     buriedColour.setText(MessageManager.getString("label.buried_index"));
1574     buriedColour.addActionListener(new java.awt.event.ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         buriedColour_actionPerformed();
1580       }
1581     });
1582     abovePIDColour.setText(MessageManager
1583             .getString("label.above_identity_percentage"));
1584     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1585     {
1586       @Override
1587       public void actionPerformed(ActionEvent e)
1588       {
1589         abovePIDColour_actionPerformed();
1590       }
1591     });
1592     userDefinedColour.setText(MessageManager
1593             .getString("action.user_defined"));
1594     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1595     {
1596       @Override
1597       public void actionPerformed(ActionEvent e)
1598       {
1599         userDefinedColour_actionPerformed(e);
1600       }
1601     });
1602     PIDColour
1603             .setText(MessageManager.getString("label.percentage_identity"));
1604     PIDColour.addActionListener(new java.awt.event.ActionListener()
1605     {
1606       @Override
1607       public void actionPerformed(ActionEvent e)
1608       {
1609         PIDColour_actionPerformed();
1610       }
1611     });
1612     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1613     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1614     {
1615       @Override
1616       public void actionPerformed(ActionEvent e)
1617       {
1618         BLOSUM62Colour_actionPerformed();
1619       }
1620     });
1621     purinePyrimidineColour.setText(MessageManager
1622             .getString("label.purine_pyrimidine"));
1623     purinePyrimidineColour
1624             .addActionListener(new java.awt.event.ActionListener()
1625             {
1626               @Override
1627               public void actionPerformed(ActionEvent e)
1628               {
1629                 purinePyrimidineColour_actionPerformed();
1630               }
1631             });
1632
1633     /*
1634      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1635      * public void actionPerformed(ActionEvent e) {
1636      * covariationColour_actionPerformed(); } });
1637      */
1638
1639     conservationMenuItem.setText(MessageManager
1640             .getString("label.conservation"));
1641     conservationMenuItem
1642             .addActionListener(new java.awt.event.ActionListener()
1643             {
1644               @Override
1645               public void actionPerformed(ActionEvent e)
1646               {
1647                 conservationMenuItem_actionPerformed();
1648               }
1649             });
1650   }
1651
1652   /**
1653    * Check for any annotations on the underlying dataset sequences (for the
1654    * current selection group) which are not 'on the alignment'.If any are found,
1655    * enable the option to add them to the alignment. The criteria for 'on the
1656    * alignment' is finding an alignment annotation on the alignment, matched on
1657    * calcId, label and sequenceRef.
1658    *
1659    * A tooltip is also constructed that displays the source (calcId) and type
1660    * (label) of the annotations that can be added.
1661    *
1662    * @param menuItem
1663    * @param forSequences
1664    */
1665   protected void configureReferenceAnnotationsMenu(
1666           JMenuItem menuItem, List<SequenceI> forSequences)
1667   {
1668     menuItem.setEnabled(false);
1669
1670     /*
1671      * Temporary store to hold distinct calcId / type pairs for the tooltip.
1672      * Using TreeMap means calcIds are shown in alphabetical order.
1673      */
1674     Map<String, String> tipEntries = new TreeMap<String, String>();
1675     final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1676     AlignmentI al = this.ap.av.getAlignment();
1677     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1678             tipEntries, candidates, al);
1679     if (!candidates.isEmpty())
1680     {
1681       StringBuilder tooltip = new StringBuilder(64);
1682       tooltip.append(MessageManager.getString("label.add_annotations_for"));
1683
1684       /*
1685        * Found annotations that could be added. Enable the menu item, and
1686        * configure its tooltip and action.
1687        */
1688       menuItem.setEnabled(true);
1689       for (String calcId : tipEntries.keySet())
1690       {
1691         tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1692       }
1693       String tooltipText = JvSwingUtils.wrapTooltip(true,
1694               tooltip.toString());
1695       menuItem.setToolTipText(tooltipText);
1696
1697       menuItem.addActionListener(new ActionListener()
1698       {
1699         @Override
1700         public void actionPerformed(ActionEvent e)
1701         {
1702           addReferenceAnnotations_actionPerformed(candidates);
1703         }
1704       });
1705     }
1706   }
1707
1708   /**
1709    * Add annotations to the sequences and to the alignment.
