src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26
  27 import jalview.analysis.*;
  28 import jalview.commands.*;
  29 import jalview.datamodel.*;
  30 import jalview.io.*;
  31 import jalview.schemes.*;
  32 import jalview.util.GroupUrlLink;
  33 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  34 import jalview.util.UrlLink;
  35
  36 /**
  37  * DOCUMENT ME!
  38  *
  39  * @author $author$
  40  * @version $Revision: 1.118 $
  41  */
  42 public class PopupMenu extends JPopupMenu
  43 {
  44   JMenu groupMenu = new JMenu();
  45
  46   JMenuItem groupName = new JMenuItem();
  47
  48   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  49
  50   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  51
  52   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  63
  64   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  65
  66   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  71
  72   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  73
  74   // protected JRadioButtonMenuItem covariationColour = new
  75   // JRadioButtonMenuItem();
  76
  77   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  78
  79   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  80
  81   AlignmentPanel ap;
  82
  83   JMenu sequenceMenu = new JMenu();
  84
  85   JMenuItem sequenceName = new JMenuItem();
  86
  87   JMenuItem sequenceDetails = new JMenuItem();
  88
  89   JMenuItem sequenceSelDetails = new JMenuItem();
  90
  91   SequenceI sequence;
  92   JMenuItem createGroupMenuItem = new JMenuItem();
  93   JMenuItem unGroupMenuItem = new JMenuItem();
  94
  95   JMenuItem outline = new JMenuItem();
  96
  97   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  98
  99   JMenu colourMenu = new JMenu();
 100
 101   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 102
 103   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 104
 105   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 106
 107   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 108
 109   JMenu editMenu = new JMenu();
 110
 111   JMenuItem cut = new JMenuItem();
 112
 113   JMenuItem copy = new JMenuItem();
 114
 115   JMenuItem upperCase = new JMenuItem();
 116
 117   JMenuItem lowerCase = new JMenuItem();
 118
 119   JMenuItem toggle = new JMenuItem();
 120
 121   JMenu pdbMenu = new JMenu();
 122
 123   JMenuItem pdbFromFile = new JMenuItem();
 124
 125   JMenuItem enterPDB = new JMenuItem();
 126
 127   JMenuItem discoverPDB = new JMenuItem();
 128
 129   JMenu outputMenu = new JMenu();
 130
 131   JMenuItem sequenceFeature = new JMenuItem();
 132
 133   JMenuItem textColour = new JMenuItem();
 134
 135   JMenu jMenu1 = new JMenu();
 136
 137   JMenu structureMenu = new JMenu();
 138
 139   JMenu viewStructureMenu = new JMenu();
 140
 141   // JMenu colStructureMenu = new JMenu();
 142   JMenuItem editSequence = new JMenuItem();
 143
 144   // JMenuItem annotationMenuItem = new JMenuItem();
 145
 146   JMenu groupLinksMenu;
 147
 148   /**
 149    * Creates a new PopupMenu object.
 150    *
 151    * @param ap
 152    *          DOCUMENT ME!
 153    * @param seq
 154    *          DOCUMENT ME!
