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.bin.Cache;
  28 import jalview.commands.ChangeCaseCommand;
  29 import jalview.commands.EditCommand;
  30 import jalview.commands.EditCommand.Action;
  31 import jalview.datamodel.AlignmentAnnotation;
  32 import jalview.datamodel.AlignmentI;
  33 import jalview.datamodel.Annotation;
  34 import jalview.datamodel.ColumnSelection;
  35 import jalview.datamodel.DBRefEntry;
  36 import jalview.datamodel.PDBEntry;
  37 import jalview.datamodel.Sequence;
  38 import jalview.datamodel.SequenceFeature;
  39 import jalview.datamodel.SequenceGroup;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.io.FormatAdapter;
  42 import jalview.io.SequenceAnnotationReport;
  43 import jalview.schemes.AnnotationColourGradient;
  44 import jalview.schemes.Blosum62ColourScheme;
  45 import jalview.schemes.BuriedColourScheme;
  46 import jalview.schemes.ClustalxColourScheme;
  47 import jalview.schemes.HelixColourScheme;
  48 import jalview.schemes.HydrophobicColourScheme;
  49 import jalview.schemes.NucleotideColourScheme;
  50 import jalview.schemes.PIDColourScheme;
  51 import jalview.schemes.PurinePyrimidineColourScheme;
  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.DBRefUtils;
  58 import jalview.util.GroupUrlLink;
  59 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  60 import jalview.util.MessageManager;
  61 import jalview.util.UrlLink;
  62
  63 import java.awt.Color;
  64 import java.awt.event.ActionEvent;
  65 import java.awt.event.ActionListener;
  66 import java.util.ArrayList;
  67 import java.util.Arrays;
  68 import java.util.Collections;
  69 import java.util.Hashtable;
  70 import java.util.LinkedHashMap;
  71 import java.util.List;
  72 import java.util.Map;
  73 import java.util.TreeMap;
  74 import java.util.Vector;
  75
  76 import javax.swing.ButtonGroup;
  77 import javax.swing.JCheckBoxMenuItem;
  78 import javax.swing.JColorChooser;
  79 import javax.swing.JMenu;
  80 import javax.swing.JMenuItem;
  81 import javax.swing.JOptionPane;
  82 import javax.swing.JPopupMenu;
  83 import javax.swing.JRadioButtonMenuItem;
  84
  85 /**
  86  * DOCUMENT ME!
  87  *
  88  * @author $author$
  89  * @version $Revision: 1.118 $
  90  */
  91 public class PopupMenu extends JPopupMenu
  92 {
  93   JMenu groupMenu = new JMenu();
  94
  95   JMenuItem groupName = new JMenuItem();
  96
  97   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  98
  99   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 100
 101   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 102
 103   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 104
 105   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 106
 107   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 108
 109   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 110
 111   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 112
 113   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
 114
 115   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 116
 117   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 118
 119   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 120
 121   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 122
 123   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 124
 125   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 126
 127   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 128
 129   AlignmentPanel ap;
 130
 131   JMenu sequenceMenu = new JMenu();
 132
 133   JMenuItem sequenceName = new JMenuItem();
 134
 135   JMenuItem sequenceDetails = new JMenuItem();
 136
 137   JMenuItem sequenceSelDetails = new JMenuItem();
 138
 139   JMenuItem makeReferenceSeq = new JMenuItem();
 140
 141   JMenuItem chooseAnnotations = new JMenuItem();
 142
 143   SequenceI sequence;
 144
 145   JMenuItem createGroupMenuItem = new JMenuItem();
 146
 147   JMenuItem unGroupMenuItem = new JMenuItem();
 148
 149   JMenuItem outline = new JMenuItem();
 150
 151   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 152
 153   JMenu colourMenu = new JMenu();
 154
 155   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 156
 157   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 158
 159   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 160
 161   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 162
 163   JMenu editMenu = new JMenu();
 164
 165   JMenuItem cut = new JMenuItem();
 166
 167   JMenuItem copy = new JMenuItem();
 168
 169   JMenuItem upperCase = new JMenuItem();
 170
 171   JMenuItem lowerCase = new JMenuItem();
 172
 173   JMenuItem toggle = new JMenuItem();
 174
 175   JMenu pdbMenu = new JMenu();
 176
 177   JMenu outputMenu = new JMenu();
 178
 179   JMenu seqShowAnnotationsMenu = new JMenu();
 180
 181   JMenu seqHideAnnotationsMenu = new JMenu();
 182
 183   JMenuItem seqAddReferenceAnnotations = new JMenuItem(
 184           MessageManager.getString("label.add_reference_annotations"));
 185
 186   JMenu groupShowAnnotationsMenu = new JMenu();
 187
 188   JMenu groupHideAnnotationsMenu = new JMenu();
 189
 190   JMenuItem groupAddReferenceAnnotations = new JMenuItem(
 191           MessageManager.getString("label.add_reference_annotations"));
 192
 193   JMenuItem sequenceFeature = new JMenuItem();
 194
 195   JMenuItem textColour = new JMenuItem();
 196
 197   JMenu jMenu1 = new JMenu();
 198
 199   JMenuItem pdbStructureDialog = new JMenuItem();
 200
 201   JMenu rnaStructureMenu = new JMenu();
 202
 203   JMenuItem editSequence = new JMenuItem();
 204
 205   JMenu groupLinksMenu;
 206
 207   JMenuItem hideInsertions = new JMenuItem();
 208
 209   /**
 210    * Creates a new PopupMenu object.
 211    *
 212    * @param ap
 213    *          DOCUMENT ME!
 214    * @param seq
 215    *          DOCUMENT ME!
 216    */
 217   public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
 218   {
 219     this(ap, seq, links, null);
 220   }
 221
 222   /**
 223    *
 224    * @param ap
 225    * @param seq
 226    * @param links
 227    * @param groupLinks
 228    */
 229   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 230           List<String> links, List<String> groupLinks)
 231   {
 232     // /////////////////////////////////////////////////////////
 233     // If this is activated from the sequence panel, the user may want to
 234     // edit or annotate a particular residue. Therefore display the residue menu
 235     //
 236     // If from the IDPanel, we must display the sequence menu
 237     // ////////////////////////////////////////////////////////
 238     this.ap = ap;
 239     sequence = seq;
 240
 241     ButtonGroup colours = new ButtonGroup();
 242     colours.add(noColourmenuItem);
 243     colours.add(clustalColour);
 244     colours.add(zappoColour);
 245     colours.add(taylorColour);
 246     colours.add(hydrophobicityColour);
 247     colours.add(helixColour);
 248     colours.add(strandColour);
 249     colours.add(turnColour);
 250     colours.add(buriedColour);
 251     colours.add(abovePIDColour);
 252     colours.add(userDefinedColour);
 253     colours.add(PIDColour);
 254     colours.add(BLOSUM62Colour);
 255     colours.add(purinePyrimidineColour);
 256     colours.add(RNAInteractionColour);
 257
 258     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 259     {
 260       JMenuItem item = new JMenuItem(
 261               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 262
 263       item.addActionListener(new java.awt.event.ActionListener()
 264       {
 265         @Override
 266         public void actionPerformed(ActionEvent e)
 267         {
 268           outputText_actionPerformed(e);
 269         }
 270       });
 271
 272       outputMenu.add(item);
 273     }
 274
 275     /*
 276      * Build menus for annotation types that may be shown or hidden, and for
 277      * 'reference annotations' that may be added to the alignment. First for the
 278      * currently selected sequence (if there is one):
 279      */
 280     final List<SequenceI> selectedSequence = (seq == null ? Collections
 281             .<SequenceI> emptyList() : Arrays.asList(seq));
 282     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
 283             seqHideAnnotationsMenu, selectedSequence);
 284     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
 285             selectedSequence);
 286
 287     /*
 288      * And repeat for the current selection group (if there is one):
 289      */
 290     final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
 291             .<SequenceI> emptyList() : ap.av.getSelectionGroup()
 292             .getSequences());
 293     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
 294             groupHideAnnotationsMenu, selectedGroup);
 295     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
 296             selectedGroup);
 297
 298     try
 299     {
 300       jbInit();
 301     } catch (Exception e)
 302     {
 303       e.printStackTrace();
 304     }
 305
 306     JMenuItem menuItem;
 307     if (seq != null)
 308     {
 309       sequenceMenu.setText(sequence.getName());
 310       if (seq == ap.av.getAlignment().getSeqrep())
 311       {
 312         makeReferenceSeq.setText(MessageManager
 313                 .getString("action.unmark_as_reference"));
 314       }
 315       else
 316       {
 317         makeReferenceSeq.setText(MessageManager
 318                 .getString("action.set_as_reference"));
 319       }
 320
 321       if (!ap.av.getAlignment().isNucleotide())
 322       {
 323         remove(rnaStructureMenu);
 324       }
 325       else
 326       {
 327         int origCount = rnaStructureMenu.getItemCount();
 328         /*
 329          * add menu items to 2D-render any alignment or sequence secondary
 330          * structure annotation
 331          */
 332         AlignmentAnnotation[] aas = ap.av.getAlignment()