1710    *
1711    * @param candidates
1712    *          a map whose keys are sequences on the alignment, and values a list
1713    *          of annotations to add to each sequence
1714    */
1715   protected void addReferenceAnnotations_actionPerformed(
1716           Map<SequenceI, List<AlignmentAnnotation>> candidates)
1717   {
1718     final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1719     final AlignmentI alignment = this.ap.getAlignment();
1720     AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1721             selectionGroup);
1722     refresh();
1723   }
1724
1725   protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1726   {
1727     if (!ap.av.getAlignment().hasSeqrep())
1728     {
1729       // initialise the display flags so the user sees something happen
1730       ap.av.setDisplayReferenceSeq(true);
1731       ap.av.setColourByReferenceSeq(true);
1732       ap.av.getAlignment().setSeqrep(sequence);
1733     }
1734     else
1735     {
1736       if (ap.av.getAlignment().getSeqrep() == sequence)
1737       {
1738         ap.av.getAlignment().setSeqrep(null);
1739       }
1740       else
1741       {
1742         ap.av.getAlignment().setSeqrep(sequence);
1743       }
1744     }
1745     refresh();
1746   }
1747
1748   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1749   {
1750     if (sequence != null)
1751     {
1752       ColumnSelection cs = ap.av.getColumnSelection();
1753       if (cs == null)
1754       {
1755         cs = new ColumnSelection();
1756       }
1757       cs.hideInsertionsFor(sequence);
1758       ap.av.setColumnSelection(cs);
1759     }
1760     refresh();
1761   }
1762   protected void sequenceSelectionDetails_actionPerformed()
1763   {
1764     createSequenceDetailsReport(ap.av.getSequenceSelection());
1765   }
1766
1767   protected void sequenceDetails_actionPerformed()
1768   {
1769     createSequenceDetailsReport(new SequenceI[]
1770     { sequence });
1771   }
1772
1773   public void createSequenceDetailsReport(SequenceI[] sequences)
1774   {
1775     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1776     StringBuffer contents = new StringBuffer();
1777     for (SequenceI seq : sequences)
1778     {
1779       contents.append("<p><h2>"
1780               + MessageManager
1781                       .formatMessage(
1782                               "label.create_sequence_details_report_annotation_for",
1783                               new Object[]
1784                               { seq.getDisplayId(true) }) + "</h2></p><p>");
1785       new SequenceAnnotationReport(null)
1786               .createSequenceAnnotationReport(
1787                       contents,
1788                       seq,
1789                       true,
1790                       true,
1791                       false,
1792                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1793                               .getSeqPanel().seqCanvas.fr
1794                               .getMinMax()
1795                               : null);
1796       contents.append("</p>");
1797     }
1798     cap.setText("<html>" + contents.toString() + "</html>");
1799
1800     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1801             "label.sequence_details_for",
1802             (sequences.length == 1 ? new Object[]
1803             { sequences[0].getDisplayId(true) } : new Object[]
1804             { MessageManager.getString("label.selection") })), 500, 400);
1805
1806   }
1807
1808   protected void showNonconserved_actionPerformed()
1809   {
1810     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1811     refresh();
1812   }
1813
1814   /**
1815    * call to refresh view after settings change
1816    */
1817   void refresh()
1818   {
1819     ap.updateAnnotation();
1820     ap.paintAlignment(true);
1821
1822     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1823   }
1824
1825   /**
1826    * DOCUMENT ME!
1827    *
1828    * @param e
1829    *          DOCUMENT ME!
1830    */
1831   protected void clustalColour_actionPerformed()
1832   {
1833     SequenceGroup sg = getGroup();
1834     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1835     refresh();
1836   }
1837
1838   /**
1839    * DOCUMENT ME!
1840    *
1841    * @param e
1842    *          DOCUMENT ME!