 155    */
 156   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 157   {
 158     this(ap, seq, links, null);
 159   }
 160
 161   /**
 162    *
 163    * @param ap
 164    * @param seq
 165    * @param links
 166    * @param groupLinks
 167    */
 168   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 169           Vector links, Vector groupLinks)
 170   {
 171     // /////////////////////////////////////////////////////////
 172     // If this is activated from the sequence panel, the user may want to
 173     // edit or annotate a particular residue. Therefore display the residue menu
 174     //
 175     // If from the IDPanel, we must display the sequence menu
 176     // ////////////////////////////////////////////////////////
 177     this.ap = ap;
 178     sequence = seq;
 179
 180     ButtonGroup colours = new ButtonGroup();
 181     colours.add(noColourmenuItem);
 182     colours.add(clustalColour);
 183     colours.add(zappoColour);
 184     colours.add(taylorColour);
 185     colours.add(hydrophobicityColour);
 186     colours.add(helixColour);
 187     colours.add(strandColour);
 188     colours.add(turnColour);
 189     colours.add(buriedColour);
 190     colours.add(abovePIDColour);
 191     colours.add(userDefinedColour);
 192     colours.add(PIDColour);
 193     colours.add(BLOSUM62Colour);
 194     colours.add(purinePyrimidineColour);
 195     // colours.add(covariationColour);
 196
 197     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 198     {
 199       JMenuItem item = new JMenuItem(
 200               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 201
 202       item.addActionListener(new java.awt.event.ActionListener()
 203       {
 204         public void actionPerformed(ActionEvent e)
 205         {
 206           outputText_actionPerformed(e);
 207         }
 208       });
 209
 210       outputMenu.add(item);
 211     }
 212
 213     try
 214     {
 215       jbInit();
 216     } catch (Exception e)
 217     {
 218       e.printStackTrace();
 219     }
 220
 221     JMenuItem menuItem;
 222     if (seq != null)
 223     {
 224       sequenceMenu.setText(sequence.getName());
 225
 226       if (seq.getDatasetSequence().getPDBId() != null
 227               && seq.getDatasetSequence().getPDBId().size() > 0)
 228       {
 229         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 230                 .elements();
 231
 232         while (e.hasMoreElements())
 233         {
 234           final PDBEntry pdb = (PDBEntry) e.nextElement();
 235
 236           menuItem = new JMenuItem();
 237           menuItem.setText(pdb.getId());
 238           menuItem.addActionListener(new java.awt.event.ActionListener()
 239           {
 240             public void actionPerformed(ActionEvent e)
 241             {
 242               // TODO re JAL-860: optionally open dialog or provide a menu entry
 243               // allowing user to open just one structure per sequence
 244               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 245               { pdb })[0], null, ap);
 246               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 247             }
 248
 249           });
 250           viewStructureMenu.add(menuItem);
 251
 252           /*
 253            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 254            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 255            * public void actionPerformed(ActionEvent e) {
 256            * colourByStructure(pdb.getId()); } });
 257            * colStructureMenu.add(menuItem);
 258            */
 259         }
 260       }
 261       else
 262       {
 263         if (ap.av.getAlignment().isNucleotide() == false)
 264         {
 265           structureMenu.remove(viewStructureMenu);
 266         }
 267         // structureMenu.remove(colStructureMenu);
 268       }
 269
 270       if (ap.av.getAlignment().isNucleotide() == true)
 271       {
 272         AlignmentAnnotation[] aa = ap.av.getAlignment()
 273                 .getAlignmentAnnotation();
 274         for (int i = 0; i < aa.length; i++)
 275         {
 276           if (aa[i].getRNAStruc() != null)
 277           {
 278             final String rnastruc = aa[i].getRNAStruc();
 279             final String structureLine = aa[i].label;
 280             menuItem = new JMenuItem();
 281             menuItem.setText("2D RNA " + structureLine);
 282             menuItem.addActionListener(new java.awt.event.ActionListener()
 283             {
 284               public void actionPerformed(ActionEvent e)
 285               {
 286                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
 287                         rnastruc, seq.getName(), ap);
 288               }
 289             });
 290             viewStructureMenu.add(menuItem);
 291           }
 292         }
 293
 294         // SequenceFeatures[] test = seq.getSequenceFeatures();
 295
 296         if (seq.getAnnotation() != null)
 297         {
 298           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 299           for (int i = 0; i < seqAnno.length; i++)