 333                 .getAlignmentAnnotation();
 334         if (aas != null)
 335         {
 336           for (final AlignmentAnnotation aa : aas)
 337           {
 338             if (aa.isValidStruc() && aa.sequenceRef == null)
 339             {
 340               /*
 341                * valid alignment RNA secondary structure annotation
 342                */
 343               menuItem = new JMenuItem();
 344               menuItem.setText(MessageManager.formatMessage(
 345                       "label.2d_rna_structure_line",
 346                       new Object[] { aa.label }));
 347               menuItem.addActionListener(new java.awt.event.ActionListener()
 348               {
 349                 @Override
 350                 public void actionPerformed(ActionEvent e)
 351                 {
 352                   new AppVarna(seq, aa, ap);
 353                 }
 354               });
 355               rnaStructureMenu.add(menuItem);
 356             }
 357           }
 358         }
 359
 360         if (seq.getAnnotation() != null)
 361         {
 362           AlignmentAnnotation seqAnns[] = seq.getAnnotation();
 363           for (final AlignmentAnnotation aa : seqAnns)
 364           {
 365             if (aa.isValidStruc())
 366             {
 367               /*
 368                * valid sequence RNA secondary structure annotation
 369                */
 370               // TODO: make rnastrucF a bit more nice
 371               menuItem = new JMenuItem();
 372               menuItem.setText(MessageManager.formatMessage(
 373                       "label.2d_rna_sequence_name",
 374                       new Object[] { seq.getName() }));
 375               menuItem.addActionListener(new java.awt.event.ActionListener()
 376               {
 377                 @Override
 378                 public void actionPerformed(ActionEvent e)
 379                 {
 380                   // TODO: VARNA does'nt print gaps in the sequence
 381                   new AppVarna(seq, aa, ap);
 382                 }
 383               });
 384               rnaStructureMenu.add(menuItem);
 385             }
 386           }
 387         }
 388         if (rnaStructureMenu.getItemCount() == origCount)
 389         {
 390           remove(rnaStructureMenu);
 391         }
 392       }
 393
 394       menuItem = new JMenuItem(
 395               MessageManager.getString("action.hide_sequences"));
 396       menuItem.addActionListener(new java.awt.event.ActionListener()
 397       {
 398         @Override
 399         public void actionPerformed(ActionEvent e)
 400         {
 401           hideSequences(false);
 402         }
 403       });
 404       add(menuItem);
 405
 406       if (ap.av.getSelectionGroup() != null
 407               && ap.av.getSelectionGroup().getSize() > 1)
 408       {
 409         menuItem = new JMenuItem(MessageManager.formatMessage(
 410                 "label.represent_group_with",
 411                 new Object[] { seq.getName() }));
 412         menuItem.addActionListener(new java.awt.event.ActionListener()
 413         {
 414           @Override
 415           public void actionPerformed(ActionEvent e)
 416           {
 417             hideSequences(true);
 418           }
 419         });
 420         sequenceMenu.add(menuItem);
 421       }
 422
 423       if (ap.av.hasHiddenRows())
 424       {
 425         final int index = ap.av.getAlignment().findIndex(seq);
 426
 427         if (ap.av.adjustForHiddenSeqs(index)
 428                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 429         {
 430           menuItem = new JMenuItem(
 431                   MessageManager.getString("action.reveal_sequences"));
 432           menuItem.addActionListener(new ActionListener()
 433           {
 434             @Override
 435             public void actionPerformed(ActionEvent e)
 436             {
 437               ap.av.showSequence(index);
 438               if (ap.overviewPanel != null)
 439               {
 440                 ap.overviewPanel.updateOverviewImage();
 441               }
 442             }
 443           });
 444           add(menuItem);
 445         }
 446       }
 447     }
 448     // for the case when no sequences are even visible
 449     if (ap.av.hasHiddenRows())
 450     {
 451       {
 452         menuItem = new JMenuItem(
 453                 MessageManager.getString("action.reveal_all"));
 454         menuItem.addActionListener(new ActionListener()
 455         {
 456           @Override
 457           public void actionPerformed(ActionEvent e)
 458           {
 459             ap.av.showAllHiddenSeqs();
 460             if (ap.overviewPanel != null)
 461             {
 462               ap.overviewPanel.updateOverviewImage();
 463             }
 464           }
 465         });
 466
 467         add(menuItem);
 468       }
 469
 470     }
 471
 472     SequenceGroup sg = ap.av.getSelectionGroup();
 473     boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
 474             .getGroups().contains(sg) : false;
 475
 476     if (sg != null && sg.getSize() > 0)
 477     {
 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().getAllPDBEntries();
 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       pdbStructureDialog.setVisible(false);
 602       rnaStructureMenu.setVisible(false);
 603     }
 604
 605     if (links != null && links.size() > 0)
 606     {
 607       addFeatureLinks(seq, links);
 608     }
 609   }
 610
 611   /**
 612    * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
 613    *
 614    * @param seq
 615    * @param links
 616    */
 617   void addFeatureLinks(final SequenceI seq, List<String> links)
 618   {
 619     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
 620     List<String> linkset = new ArrayList<String>();
 621     for (String link : links)
 622     {
 623       UrlLink urlLink = null;
 624       try
 625       {
 626         urlLink = new UrlLink(link);
 627       } catch (Exception foo)
 628       {
 629         Cache.log.error("Exception for URLLink '" + link + "'", foo);
 630         continue;
 631       }
 632       ;
 633       if (!urlLink.isValid())
 634       {
 635         Cache.log.error(urlLink.getInvalidMessage());
 636         continue;
 637       }
 638       final String label = urlLink.getLabel();
 639       if (seq != null && urlLink.isDynamic())
 640       {
 641
 642         // collect matching db-refs
 643         DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
 644                 new String[] { urlLink.getTarget() });
 645         // collect id string too
 646         String id = seq.getName();
 647         String descr = seq.getDescription();
 648         if (descr != null && descr.length() < 1)
 649         {
 650           descr = null;
 651         }
 652
 653         if (dbr != null)
 654         {
 655           for (int r = 0; r < dbr.length; r++)
 656           {
 657             if (id != null && dbr[r].getAccessionId().equals(id))
 658             {
 659               // suppress duplicate link creation for the bare sequence ID
 660               // string with this link
 661               id = null;
 662             }
 663             // create Bare ID link for this URL
 664             String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
 665             if (urls != null)
 666             {
 667               for (int u = 0; u < urls.length; u += 2)
 668               {
 669                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 670                 {
 671                   linkset.add(urls[u] + "|" + urls[u + 1]);
 672                   addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 673                 }
 674               }
 675             }
 676           }
 677         }
 678         if (id != null)
 679         {
 680           // create Bare ID link for this URL
 681           String[] urls = urlLink.makeUrls(id, true);
 682           if (urls != null)
 683           {
 684             for (int u = 0; u < urls.length; u += 2)
 685             {
 686               if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 687               {
 688                 linkset.add(urls[u] + "|" + urls[u + 1]);
 689                 addshowLink(linkMenu, label, urls[u + 1]);
 690               }
 691             }
 692           }
 693         }
 694         // Create urls from description but only for URL links which are regex
 695         // links
 696         if (descr != null && urlLink.getRegexReplace() != null)
 697         {
 698           // create link for this URL from description where regex matches
 699           String[] urls = urlLink.makeUrls(descr, true);
 700           if (urls != null)
 701           {
 702             for (int u = 0; u < urls.length; u += 2)
 703             {
 704               if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 705               {
 706                 linkset.add(urls[u] + "|" + urls[u + 1]);
 707                 addshowLink(linkMenu, label, urls[u + 1]);
 708               }
 709             }
 710           }
 711         }
 712       }
 713       else
 714       {
 715         if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 716         {
 717           linkset.add(label + "|" + urlLink.getUrl_prefix());
 718           // Add a non-dynamic link
 719           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 720         }
 721       }
 722     }
 723     if (sequence != null)
 724     {
 725       sequenceMenu.add(linkMenu);
 726     }
 727     else
 728     {
 729       add(linkMenu);
 730     }
 731   }
 732
 733   /**
 734    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
 735    * "All" is added first, followed by a separator. Then add any annotation
 736    * types associated with the current selection. Separate menus are built for
 737    * the selected sequence group (if any), and the selected sequence.