1843    */
1844   protected void zappoColour_actionPerformed()
1845   {
1846     getGroup().cs = new ZappoColourScheme();
1847     refresh();
1848   }
1849
1850   /**
1851    * DOCUMENT ME!
1852    *
1853    * @param e
1854    *          DOCUMENT ME!
1855    */
1856   protected void taylorColour_actionPerformed()
1857   {
1858     getGroup().cs = new TaylorColourScheme();
1859     refresh();
1860   }
1861
1862   /**
1863    * DOCUMENT ME!
1864    *
1865    * @param e
1866    *          DOCUMENT ME!
1867    */
1868   protected void hydrophobicityColour_actionPerformed()
1869   {
1870     getGroup().cs = new HydrophobicColourScheme();
1871     refresh();
1872   }
1873
1874   /**
1875    * DOCUMENT ME!
1876    *
1877    * @param e
1878    *          DOCUMENT ME!
1879    */
1880   protected void helixColour_actionPerformed()
1881   {
1882     getGroup().cs = new HelixColourScheme();
1883     refresh();
1884   }
1885
1886   /**
1887    * DOCUMENT ME!
1888    *
1889    * @param e
1890    *          DOCUMENT ME!
1891    */
1892   protected void strandColour_actionPerformed()
1893   {
1894     getGroup().cs = new StrandColourScheme();
1895     refresh();
1896   }
1897
1898   /**
1899    * DOCUMENT ME!
1900    *
1901    * @param e
1902    *          DOCUMENT ME!
1903    */
1904   protected void turnColour_actionPerformed()
1905   {
1906     getGroup().cs = new TurnColourScheme();
1907     refresh();
1908   }
1909
1910   /**
1911    * DOCUMENT ME!
1912    *
1913    * @param e
1914    *          DOCUMENT ME!
1915    */
1916   protected void buriedColour_actionPerformed()
1917   {
1918     getGroup().cs = new BuriedColourScheme();
1919     refresh();
1920   }
1921
1922   /**
1923    * DOCUMENT ME!
1924    *
1925    * @param e
1926    *          DOCUMENT ME!
1927    */
1928   public void nucleotideMenuItem_actionPerformed()
1929   {
1930     getGroup().cs = new NucleotideColourScheme();
1931     refresh();
1932   }
1933
1934   protected void purinePyrimidineColour_actionPerformed()
1935   {
1936     getGroup().cs = new PurinePyrimidineColourScheme();
1937     refresh();
1938   }
1939
1940   /*
1941    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1942    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1943    */
1944   /**
1945    * DOCUMENT ME!
1946    *
1947    * @param e
1948    *          DOCUMENT ME!
1949    */
1950   protected void abovePIDColour_actionPerformed()
1951   {
1952     SequenceGroup sg = getGroup();
1953     if (sg.cs == null)
1954     {
1955       return;
1956     }
1957
1958     if (abovePIDColour.isSelected())
1959     {
1960       sg.cs.setConsensus(AAFrequency.calculate(
1961               sg.getSequences(ap.av.getHiddenRepSequences()),
1962               sg.getStartRes(), sg.getEndRes() + 1));
1963
1964       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1965               .getName());
1966
1967       sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1968
1969       SliderPanel.showPIDSlider();
1970     }
1971     else
1972     // remove PIDColouring
1973     {
1974       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1975     }
1976
1977     refresh();
1978   }
1979
1980   /**
1981    * DOCUMENT ME!
1982    *
1983    * @param e
1984    *          DOCUMENT ME!
1985    */
1986   protected void userDefinedColour_actionPerformed(ActionEvent e)
1987   {
1988     SequenceGroup sg = getGroup();
1989
1990     if (e.getSource().equals(userDefinedColour))
1991     {
1992       new UserDefinedColours(ap, sg);
1993     }
1994     else
1995     {
1996       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1997               .getUserColourSchemes().get(e.getActionCommand());
1998
1999       sg.cs = udc;
2000     }
2001     refresh();
2002   }
2003
2004   /**
2005    * Open a panel where the user can choose which types of sequence annotation
2006    * to show or hide.