 738    * <p>
 739    * Some annotation rows are always rendered together - these can be identified
 740    * by a common graphGroup property > -1. Only one of each group will be marked
 741    * as visible (to avoid duplication of the display). For such groups we add a
 742    * composite type name, e.g.
 743    * <p>
 744    * IUPredWS (Long), IUPredWS (Short)
 745    *
 746    * @param seq
 747    */
 748   protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
 749           List<SequenceI> forSequences)
 750   {
 751     showMenu.removeAll();
 752     hideMenu.removeAll();
 753
 754     final List<String> all = Arrays.asList(new String[] { MessageManager
 755             .getString("label.all") });
 756     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
 757     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
 758             false);
 759     showMenu.addSeparator();
 760     hideMenu.addSeparator();
 761
 762     final AlignmentAnnotation[] annotations = ap.getAlignment()
 763             .getAlignmentAnnotation();
 764
 765     /*
 766      * Find shown/hidden annotations types, distinguished by source (calcId),
 767      * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
 768      * the insertion order, which is the order of the annotations on the
 769      * alignment.
 770      */
 771     Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
 772     Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
 773     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
 774             AlignmentAnnotationUtils.asList(annotations), forSequences);
 775
 776     for (String calcId : hiddenTypes.keySet())
 777     {
 778       for (List<String> type : hiddenTypes.get(calcId))
 779       {
 780         addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
 781                 false, true);
 782       }
 783     }
 784     // grey out 'show annotations' if none are hidden
 785     showMenu.setEnabled(!hiddenTypes.isEmpty());
 786
 787     for (String calcId : shownTypes.keySet())
 788     {
 789       for (List<String> type : shownTypes.get(calcId))
 790       {
 791         addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
 792                 false, false);
 793       }
 794     }
 795     // grey out 'hide annotations' if none are shown
 796     hideMenu.setEnabled(!shownTypes.isEmpty());
 797   }
 798
 799   /**
 800    * Returns a list of sequences - either the current selection group (if there
 801    * is one), else the specified single sequence.
 802    *
 803    * @param seq
 804    * @return
 805    */
 806   protected List<SequenceI> getSequenceScope(SequenceI seq)
 807   {
 808     List<SequenceI> forSequences = null;
 809     final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
 810     if (selectionGroup != null && selectionGroup.getSize() > 0)
 811     {
 812       forSequences = selectionGroup.getSequences();
 813     }
 814     else
 815     {
 816       forSequences = seq == null ? Collections.<SequenceI> emptyList()
 817               : Arrays.asList(seq);
 818     }
 819     return forSequences;
 820   }
 821
 822   /**
 823    * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
 824    * menus.
 825    *
 826    * @param showOrHideMenu
 827    *          the menu to add to
 828    * @param forSequences
 829    *          the sequences whose annotations may be shown or hidden
 830    * @param calcId
 831    * @param types
 832    *          the label to add
 833    * @param allTypes
 834    *          if true this is a special label meaning 'All'
 835    * @param actionIsShow
 836    *          if true, the select menu item action is to show the annotation
 837    *          type, else hide
 838    */
 839   protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
 840           final List<SequenceI> forSequences, String calcId,
 841           final List<String> types, final boolean allTypes,
 842           final boolean actionIsShow)
 843   {
 844     String label = types.toString(); // [a, b, c]
 845     label = label.substring(1, label.length() - 1); // a, b, c
 846     final JMenuItem item = new JMenuItem(label);
 847     item.setToolTipText(calcId);
 848     item.addActionListener(new java.awt.event.ActionListener()
 849     {
 850       @Override
 851       public void actionPerformed(ActionEvent e)
 852       {
 853         AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
 854                 types, forSequences, allTypes, actionIsShow);
 855         refresh();
 856       }
 857     });
 858     showOrHideMenu.add(item);
 859   }
 860
 861   private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
 862   {
 863
 864     // TODO: usability: thread off the generation of group url content so root
 865     // menu appears asap
 866     // sequence only URLs
 867     // ID/regex match URLs
 868     groupLinksMenu = new JMenu(
 869             MessageManager.getString("action.group_link"));
 870     // three types of url that might be created.
 871     JMenu[] linkMenus = new JMenu[] { null,
 872         new JMenu(MessageManager.getString("action.ids")),
 873         new JMenu(MessageManager.getString("action.sequences")),
 874         new JMenu(MessageManager.getString("action.ids_sequences")) };
 875
 876     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 877     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 878     Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
 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.getDBRefs();
 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 = commonDbrefs.get(src);
 899           if (sarray == null)
 900           {
 901             sarray = new Object[2];
 902             sarray[0] = new int[] { 0 };
 903             sarray[1] = new String[seqs.length];
 904
 905             commonDbrefs.put(src, sarray);
 906           }
 907
 908           if (((String[]) sarray[1])[sq] == null)
 909           {
 910             if (!dbr[d].hasMap()
 911                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 912             {
 913               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 914               ((int[]) sarray[0])[0]++;
 915             }
 916           }
 917         }
 918       }
 919     }
 920     // now create group links for all distinct ID/sequence sets.
 921     boolean addMenu = false; // indicates if there are any group links to give
 922                              // to user
 923     for (String link : groupLinks)
 924     {
 925       GroupUrlLink urlLink = null;
 926       try
 927       {
 928         urlLink = new GroupUrlLink(link);
 929       } catch (Exception foo)
 930       {
 931         Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
 932         continue;
 933       }
 934       ;
 935       if (!urlLink.isValid())
 936       {
 937         Cache.log.error(urlLink.getInvalidMessage());
 938         continue;
 939       }
 940       final String label = urlLink.getLabel();
 941       boolean usingNames = false;
 942       // Now see which parts of the group apply for this URL
 943       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 944       Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
 945       String[] seqstr, ids; // input to makeUrl
 946       if (idset != null)
 947       {
 948         int numinput = ((int[]) idset[0])[0];
 949         String[] allids = ((String[]) idset[1]);
 950         seqstr = new String[numinput];
 951         ids = new String[numinput];
 952         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 953         {
 954           if (allids[sq] != null)
 955           {
 956             ids[idcount] = allids[sq];
 957             seqstr[idcount++] = idandseqs[1][sq];
 958           }
 959         }
 960       }
 961       else
 962       {
 963         // just use the id/seq set
 964         seqstr = idandseqs[1];
 965         ids = idandseqs[0];
 966         usingNames = true;
 967       }
 968       // and try and make the groupURL!
 969
 970       Object[] urlset = null;
 971       try
 972       {
 973         urlset = urlLink.makeUrlStubs(ids, seqstr,
 974                 "FromJalview" + System.currentTimeMillis(), false);
 975       } catch (UrlStringTooLongException e)
 976       {
 977       }
 978       if (urlset != null)
 979       {
 980         int type = urlLink.getGroupURLType() & 3;
 981         // first two bits ofurlLink type bitfield are sequenceids and sequences
 982         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 983         addshowLink(linkMenus[type], label
 984                 + (((type & 1) == 1) ? ("("
 985                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 986                 urlLink, urlset);
 987         addMenu = true;
 988       }
 989     }
 990     if (addMenu)
 991     {
 992       groupLinksMenu = new JMenu(
 993               MessageManager.getString("action.group_link"));
 994       for (int m = 0; m < linkMenus.length; m++)
 995       {
 996         if (linkMenus[m] != null
 997                 && linkMenus[m].getMenuComponentCount() > 0)
 998         {
 999           groupLinksMenu.add(linkMenus[m]);
1000         }
1001       }
1002
1003       groupMenu.add(groupLinksMenu);
1004     }
1005   }
1006
1007   /**
1008    * add a show URL menu item to the given linkMenu
1009    *
1010    * @param linkMenu
1011    * @param label
1012    *          - menu label string
1013    * @param url
1014    *          - url to open
1015    */
1016   private void addshowLink(JMenu linkMenu, String label, final String url)
1017   {
1018     JMenuItem item = new JMenuItem(label);
1019     item.setToolTipText(MessageManager.formatMessage(
1020             "label.open_url_param", new Object[] { url }));
1021     item.addActionListener(new java.awt.event.ActionListener()
1022     {
1023       @Override
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         new Thread(new Runnable()
1027         {
1028
1029           @Override
1030           public void run()
1031           {
1032             showLink(url);
1033           }
1034
1035         }).start();
1036       }
1037     });
1038
1039     linkMenu.add(item);
1040   }
1041
1042   /**
1043    * add a late bound groupURL item to the given linkMenu
1044    *
1045    * @param linkMenu
1046    * @param label
1047    *          - menu label string
1048    * @param urlgenerator
1049    *          GroupURLLink used to generate URL
1050    * @param urlstub
1051    *          Object array returned from the makeUrlStubs function.