2007    *
2008    * @param e
2009    */
2010   protected void chooseAnnotations_actionPerformed(ActionEvent e)
2011   {
2012     // todo correct way to guard against opening a duplicate panel?
2013     new AnnotationChooser(ap);
2014   }
2015
2016   /**
2017    * DOCUMENT ME!
2018    *
2019    * @param e
2020    *          DOCUMENT ME!
2021    */
2022   protected void PIDColour_actionPerformed()
2023   {
2024     SequenceGroup sg = getGroup();
2025     sg.cs = new PIDColourScheme();
2026     sg.cs.setConsensus(AAFrequency.calculate(
2027             sg.getSequences(ap.av.getHiddenRepSequences()),
2028             sg.getStartRes(), sg.getEndRes() + 1));
2029     refresh();
2030   }
2031
2032   /**
2033    * DOCUMENT ME!
2034    *
2035    * @param e
2036    *          DOCUMENT ME!
2037    */
2038   protected void BLOSUM62Colour_actionPerformed()
2039   {
2040     SequenceGroup sg = getGroup();
2041
2042     sg.cs = new Blosum62ColourScheme();
2043
2044     sg.cs.setConsensus(AAFrequency.calculate(
2045             sg.getSequences(ap.av.getHiddenRepSequences()),
2046             sg.getStartRes(), sg.getEndRes() + 1));
2047
2048     refresh();
2049   }
2050
2051   /**
2052    * DOCUMENT ME!
2053    *
2054    * @param e
2055    *          DOCUMENT ME!
2056    */
2057   protected void noColourmenuItem_actionPerformed()
2058   {
2059     getGroup().cs = null;
2060     refresh();
2061   }
2062
2063   /**
2064    * DOCUMENT ME!
2065    *
2066    * @param e
2067    *          DOCUMENT ME!
2068    */
2069   protected void conservationMenuItem_actionPerformed()
2070   {
2071     SequenceGroup sg = getGroup();
2072     if (sg.cs == null)
2073     {
2074       return;
2075     }
2076
2077     if (conservationMenuItem.isSelected())
2078     {
2079       // JBPNote: Conservation name shouldn't be i18n translated
2080       Conservation c = new Conservation("Group",
2081               ResidueProperties.propHash, 3, sg.getSequences(ap.av
2082                       .getHiddenRepSequences()), sg.getStartRes(),
2083               sg.getEndRes() + 1);
2084
2085       c.calculate();
2086       c.verdict(false, ap.av.getConsPercGaps());
2087
2088       sg.cs.setConservation(c);
2089
2090       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2091       SliderPanel.showConservationSlider();
2092     }
2093     else
2094     // remove ConservationColouring
2095     {
2096       sg.cs.setConservation(null);
2097     }
2098
2099     refresh();
2100   }
2101
2102   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2103   {
2104     SequenceGroup sg = getGroup();
2105     if (sg == null)
2106     {
2107       return;
2108     }
2109
2110     AnnotationColourGradient acg = new AnnotationColourGradient(
2111             sequence.getAnnotation()[0], null,
2112             AnnotationColourGradient.NO_THRESHOLD);
2113
2114     acg.setPredefinedColours(true);
2115     sg.cs = acg;
2116
2117     refresh();
2118   }
2119
2120   /**
2121    * DOCUMENT ME!
2122    *
2123    * @param e
2124    *          DOCUMENT ME!
2125    */
2126   protected void groupName_actionPerformed()
2127   {
2128
2129     SequenceGroup sg = getGroup();
2130     EditNameDialog dialog = new EditNameDialog(sg.getName(),
2131             sg.getDescription(), "       "
2132                     + MessageManager.getString("label.group_name") + " ",
2133             MessageManager.getString("label.group_description") + " ",
2134             MessageManager.getString("label.edit_group_name_description"),
2135             ap.alignFrame);
2136
2137     if (!dialog.accept)
2138     {
2139       return;
2140     }
2141
2142     sg.setName(dialog.getName());
2143     sg.setDescription(dialog.getDescription());
2144     refresh();
2145   }
2146
2147   /**
2148    * Get selection group - adding it to the alignment if necessary.