1052    */
1053   private void addshowLink(JMenu linkMenu, String label,
1054           final GroupUrlLink urlgenerator, final Object[] urlstub)
1055   {
1056     JMenuItem item = new JMenuItem(label);
1057     item.setToolTipText(MessageManager.formatMessage(
1058             "label.open_url_seqs_param",
1059             new Object[] { urlgenerator.getUrl_prefix(),
1060                 urlgenerator.getNumberInvolved(urlstub) }));
1061     // TODO: put in info about what is being sent.
1062     item.addActionListener(new ActionListener()
1063     {
1064       @Override
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         new Thread(new Runnable()
1068         {
1069
1070           @Override
1071           public void run()
1072           {
1073             try
1074             {
1075               showLink(urlgenerator.constructFrom(urlstub));
1076             } catch (UrlStringTooLongException e2)
1077             {
1078             }
1079           }
1080
1081         }).start();
1082       }
1083     });
1084
1085     linkMenu.add(item);
1086   }
1087
1088   /**
1089    * DOCUMENT ME!
1090    *
1091    * @throws Exception
1092    *           DOCUMENT ME!
1093    */
1094   private void jbInit() throws Exception
1095   {
1096     groupMenu.setText(MessageManager.getString("label.selection"));
1097     groupName.setText(MessageManager.getString("label.name"));
1098     groupName.addActionListener(new java.awt.event.ActionListener()
1099     {
1100       @Override
1101       public void actionPerformed(ActionEvent e)
1102       {
1103         groupName_actionPerformed();
1104       }
1105     });
1106     sequenceMenu.setText(MessageManager.getString("label.sequence"));
1107     sequenceName.setText(MessageManager
1108             .getString("label.edit_name_description"));
1109     sequenceName.addActionListener(new java.awt.event.ActionListener()
1110     {
1111       @Override
1112       public void actionPerformed(ActionEvent e)
1113       {
1114         sequenceName_actionPerformed();
1115       }
1116     });
1117     chooseAnnotations.setText(MessageManager
1118             .getString("action.choose_annotations"));
1119     chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1120     {
1121       @Override
1122       public void actionPerformed(ActionEvent e)
1123       {
1124         chooseAnnotations_actionPerformed(e);
1125       }
1126     });
1127     sequenceDetails.setText(MessageManager
1128             .getString("label.sequence_details"));
1129     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1130     {
1131       @Override
1132       public void actionPerformed(ActionEvent e)
1133       {
1134         sequenceDetails_actionPerformed();
1135       }
1136     });
1137     sequenceSelDetails.setText(MessageManager
1138             .getString("label.sequence_details"));
1139     sequenceSelDetails
1140             .addActionListener(new java.awt.event.ActionListener()
1141             {
1142               @Override
1143               public void actionPerformed(ActionEvent e)
1144               {
1145                 sequenceSelectionDetails_actionPerformed();
1146               }
1147             });
1148     PIDColour.setFocusPainted(false);
1149     unGroupMenuItem
1150             .setText(MessageManager.getString("action.remove_group"));
1151     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1152     {
1153       @Override
1154       public void actionPerformed(ActionEvent e)
1155       {
1156         unGroupMenuItem_actionPerformed();
1157       }
1158     });
1159     createGroupMenuItem.setText(MessageManager
1160             .getString("action.create_group"));
1161     createGroupMenuItem
1162             .addActionListener(new java.awt.event.ActionListener()
1163             {
1164               @Override
1165               public void actionPerformed(ActionEvent e)
1166               {
1167                 createGroupMenuItem_actionPerformed();
1168               }
1169             });
1170
1171     outline.setText(MessageManager.getString("action.border_colour"));
1172     outline.addActionListener(new java.awt.event.ActionListener()
1173     {
1174       @Override
1175       public void actionPerformed(ActionEvent e)
1176       {
1177         outline_actionPerformed();
1178       }
1179     });
1180     nucleotideMenuItem
1181             .setText(MessageManager.getString("label.nucleotide"));
1182     nucleotideMenuItem.addActionListener(new ActionListener()
1183     {
1184       @Override
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         nucleotideMenuItem_actionPerformed();
1188       }
1189     });
1190     colourMenu.setText(MessageManager.getString("label.group_colour"));
1191     showBoxes.setText(MessageManager.getString("action.boxes"));
1192     showBoxes.setState(true);
1193     showBoxes.addActionListener(new ActionListener()
1194     {
1195       @Override
1196       public void actionPerformed(ActionEvent e)
1197       {
1198         showBoxes_actionPerformed();
1199       }
1200     });
1201     showText.setText(MessageManager.getString("action.text"));
1202     showText.setState(true);
1203     showText.addActionListener(new ActionListener()
1204     {
1205       @Override
1206       public void actionPerformed(ActionEvent e)
1207       {
1208         showText_actionPerformed();
1209       }
1210     });
1211     showColourText.setText(MessageManager.getString("label.colour_text"));
1212     showColourText.addActionListener(new ActionListener()
1213     {
1214       @Override
1215       public void actionPerformed(ActionEvent e)
1216       {
1217         showColourText_actionPerformed();
1218       }
1219     });
1220     displayNonconserved.setText(MessageManager
1221             .getString("label.show_non_conversed"));
1222     displayNonconserved.setState(true);
1223     displayNonconserved.addActionListener(new ActionListener()
1224     {
1225       @Override
1226       public void actionPerformed(ActionEvent e)
1227       {
1228         showNonconserved_actionPerformed();
1229       }
1230     });
1231     editMenu.setText(MessageManager.getString("action.edit"));
1232     cut.setText(MessageManager.getString("action.cut"));
1233     cut.addActionListener(new ActionListener()
1234     {
1235       @Override
1236       public void actionPerformed(ActionEvent e)
1237       {
1238         cut_actionPerformed();
1239       }
1240     });
1241     upperCase.setText(MessageManager.getString("label.to_upper_case"));
1242     upperCase.addActionListener(new ActionListener()
1243     {
1244       @Override
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         changeCase(e);
1248       }
1249     });
1250     copy.setText(MessageManager.getString("action.copy"));
1251     copy.addActionListener(new ActionListener()
1252     {
1253       @Override
1254       public void actionPerformed(ActionEvent e)
1255       {
1256         copy_actionPerformed();
1257       }
1258     });
1259     lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1260     lowerCase.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         changeCase(e);
1266       }
1267     });
1268     toggle.setText(MessageManager.getString("label.toggle_case"));
1269     toggle.addActionListener(new ActionListener()
1270     {
1271       @Override
1272       public void actionPerformed(ActionEvent e)
1273       {
1274         changeCase(e);
1275       }
1276     });
1277     outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1278             + "...");
1279     seqShowAnnotationsMenu.setText(MessageManager
1280             .getString("label.show_annotations"));
1281     seqHideAnnotationsMenu.setText(MessageManager
1282             .getString("label.hide_annotations"));
1283     groupShowAnnotationsMenu.setText(MessageManager
1284             .getString("label.show_annotations"));
1285     groupHideAnnotationsMenu.setText(MessageManager
1286             .getString("label.hide_annotations"));
1287     sequenceFeature.setText(MessageManager
1288             .getString("label.create_sequence_feature"));
1289     sequenceFeature.addActionListener(new ActionListener()
1290     {
1291       @Override
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         sequenceFeature_actionPerformed();
1295       }
1296     });
1297     textColour.setText(MessageManager.getString("label.text_colour"));
1298     textColour.addActionListener(new ActionListener()
1299     {
1300       @Override
1301       public void actionPerformed(ActionEvent e)
1302       {
1303         textColour_actionPerformed();
1304       }
1305     });
1306     jMenu1.setText(MessageManager.getString("label.group"));
1307     pdbStructureDialog.setText(MessageManager
1308             .getString("label.show_pdbstruct_dialog"));
1309     pdbStructureDialog.addActionListener(new ActionListener()
1310     {
1311       @Override
1312       public void actionPerformed(ActionEvent actionEvent)
1313       {
1314         SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1315         if (ap.av.getSelectionGroup() != null)
1316         {
1317           selectedSeqs = ap.av.getSequenceSelection();
1318         }
1319         new StructureChooser(selectedSeqs, sequence, ap);
1320       }
1321     });
1322
1323     rnaStructureMenu.setText(MessageManager
1324             .getString("label.view_rna_structure"));
1325
1326     // colStructureMenu.setText("Colour By Structure");
1327     editSequence.setText(MessageManager.getString("label.edit_sequence")
1328             + "...");
1329     editSequence.addActionListener(new ActionListener()
1330     {
1331       @Override
1332       public void actionPerformed(ActionEvent actionEvent)
1333       {
1334         editSequence_actionPerformed(actionEvent);
1335       }
1336     });
1337     makeReferenceSeq.setText(MessageManager
1338             .getString("label.mark_as_representative"));
1339     makeReferenceSeq.addActionListener(new ActionListener()
1340     {
1341
1342       @Override