2149    *
2150    * @return sequence group to operate on
2151    */
2152   SequenceGroup getGroup()
2153   {
2154     SequenceGroup sg = ap.av.getSelectionGroup();
2155     // this method won't add a new group if it already exists
2156     if (sg != null)
2157     {
2158       ap.av.getAlignment().addGroup(sg);
2159     }
2160
2161     return sg;
2162   }
2163
2164   /**
2165    * DOCUMENT ME!
2166    *
2167    * @param e
2168    *          DOCUMENT ME!
2169    */
2170   void sequenceName_actionPerformed()
2171   {
2172     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2173             sequence.getDescription(),
2174             "       " + MessageManager.getString("label.sequence_name")
2175                     + " ",
2176             MessageManager.getString("label.sequence_description") + " ",
2177             MessageManager
2178                     .getString("label.edit_sequence_name_description"),
2179             ap.alignFrame);
2180
2181     if (!dialog.accept)
2182     {
2183       return;
2184     }
2185
2186     if (dialog.getName() != null)
2187     {
2188       if (dialog.getName().indexOf(" ") > -1)
2189       {
2190         JOptionPane
2191                 .showMessageDialog(
2192                         ap,
2193                         MessageManager
2194                                 .getString("label.spaces_converted_to_backslashes"),
2195                         MessageManager
2196                                 .getString("label.no_spaces_allowed_sequence_name"),
2197                         JOptionPane.WARNING_MESSAGE);
2198       }
2199
2200       sequence.setName(dialog.getName().replace(' ', '_'));
2201       ap.paintAlignment(false);
2202     }
2203
2204     sequence.setDescription(dialog.getDescription());
2205
2206     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2207             .getSequences());
2208
2209   }
2210
2211   /**
2212    * DOCUMENT ME!
2213    *
2214    * @param e
2215    *          DOCUMENT ME!
2216    */
2217   void unGroupMenuItem_actionPerformed()
2218   {
2219     SequenceGroup sg = ap.av.getSelectionGroup();
2220     ap.av.getAlignment().deleteGroup(sg);
2221     ap.av.setSelectionGroup(null);
2222     refresh();
2223   }
2224
2225   void createGroupMenuItem_actionPerformed()
2226   {
2227     getGroup(); // implicitly creates group - note - should apply defaults / use
2228                 // standard alignment window logic for this
2229     refresh();
2230   }
2231
2232   /**
2233    * DOCUMENT ME!
2234    *
2235    * @param e
2236    *          DOCUMENT ME!
2237    */
2238   protected void outline_actionPerformed()
2239   {
2240     SequenceGroup sg = getGroup();
2241     Color col = JColorChooser.showDialog(this,
2242             MessageManager.getString("label.select_outline_colour"),
2243             Color.BLUE);
2244
2245     if (col != null)
2246     {
2247       sg.setOutlineColour(col);
2248     }
2249
2250     refresh();
2251   }
2252
2253   /**
2254    * DOCUMENT ME!
2255    *
2256    * @param e
2257    *          DOCUMENT ME!
2258    */
2259   public void showBoxes_actionPerformed()
2260   {
2261     getGroup().setDisplayBoxes(showBoxes.isSelected());
2262     refresh();
2263   }
2264
2265   /**
2266    * DOCUMENT ME!
2267    *
2268    * @param e
2269    *          DOCUMENT ME!
2270    */
2271   public void showText_actionPerformed()
2272   {
2273     getGroup().setDisplayText(showText.isSelected());
2274     refresh();
2275   }
2276
2277   /**
2278    * DOCUMENT ME!
2279    *
2280    * @param e
2281    *          DOCUMENT ME!
2282    */
2283   public void showColourText_actionPerformed()
2284   {
2285     getGroup().setColourText(showColourText.isSelected());
2286     refresh();
2287   }
2288
2289   public void showLink(String url)
2290   {
2291     try
2292     {
2293       jalview.util.BrowserLauncher.openURL(url);
2294     } catch (Exception ex)
2295     {
2296       JOptionPane.showInternalMessageDialog(Desktop.desktop,
2297               MessageManager.getString("label.web_browser_not_found_unix"),
2298               MessageManager.getString("label.web_browser_not_found"),
2299               JOptionPane.WARNING_MESSAGE);
2300
2301       ex.printStackTrace();
2302     }
2303   }
2304
2305   void hideSequences(boolean representGroup)
2306   {
2307     SequenceGroup sg = ap.av.getSelectionGroup();
2308     if (sg == null || sg.getSize() < 1)
2309     {
2310       ap.av.hideSequence(new SequenceI[]
2311       { sequence });
2312       return;
2313     }
2314
2315     ap.av.setSelectionGroup(null);
2316
2317     if (representGroup)
2318     {
2319       ap.av.hideRepSequences(sequence, sg);
2320
2321       return;
2322     }
2323
2324     int gsize = sg.getSize();
2325     SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
2326
2327     ap.av.hideSequence(hseqs);
2328     // refresh(); TODO: ? needed ?
2329     ap.av.sendSelection();
2330   }
2331
2332   public void copy_actionPerformed()
2333   {
2334     ap.alignFrame.copy_actionPerformed(null);
2335   }
2336
2337   public void cut_actionPerformed()
2338   {
2339     ap.alignFrame.cut_actionPerformed(null);
2340   }
2341
2342   void changeCase(ActionEvent e)
2343   {
2344     Object source = e.getSource();
2345     SequenceGroup sg = ap.av.getSelectionGroup();
2346
2347     if (sg != null)
2348     {
2349       List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2350               sg.getStartRes(),
2351               sg.getEndRes() + 1);
2352
2353       String description;
2354       int caseChange;
2355
2356       if (source == toggle)
2357       {
2358         description = MessageManager.getString("label.toggle_case");
2359         caseChange = ChangeCaseCommand.TOGGLE_CASE;
2360       }
2361       else if (source == upperCase)
2362       {
2363         description = MessageManager.getString("label.to_upper_case");
2364         caseChange = ChangeCaseCommand.TO_UPPER;
2365       }
2366       else
2367       {
2368         description = MessageManager.getString("label.to_lower_case");
2369         caseChange = ChangeCaseCommand.TO_LOWER;
2370       }
2371
2372       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2373               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2374               startEnd, caseChange);
2375
2376       ap.alignFrame.addHistoryItem(caseCommand);
2377
2378       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2379               .getSequences());
2380
2381     }
2382   }
2383
2384   public void outputText_actionPerformed(ActionEvent e)
2385   {
2386     CutAndPasteTransfer cap = new CutAndPasteTransfer();
2387     cap.setForInput(null);
2388     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2389             "label.alignment_output_command", new Object[]
2390             { e.getActionCommand() }), 600, 500);
2391
2392     String[] omitHidden = null;
2393
2394     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2395     // or we simply trust the user wants
2396     // wysiwig behaviour
2397
2398     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2399             ap.av, true));
2400   }
2401
2402   public void pdbFromFile_actionPerformed()
2403   {
2404     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2405             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2406     chooser.setFileView(new jalview.io.JalviewFileView());
2407     chooser.setDialogTitle(MessageManager.formatMessage(
2408             "label.select_pdb_file_for", new Object[]
2409             { sequence.getDisplayId(false) }));
2410     chooser.setToolTipText(MessageManager.formatMessage(
2411             "label.load_pdb_file_associate_with_sequence", new Object[]
2412             { sequence.getDisplayId(false) }));
2413
2414     int value = chooser.showOpenDialog(null);
2415
2416     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2417     {
2418       String choice = chooser.getSelectedFile().getPath();
2419       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2420       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2421               jalview.io.AppletFormatAdapter.FILE, sequence, true,