1343       public void actionPerformed(ActionEvent actionEvent)
1344       {
1345         makeReferenceSeq_actionPerformed(actionEvent);
1346
1347       }
1348     });
1349     hideInsertions.setText(MessageManager
1350             .getString("label.hide_insertions"));
1351     hideInsertions.addActionListener(new ActionListener()
1352     {
1353
1354       @Override
1355       public void actionPerformed(ActionEvent e)
1356       {
1357         hideInsertions_actionPerformed(e);
1358       }
1359     });
1360     /*
1361      * annotationMenuItem.setText("By Annotation");
1362      * annotationMenuItem.addActionListener(new ActionListener() { public void
1363      * actionPerformed(ActionEvent actionEvent) {
1364      * annotationMenuItem_actionPerformed(actionEvent); } });
1365      */
1366     groupMenu.add(sequenceSelDetails);
1367     add(groupMenu);
1368     add(sequenceMenu);
1369     add(rnaStructureMenu);
1370     add(pdbStructureDialog);
1371     if (sequence != null)
1372     {
1373       add(hideInsertions);
1374     }
1375     // annotations configuration panel suppressed for now
1376     // groupMenu.add(chooseAnnotations);
1377
1378     /*
1379      * Add show/hide annotations to the Sequence menu, and to the Selection menu
1380      * (if a selection group is in force).
1381      */
1382     sequenceMenu.add(seqShowAnnotationsMenu);
1383     sequenceMenu.add(seqHideAnnotationsMenu);
1384     sequenceMenu.add(seqAddReferenceAnnotations);
1385     groupMenu.add(groupShowAnnotationsMenu);
1386     groupMenu.add(groupHideAnnotationsMenu);
1387     groupMenu.add(groupAddReferenceAnnotations);
1388     groupMenu.add(editMenu);
1389     groupMenu.add(outputMenu);
1390     groupMenu.add(sequenceFeature);
1391     groupMenu.add(createGroupMenuItem);
1392     groupMenu.add(unGroupMenuItem);
1393     groupMenu.add(jMenu1);
1394     sequenceMenu.add(sequenceName);
1395     sequenceMenu.add(sequenceDetails);
1396     sequenceMenu.add(makeReferenceSeq);
1397     colourMenu.add(textColour);
1398     colourMenu.add(noColourmenuItem);
1399     colourMenu.add(clustalColour);
1400     colourMenu.add(BLOSUM62Colour);
1401     colourMenu.add(PIDColour);
1402     colourMenu.add(zappoColour);
1403     colourMenu.add(taylorColour);
1404     colourMenu.add(hydrophobicityColour);
1405     colourMenu.add(helixColour);
1406     colourMenu.add(strandColour);
1407     colourMenu.add(turnColour);
1408     colourMenu.add(buriedColour);
1409     colourMenu.add(nucleotideMenuItem);
1410     if (ap.getAlignment().isNucleotide())
1411     {
1412       // JBPNote - commented since the colourscheme isn't functional
1413       colourMenu.add(purinePyrimidineColour);
1414     }
1415     colourMenu.add(userDefinedColour);
1416
1417     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1418     {
1419       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1420               .getUserColourSchemes().keys();
1421
1422       while (userColours.hasMoreElements())
1423       {
1424         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1425         item.addActionListener(new ActionListener()
1426         {
1427           @Override
1428           public void actionPerformed(ActionEvent evt)
1429           {
1430             userDefinedColour_actionPerformed(evt);
1431           }
1432         });
1433         colourMenu.add(item);
1434       }
1435     }
1436
1437     colourMenu.addSeparator();
1438     colourMenu.add(abovePIDColour);
1439     colourMenu.add(conservationMenuItem);
1440     editMenu.add(copy);
1441     editMenu.add(cut);
1442     editMenu.add(editSequence);
1443     editMenu.add(upperCase);
1444     editMenu.add(lowerCase);
1445     editMenu.add(toggle);
1446     // JBPNote: These shouldn't be added here - should appear in a generic
1447     // 'apply web service to this sequence menu'
1448     // pdbMenu.add(RNAFold);
1449     // pdbMenu.add(ContraFold);
1450     jMenu1.add(groupName);
1451     jMenu1.add(colourMenu);
1452     jMenu1.add(showBoxes);
1453     jMenu1.add(showText);
1454     jMenu1.add(showColourText);
1455     jMenu1.add(outline);
1456     jMenu1.add(displayNonconserved);
1457     noColourmenuItem.setText(MessageManager.getString("label.none"));
1458     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1459     {
1460       @Override
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         noColourmenuItem_actionPerformed();
1464       }
1465     });
1466
1467     clustalColour.setText(MessageManager
1468             .getString("label.clustalx_colours"));
1469     clustalColour.addActionListener(new java.awt.event.ActionListener()
1470     {
1471       @Override
1472       public void actionPerformed(ActionEvent e)
1473       {
1474         clustalColour_actionPerformed();
1475       }
1476     });
1477     zappoColour.setText(MessageManager.getString("label.zappo"));
1478     zappoColour.addActionListener(new java.awt.event.ActionListener()
1479     {
1480       @Override
1481       public void actionPerformed(ActionEvent e)
1482       {
1483         zappoColour_actionPerformed();
1484       }
1485     });
1486     taylorColour.setText(MessageManager.getString("label.taylor"));
1487     taylorColour.addActionListener(new java.awt.event.ActionListener()
1488     {
1489       @Override
1490       public void actionPerformed(ActionEvent e)
1491       {
1492         taylorColour_actionPerformed();
1493       }
1494     });
1495     hydrophobicityColour.setText(MessageManager
1496             .getString("label.hydrophobicity"));
1497     hydrophobicityColour
1498             .addActionListener(new java.awt.event.ActionListener()
1499             {
1500               @Override
1501               public void actionPerformed(ActionEvent e)
1502               {
1503                 hydrophobicityColour_actionPerformed();
1504               }
1505             });
1506     helixColour.setText(MessageManager.getString("label.helix_propensity"));
1507     helixColour.addActionListener(new java.awt.event.ActionListener()
1508     {
1509       @Override
1510       public void actionPerformed(ActionEvent e)
1511       {
1512         helixColour_actionPerformed();
1513       }
1514     });
1515     strandColour.setText(MessageManager
1516             .getString("label.strand_propensity"));
1517     strandColour.addActionListener(new java.awt.event.ActionListener()
1518     {
1519       @Override
1520       public void actionPerformed(ActionEvent e)
1521       {
1522         strandColour_actionPerformed();
1523       }
1524     });
1525     turnColour.setText(MessageManager.getString("label.turn_propensity"));
1526     turnColour.addActionListener(new java.awt.event.ActionListener()
1527     {
1528       @Override
1529       public void actionPerformed(ActionEvent e)
1530       {
1531         turnColour_actionPerformed();
1532       }
1533     });
1534     buriedColour.setText(MessageManager.getString("label.buried_index"));
1535     buriedColour.addActionListener(new java.awt.event.ActionListener()
1536     {
1537       @Override
1538       public void actionPerformed(ActionEvent e)
1539       {
1540         buriedColour_actionPerformed();
1541       }
1542     });
1543     abovePIDColour.setText(MessageManager
1544             .getString("label.above_identity_percentage"));
1545     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1546     {
1547       @Override
1548       public void actionPerformed(ActionEvent e)
1549       {
1550         abovePIDColour_actionPerformed();
1551       }
1552     });
1553     userDefinedColour.setText(MessageManager
1554             .getString("action.user_defined"));
1555     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1556     {
1557       @Override
1558       public void actionPerformed(ActionEvent e)
1559       {
1560         userDefinedColour_actionPerformed(e);
1561       }
1562     });
1563     PIDColour
1564             .setText(MessageManager.getString("label.percentage_identity"));
1565     PIDColour.addActionListener(new java.awt.event.ActionListener()
1566     {
1567       @Override
1568       public void actionPerformed(ActionEvent e)
1569       {
1570         PIDColour_actionPerformed();
1571       }
1572     });
1573     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1574     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1575     {
1576       @Override
1577       public void actionPerformed(ActionEvent e)
1578       {
1579         BLOSUM62Colour_actionPerformed();
1580       }
1581     });
1582     purinePyrimidineColour.setText(MessageManager
1583             .getString("label.purine_pyrimidine"));
1584     purinePyrimidineColour
1585             .addActionListener(new java.awt.event.ActionListener()
1586             {
1587               @Override
1588               public void actionPerformed(ActionEvent e)
1589               {
1590                 purinePyrimidineColour_actionPerformed();
1591               }
1592             });
1593
1594     /*
1595      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1596      * public void actionPerformed(ActionEvent e) {
1597      * covariationColour_actionPerformed(); } });
1598      */
1599
1600     conservationMenuItem.setText(MessageManager
1601             .getString("label.conservation"));
1602     conservationMenuItem
1603             .addActionListener(new java.awt.event.ActionListener()
1604             {
1605               @Override
1606               public void actionPerformed(ActionEvent e)
1607               {
1608                 conservationMenuItem_actionPerformed();
1609               }
1610             });
1611   }
1612
1613   /**
1614    * Check for any annotations on the underlying dataset sequences (for the
1615    * current selection group) which are not 'on the alignment'.If any are found,
1616    * enable the option to add them to the alignment. The criteria for 'on the
1617    * alignment' is finding an alignment annotation on the alignment, matched on
1618    * calcId, label and sequenceRef.
1619    *
1620    * A tooltip is also constructed that displays the source (calcId) and type
1621    * (label) of the annotations that can be added.
1622    *
1623    * @param menuItem
1624    * @param forSequences
1625    */
1626   protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1627           List<SequenceI> forSequences)
1628   {
1629     menuItem.setEnabled(false);
1630
1631     /*
1632      * Temporary store to hold distinct calcId / type pairs for the tooltip.
1633      * Using TreeMap means calcIds are shown in alphabetical order.
1634      */
1635     Map<String, String> tipEntries = new TreeMap<String, String>();
1636     final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1637     AlignmentI al = this.ap.av.getAlignment();
1638     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1639             tipEntries, candidates, al);
1640     if (!candidates.isEmpty())
1641     {
1642       StringBuilder tooltip = new StringBuilder(64);
1643       tooltip.append(MessageManager.getString("label.add_annotations_for"));
1644
1645       /*
1646        * Found annotations that could be added. Enable the menu item, and
1647        * configure its tooltip and action.
1648        */
1649       menuItem.setEnabled(true);
1650       for (String calcId : tipEntries.keySet())
1651       {
1652         tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1653       }
1654       String tooltipText = JvSwingUtils.wrapTooltip(true,
1655               tooltip.toString());
1656       menuItem.setToolTipText(tooltipText);
1657
1658       menuItem.addActionListener(new ActionListener()
1659       {
1660         @Override
1661         public void actionPerformed(ActionEvent e)
1662         {
1663           addReferenceAnnotations_actionPerformed(candidates);
1664         }
1665       });
1666     }
1667   }
1668
1669   /**
1670    * Add annotations to the sequences and to the alignment.
1671    *
1672    * @param candidates
1673    *          a map whose keys are sequences on the alignment, and values a list
1674    *          of annotations to add to each sequence
1675    */
1676   protected void addReferenceAnnotations_actionPerformed(
1677           Map<SequenceI, List<AlignmentAnnotation>> candidates)
1678   {
1679     final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1680     final AlignmentI alignment = this.ap.getAlignment();
1681     AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1682             selectionGroup);
1683     refresh();
1684   }
1685
1686   protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1687   {
1688     if (!ap.av.getAlignment().hasSeqrep())
1689     {
1690       // initialise the display flags so the user sees something happen
1691       ap.av.setDisplayReferenceSeq(true);
1692       ap.av.setColourByReferenceSeq(true);
1693       ap.av.getAlignment().setSeqrep(sequence);
1694     }
1695     else
1696     {
1697       if (ap.av.getAlignment().getSeqrep() == sequence)
1698       {
1699         ap.av.getAlignment().setSeqrep(null);
1700       }
1701       else
1702       {
1703         ap.av.getAlignment().setSeqrep(sequence);
1704       }
1705     }
1706     refresh();
1707   }
1708
1709   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1710   {
1711     if (sequence != null)
1712     {
1713       ColumnSelection cs = ap.av.getColumnSelection();
1714       if (cs == null)
1715       {
1716         cs = new ColumnSelection();
1717       }
1718       cs.hideInsertionsFor(sequence);
1719       ap.av.setColumnSelection(cs);
1720     }
1721     refresh();
1722   }
1723
1724   protected void sequenceSelectionDetails_actionPerformed()
1725   {
1726     createSequenceDetailsReport(ap.av.getSequenceSelection());
1727   }
1728
1729   protected void sequenceDetails_actionPerformed()
1730   {
1731     createSequenceDetailsReport(new SequenceI[] { sequence });
1732   }
1733
1734   public void createSequenceDetailsReport(SequenceI[] sequences)
1735   {
1736     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1737     StringBuffer contents = new StringBuffer();
1738     for (SequenceI seq : sequences)
1739     {
1740       contents.append("<p><h2>"
1741               + MessageManager
1742                       .formatMessage(
1743                               "label.create_sequence_details_report_annotation_for",
1744                               new Object[] { seq.getDisplayId(true) })
1745               + "</h2></p><p>");
1746       new SequenceAnnotationReport(null)
1747               .createSequenceAnnotationReport(
1748                       contents,
1749                       seq,
1750                       true,
1751                       true,
1752                       false,
1753                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1754                               .getSeqPanel().seqCanvas.fr.getMinMax()
1755                               : null);
1756       contents.append("</p>");
1757     }
1758     cap.setText("<html>" + contents.toString() + "</html>");
1759
1760     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1761             "label.sequence_details_for",
1762             (sequences.length == 1 ? new Object[] { sequences[0]
1763                     .getDisplayId(true) } : new Object[] { MessageManager
1764                     .getString("label.selection") })), 500, 400);
1765
1766   }
1767
1768   protected void showNonconserved_actionPerformed()
1769   {
1770     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1771     refresh();
1772   }
1773
1774   /**
1775    * call to refresh view after settings change
1776    */
1777   void refresh()
1778   {
1779     ap.updateAnnotation();
1780     ap.paintAlignment(true);
1781
1782     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1783   }
1784
1785   /**
1786    * DOCUMENT ME!
1787    *
1788    * @param e
1789    *          DOCUMENT ME!
1790    */
1791   protected void clustalColour_actionPerformed()
1792   {
1793     SequenceGroup sg = getGroup();
1794     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1795     refresh();
1796   }
1797
1798   /**
1799    * DOCUMENT ME!
1800    *
1801    * @param e
1802    *          DOCUMENT ME!
1803    */
1804   protected void zappoColour_actionPerformed()
1805   {
1806     getGroup().cs = new ZappoColourScheme();
1807     refresh();
1808   }
1809
1810   /**
1811    * DOCUMENT ME!
1812    *
1813    * @param e
1814    *          DOCUMENT ME!
1815    */
1816   protected void taylorColour_actionPerformed()
1817   {
1818     getGroup().cs = new TaylorColourScheme();
1819     refresh();
1820   }
1821
1822   /**
1823    * DOCUMENT ME!