2422               Desktop.instance);
2423     }
2424
2425   }
2426
2427
2428   public void enterPDB_actionPerformed()
2429   {
2430     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2431             MessageManager.getString("label.enter_pdb_id"),
2432             MessageManager.getString("label.enter_pdb_id"),
2433             JOptionPane.QUESTION_MESSAGE);
2434
2435     if (id != null && id.length() > 0)
2436     {
2437       PDBEntry entry = new PDBEntry();
2438       entry.setId(id.toUpperCase());
2439       sequence.getDatasetSequence().addPDBId(entry);
2440     }
2441   }
2442
2443   public void discoverPDB_actionPerformed()
2444   {
2445
2446     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2447     { sequence }
2448             : ap.av.getSequenceSelection());
2449     Thread discpdb = new Thread(new Runnable()
2450     {
2451       @Override
2452       public void run()
2453       {
2454
2455         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2456                 .fetchDBRefs(false);
2457       }
2458
2459     });
2460     discpdb.start();
2461   }
2462
2463   public void sequenceFeature_actionPerformed()
2464   {
2465     SequenceGroup sg = ap.av.getSelectionGroup();
2466     if (sg == null)
2467     {
2468       return;
2469     }
2470
2471     int rsize = 0, gSize = sg.getSize();
2472     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2473     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2474
2475     for (int i = 0; i < gSize; i++)
2476     {
2477       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2478       int end = sg.findEndRes(sg.getSequenceAt(i));
2479       if (start <= end)
2480       {
2481         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2482         features[rsize] = new SequenceFeature(null, null, null, start, end,
2483                 "Jalview");
2484         rsize++;
2485       }
2486     }
2487     rseqs = new SequenceI[rsize];
2488     tfeatures = new SequenceFeature[rsize];
2489     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2490     System.arraycopy(features, 0, tfeatures, 0, rsize);
2491     features = tfeatures;
2492     seqs = rseqs;
2493     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2494             features, true, ap))
2495     {
2496       ap.alignFrame.setShowSeqFeatures(true);
2497       ap.highlightSearchResults(null);
2498     }
2499   }
2500
2501   public void textColour_actionPerformed()
2502   {
2503     SequenceGroup sg = getGroup();
2504     if (sg != null)
2505     {
2506       new TextColourChooser().chooseColour(ap, sg);
2507     }
2508   }
2509
2510   public void colourByStructure(String pdbid)
2511   {
2512     Annotation[] anots = ap.av.getStructureSelectionManager()
2513             .colourSequenceFromStructure(sequence, pdbid);
2514
2515     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2516             "Coloured by " + pdbid, anots);
2517
2518     ap.av.getAlignment().addAnnotation(an);
2519     an.createSequenceMapping(sequence, 0, true);
2520     // an.adjustForAlignment();
2521     ap.av.getAlignment().setAnnotationIndex(an, 0);
2522
2523     ap.adjustAnnotationHeight();
2524
2525     sequence.addAlignmentAnnotation(an);
2526
2527   }
2528
2529   public void editSequence_actionPerformed(ActionEvent actionEvent)
2530   {
2531     SequenceGroup sg = ap.av.getSelectionGroup();
2532
2533     if (sg != null)
2534     {
2535       if (sequence == null)
2536       {
2537         sequence = sg.getSequenceAt(0);
2538       }
2539
2540       EditNameDialog dialog = new EditNameDialog(
2541               sequence.getSequenceAsString(sg.getStartRes(),
2542                       sg.getEndRes() + 1), null,
2543               MessageManager.getString("label.edit_sequence"), null,
2544               MessageManager.getString("label.edit_sequence"),
2545               ap.alignFrame);
2546
2547       if (dialog.accept)
2548       {
2549         EditCommand editCommand = new EditCommand(
2550                 MessageManager.getString("label.edit_sequences"),
2551                 Action.REPLACE, dialog.getName().replace(' ',
2552                         ap.av.getGapCharacter()),
2553                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2554                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2555
2556         ap.alignFrame.addHistoryItem(editCommand);
2557
2558         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2559                 .getSequences());
2560       }
2561     }
2562   }
2563
2564 }