1824    *
1825    * @param e
1826    *          DOCUMENT ME!
1827    */
1828   protected void hydrophobicityColour_actionPerformed()
1829   {
1830     getGroup().cs = new HydrophobicColourScheme();
1831     refresh();
1832   }
1833
1834   /**
1835    * DOCUMENT ME!
1836    *
1837    * @param e
1838    *          DOCUMENT ME!
1839    */
1840   protected void helixColour_actionPerformed()
1841   {
1842     getGroup().cs = new HelixColourScheme();
1843     refresh();
1844   }
1845
1846   /**
1847    * DOCUMENT ME!
1848    *
1849    * @param e
1850    *          DOCUMENT ME!
1851    */
1852   protected void strandColour_actionPerformed()
1853   {
1854     getGroup().cs = new StrandColourScheme();
1855     refresh();
1856   }
1857
1858   /**
1859    * DOCUMENT ME!
1860    *
1861    * @param e
1862    *          DOCUMENT ME!
1863    */
1864   protected void turnColour_actionPerformed()
1865   {
1866     getGroup().cs = new TurnColourScheme();
1867     refresh();
1868   }
1869
1870   /**
1871    * DOCUMENT ME!
1872    *
1873    * @param e
1874    *          DOCUMENT ME!
1875    */
1876   protected void buriedColour_actionPerformed()
1877   {
1878     getGroup().cs = new BuriedColourScheme();
1879     refresh();
1880   }
1881
1882   /**
1883    * DOCUMENT ME!
1884    *
1885    * @param e
1886    *          DOCUMENT ME!
1887    */
1888   public void nucleotideMenuItem_actionPerformed()
1889   {
1890     getGroup().cs = new NucleotideColourScheme();
1891     refresh();
1892   }
1893
1894   protected void purinePyrimidineColour_actionPerformed()
1895   {
1896     getGroup().cs = new PurinePyrimidineColourScheme();
1897     refresh();
1898   }
1899
1900   /*
1901    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1902    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1903    */
1904   /**
1905    * DOCUMENT ME!
1906    *
1907    * @param e
1908    *          DOCUMENT ME!
1909    */
1910   protected void abovePIDColour_actionPerformed()
1911   {
1912     SequenceGroup sg = getGroup();
1913     if (sg.cs == null)
1914     {
1915       return;
1916     }
1917
1918     if (abovePIDColour.isSelected())
1919     {
1920       sg.cs.setConsensus(AAFrequency.calculate(
1921               sg.getSequences(ap.av.getHiddenRepSequences()),
1922               sg.getStartRes(), sg.getEndRes() + 1));
1923
1924       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1925               .getName());
1926
1927       sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1928
1929       SliderPanel.showPIDSlider();
1930     }
1931     else
1932     // remove PIDColouring
1933     {
1934       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1935     }
1936
1937     refresh();
1938   }
1939
1940   /**
1941    * DOCUMENT ME!
1942    *
1943    * @param e
1944    *          DOCUMENT ME!
1945    */
1946   protected void userDefinedColour_actionPerformed(ActionEvent e)
1947   {
1948     SequenceGroup sg = getGroup();
1949
1950     if (e.getSource().equals(userDefinedColour))
1951     {
1952       new UserDefinedColours(ap, sg);
1953     }
1954     else
1955     {
1956       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1957               .getUserColourSchemes().get(e.getActionCommand());
1958
1959       sg.cs = udc;
1960     }
1961     refresh();
1962   }
1963
1964   /**
1965    * Open a panel where the user can choose which types of sequence annotation
1966    * to show or hide.
1967    *
1968    * @param e
1969    */
1970   protected void chooseAnnotations_actionPerformed(ActionEvent e)
1971   {
1972     // todo correct way to guard against opening a duplicate panel?
1973     new AnnotationChooser(ap);
1974   }
1975
1976   /**
1977    * DOCUMENT ME!
1978    *
1979    * @param e
1980    *          DOCUMENT ME!
1981    */
1982   protected void PIDColour_actionPerformed()
1983   {
1984     SequenceGroup sg = getGroup();
1985     sg.cs = new PIDColourScheme();
1986     sg.cs.setConsensus(AAFrequency.calculate(
1987             sg.getSequences(ap.av.getHiddenRepSequences()),
1988             sg.getStartRes(), sg.getEndRes() + 1));
1989     refresh();
1990   }
1991
1992   /**
1993    * DOCUMENT ME!
1994    *
1995    * @param e
1996    *          DOCUMENT ME!
1997    */
1998   protected void BLOSUM62Colour_actionPerformed()
1999   {
2000     SequenceGroup sg = getGroup();
2001
2002     sg.cs = new Blosum62ColourScheme();
2003
2004     sg.cs.setConsensus(AAFrequency.calculate(
2005             sg.getSequences(ap.av.getHiddenRepSequences()),
2006             sg.getStartRes(), sg.getEndRes() + 1));
2007
2008     refresh();
2009   }
2010
2011   /**
2012    * DOCUMENT ME!
2013    *
2014    * @param e
2015    *          DOCUMENT ME!
2016    */
2017   protected void noColourmenuItem_actionPerformed()
2018   {
2019     getGroup().cs = null;
2020     refresh();
2021   }
2022
2023   /**
2024    * DOCUMENT ME!
2025    *
2026    * @param e
2027    *          DOCUMENT ME!
2028    */
2029   protected void conservationMenuItem_actionPerformed()
2030   {
2031     SequenceGroup sg = getGroup();
2032     if (sg.cs == null)
2033     {
2034       return;
2035     }
2036
2037     if (conservationMenuItem.isSelected())
2038     {
2039       // JBPNote: Conservation name shouldn't be i18n translated
2040       Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
2041               .getHiddenRepSequences()), sg.getStartRes(),
2042               sg.getEndRes() + 1);
2043
2044       c.calculate();
2045       c.verdict(false, ap.av.getConsPercGaps());
2046
2047       sg.cs.setConservation(c);
2048
2049       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2050       SliderPanel.showConservationSlider();
2051     }
2052     else
2053     // remove ConservationColouring
2054     {
2055       sg.cs.setConservation(null);
2056     }
2057
2058     refresh();
2059   }
2060
2061   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2062   {
2063     SequenceGroup sg = getGroup();
2064     if (sg == null)
2065     {
2066       return;
2067     }
2068
2069     AnnotationColourGradient acg = new AnnotationColourGradient(
2070             sequence.getAnnotation()[0], null,
2071             AnnotationColourGradient.NO_THRESHOLD);
2072
2073     acg.setPredefinedColours(true);
2074     sg.cs = acg;
2075
2076     refresh();
2077   }
2078
2079   /**
2080    * DOCUMENT ME!
2081    *
2082    * @param e
2083    *          DOCUMENT ME!
2084    */
2085   protected void groupName_actionPerformed()
2086   {
2087
2088     SequenceGroup sg = getGroup();
2089     EditNameDialog dialog = new EditNameDialog(sg.getName(),
2090             sg.getDescription(), "       "
2091                     + MessageManager.getString("label.group_name") + " ",
2092             MessageManager.getString("label.group_description") + " ",
2093             MessageManager.getString("label.edit_group_name_description"),
2094             ap.alignFrame);
2095
2096     if (!dialog.accept)
2097     {
2098       return;
2099     }
2100
2101     sg.setName(dialog.getName());
2102     sg.setDescription(dialog.getDescription());
2103     refresh();
2104   }
2105
2106   /**
2107    * Get selection group - adding it to the alignment if necessary.
2108    *
2109    * @return sequence group to operate on
2110    */
2111   SequenceGroup getGroup()
2112   {
2113     SequenceGroup sg = ap.av.getSelectionGroup();
2114     // this method won't add a new group if it already exists
2115     if (sg != null)
2116     {
2117       ap.av.getAlignment().addGroup(sg);
2118     }
2119
2120     return sg;
2121   }
2122
2123   /**
2124    * DOCUMENT ME!
2125    *
2126    * @param e
2127    *          DOCUMENT ME!
2128    */
2129   void sequenceName_actionPerformed()
2130   {
2131     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2132             sequence.getDescription(),
2133             "       " + MessageManager.getString("label.sequence_name")
2134                     + " ",
2135             MessageManager.getString("label.sequence_description") + " ",
2136             MessageManager
2137                     .getString("label.edit_sequence_name_description"),
2138             ap.alignFrame);
2139
2140     if (!dialog.accept)
2141     {
2142       return;
2143     }
2144
2145     if (dialog.getName() != null)
2146     {
2147       if (dialog.getName().indexOf(" ") > -1)
2148       {
2149         JOptionPane
2150                 .showMessageDialog(
2151                         ap,
2152                         MessageManager
2153                                 .getString("label.spaces_converted_to_backslashes"),
2154                         MessageManager
2155                                 .getString("label.no_spaces_allowed_sequence_name"),
2156                         JOptionPane.WARNING_MESSAGE);
2157       }
2158
2159       sequence.setName(dialog.getName().replace(' ', '_'));
2160       ap.paintAlignment(false);
2161     }
2162
2163     sequence.setDescription(dialog.getDescription());
2164
2165     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2166             .getSequences());
2167
2168   }
2169
2170   /**
2171    * DOCUMENT ME!
2172    *
2173    * @param e
2174    *          DOCUMENT ME!
2175    */
2176   void unGroupMenuItem_actionPerformed()
2177   {
2178     SequenceGroup sg = ap.av.getSelectionGroup();
2179     ap.av.getAlignment().deleteGroup(sg);
2180     ap.av.setSelectionGroup(null);
2181     refresh();
2182   }
2183
2184   void createGroupMenuItem_actionPerformed()
2185   {
2186     getGroup(); // implicitly creates group - note - should apply defaults / use
2187                 // standard alignment window logic for this
2188     refresh();
2189   }
2190
2191   /**
2192    * DOCUMENT ME!
2193    *
2194    * @param e
2195    *          DOCUMENT ME!
2196    */
2197   protected void outline_actionPerformed()
2198   {
2199     SequenceGroup sg = getGroup();
2200     Color col = JColorChooser.showDialog(this,
2201             MessageManager.getString("label.select_outline_colour"),
2202             Color.BLUE);
2203
2204     if (col != null)
2205     {
2206       sg.setOutlineColour(col);
2207     }
2208
2209     refresh();
2210   }
2211
2212   /**
2213    * DOCUMENT ME!
2214    *
2215    * @param e
2216    *          DOCUMENT ME!
2217    */
2218   public void showBoxes_actionPerformed()
2219   {
2220     getGroup().setDisplayBoxes(showBoxes.isSelected());
2221     refresh();
2222   }
2223
2224   /**
2225    * DOCUMENT ME!
2226    *
2227    * @param e
2228    *          DOCUMENT ME!
2229    */
2230   public void showText_actionPerformed()
2231   {
2232     getGroup().setDisplayText(showText.isSelected());
2233     refresh();
2234   }
2235
2236   /**
2237    * DOCUMENT ME!
2238    *
2239    * @param e
2240    *          DOCUMENT ME!
2241    */
2242   public void showColourText_actionPerformed()
2243   {
2244     getGroup().setColourText(showColourText.isSelected());
2245     refresh();
2246   }
2247
2248   public void showLink(String url)
2249   {
2250     try
2251     {
2252       jalview.util.BrowserLauncher.openURL(url);
2253     } catch (Exception ex)
2254     {
2255       JOptionPane.showInternalMessageDialog(Desktop.desktop,
2256               MessageManager.getString("label.web_browser_not_found_unix"),
2257               MessageManager.getString("label.web_browser_not_found"),
2258               JOptionPane.WARNING_MESSAGE);
2259
2260       ex.printStackTrace();
2261     }
2262   }
2263
2264   void hideSequences(boolean representGroup)
2265   {
2266     ap.av.hideSequences(sequence, representGroup);
2267   }
2268
2269   public void copy_actionPerformed()
2270   {
2271     ap.alignFrame.copy_actionPerformed(null);
2272   }
2273
2274   public void cut_actionPerformed()
2275   {
2276     ap.alignFrame.cut_actionPerformed(null);
2277   }
2278
2279   void changeCase(ActionEvent e)
2280   {
2281     Object source = e.getSource();
2282     SequenceGroup sg = ap.av.getSelectionGroup();
2283
2284     if (sg != null)
2285     {
2286       List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2287               sg.getStartRes(), sg.getEndRes() + 1);
2288
2289       String description;
2290       int caseChange;
2291
2292       if (source == toggle)
2293       {
2294         description = MessageManager.getString("label.toggle_case");
2295         caseChange = ChangeCaseCommand.TOGGLE_CASE;
2296       }
2297       else if (source == upperCase)
2298       {
2299         description = MessageManager.getString("label.to_upper_case");
2300         caseChange = ChangeCaseCommand.TO_UPPER;
2301       }
2302       else
2303       {
2304         description = MessageManager.getString("label.to_lower_case");
2305         caseChange = ChangeCaseCommand.TO_LOWER;
2306       }
2307
2308       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2309               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2310               startEnd, caseChange);
2311
2312       ap.alignFrame.addHistoryItem(caseCommand);
2313
2314       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2315               .getSequences());
2316
2317     }
2318   }
2319
2320   public void outputText_actionPerformed(ActionEvent e)
2321   {
2322     CutAndPasteTransfer cap = new CutAndPasteTransfer();
2323     cap.setForInput(null);
2324     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2325             "label.alignment_output_command",
2326             new Object[] { e.getActionCommand() }), 600, 500);
2327
2328     String[] omitHidden = null;
2329
2330     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2331     // or we simply trust the user wants
2332     // wysiwig behaviour
2333
2334     cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
2335             ap, true));
2336   }
2337
2338   public void sequenceFeature_actionPerformed()
2339   {
2340     SequenceGroup sg = ap.av.getSelectionGroup();
2341     if (sg == null)
2342     {
2343       return;
2344     }
2345
2346     int rsize = 0, gSize = sg.getSize();
2347     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2348     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2349
2350     for (int i = 0; i < gSize; i++)
2351     {
2352       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2353       int end = sg.findEndRes(sg.getSequenceAt(i));
2354       if (start <= end)
2355       {
2356         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2357         features[rsize] = new SequenceFeature(null, null, null, start, end,
2358                 "Jalview");
2359         rsize++;
2360       }
2361     }
2362     rseqs = new SequenceI[rsize];
2363     tfeatures = new SequenceFeature[rsize];
2364     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2365     System.arraycopy(features, 0, tfeatures, 0, rsize);
2366     features = tfeatures;
2367     seqs = rseqs;
2368     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2369             features, true, ap))
2370     {
2371       ap.alignFrame.setShowSeqFeatures(true);
2372       ap.highlightSearchResults(null);
2373     }
2374   }
2375
2376   public void textColour_actionPerformed()
2377   {
2378     SequenceGroup sg = getGroup();
2379     if (sg != null)
2380     {
2381       new TextColourChooser().chooseColour(ap, sg);
2382     }
2383   }
2384
2385   public void colourByStructure(String pdbid)
2386   {
2387     Annotation[] anots = ap.av.getStructureSelectionManager()
2388             .colourSequenceFromStructure(sequence, pdbid);
2389
2390     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2391             "Coloured by " + pdbid, anots);
2392
2393     ap.av.getAlignment().addAnnotation(an);
2394     an.createSequenceMapping(sequence, 0, true);
2395     // an.adjustForAlignment();
2396     ap.av.getAlignment().setAnnotationIndex(an, 0);
2397
2398     ap.adjustAnnotationHeight();
2399
2400     sequence.addAlignmentAnnotation(an);
2401
2402   }
2403
2404   public void editSequence_actionPerformed(ActionEvent actionEvent)
2405   {
2406     SequenceGroup sg = ap.av.getSelectionGroup();
2407
2408     if (sg != null)
2409     {
2410       if (sequence == null)
2411       {
2412         sequence = sg.getSequenceAt(0);
2413       }
2414
2415       EditNameDialog dialog = new EditNameDialog(
2416               sequence.getSequenceAsString(sg.getStartRes(),
2417                       sg.getEndRes() + 1), null,
2418               MessageManager.getString("label.edit_sequence"), null,
2419               MessageManager.getString("label.edit_sequence"),
2420               ap.alignFrame);
2421
2422       if (dialog.accept)
2423       {
2424         EditCommand editCommand = new EditCommand(
2425                 MessageManager.getString("label.edit_sequences"),
2426                 Action.REPLACE, dialog.getName().replace(' ',
2427                         ap.av.getGapCharacter()),
2428                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2429                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2430
2431         ap.alignFrame.addHistoryItem(editCommand);
2432
2433         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2434                 .getSequences());
2435       }
2436     }
2437   }
2438
2439 }