 300           {
 301             if (seqAnno[i].getRNAStruc() != null)
 302             {
 303               final String rnastruc = seqAnno[i].getRNAStruc();
 304
 305               // TODO: make rnastrucF a bit more nice
 306               menuItem = new JMenuItem();
 307               menuItem.setText("2D RNA - " + seq.getName());
 308               menuItem.addActionListener(new java.awt.event.ActionListener()
 309               {
 310                 public void actionPerformed(ActionEvent e)
 311                 {
 312                   // TODO: VARNA does'nt print gaps in the sequence
 313                   new AppVarna(seq.getName() + " structure", seq, seq
 314                           .getSequenceAsString(), rnastruc, seq.getName(),
 315                           ap);
 316                 }
 317               });
 318               viewStructureMenu.add(menuItem);
 319             }
 320           }
 321         }
 322
 323       }
 324
 325       menuItem = new JMenuItem("Hide Sequences");
 326       menuItem.addActionListener(new java.awt.event.ActionListener()
 327       {
 328         public void actionPerformed(ActionEvent e)
 329         {
 330           hideSequences(false);
 331         }
 332       });
 333       add(menuItem);
 334
 335       if (ap.av.getSelectionGroup() != null
 336               && ap.av.getSelectionGroup().getSize() > 1)
 337       {
 338         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 339         menuItem.addActionListener(new java.awt.event.ActionListener()
 340         {
 341           public void actionPerformed(ActionEvent e)
 342           {
 343             hideSequences(true);
 344           }
 345         });
 346         sequenceMenu.add(menuItem);
 347       }
 348
 349       if (ap.av.hasHiddenRows())
 350       {
 351         final int index = ap.av.getAlignment().findIndex(seq);
 352
 353         if (ap.av.adjustForHiddenSeqs(index)
 354                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 355         {
 356           menuItem = new JMenuItem("Reveal Sequences");
 357           menuItem.addActionListener(new ActionListener()
 358           {
 359             public void actionPerformed(ActionEvent e)
 360             {
 361               ap.av.showSequence(index);
 362               if (ap.overviewPanel != null)
 363               {
 364                 ap.overviewPanel.updateOverviewImage();
 365               }
 366             }
 367           });
 368           add(menuItem);
 369         }
 370       }
 371     }
 372     // for the case when no sequences are even visible
 373     if (ap.av.hasHiddenRows())
 374     {
 375       {
 376         menuItem = new JMenuItem("Reveal All");
 377         menuItem.addActionListener(new ActionListener()
 378         {
 379           public void actionPerformed(ActionEvent e)
 380           {
 381             ap.av.showAllHiddenSeqs();
 382             if (ap.overviewPanel != null)
 383             {
 384               ap.overviewPanel.updateOverviewImage();
 385             }
 386           }
 387         });
 388
 389         add(menuItem);
 390       }
 391
 392     }
 393
 394     SequenceGroup sg = ap.av.getSelectionGroup();
 395     boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
 396
 397     if (sg != null && sg.getSize() > 0)
 398     {
 399       groupName.setText("Name: " + sg.getName());
 400       groupName.setText("Edit name and description of current group.");
 401
 402       if (sg.cs instanceof ZappoColourScheme)
 403       {
 404         zappoColour.setSelected(true);
 405       }
 406       else if (sg.cs instanceof TaylorColourScheme)
 407       {
 408         taylorColour.setSelected(true);
 409       }
 410       else if (sg.cs instanceof PIDColourScheme)
 411       {
 412         PIDColour.setSelected(true);
 413       }
 414       else if (sg.cs instanceof Blosum62ColourScheme)
 415       {
 416         BLOSUM62Colour.setSelected(true);
 417       }
 418       else if (sg.cs instanceof UserColourScheme)
 419       {
 420         userDefinedColour.setSelected(true);
 421       }
 422       else if (sg.cs instanceof HydrophobicColourScheme)
 423       {
 424         hydrophobicityColour.setSelected(true);
 425       }
 426       else if (sg.cs instanceof HelixColourScheme)
 427       {
 428         helixColour.setSelected(true);
 429       }
 430       else if (sg.cs instanceof StrandColourScheme)
 431       {
 432         strandColour.setSelected(true);
 433       }
 434       else if (sg.cs instanceof TurnColourScheme)
 435       {
 436         turnColour.setSelected(true);
 437       }
 438       else if (sg.cs instanceof BuriedColourScheme)
 439       {
 440         buriedColour.setSelected(true);
 441       }
 442       else if (sg.cs instanceof ClustalxColourScheme)
 443       {
 444         clustalColour.setSelected(true);
 445       }
 446       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 447       {
 448         purinePyrimidineColour.setSelected(true);
 449       }
 450       /*
 451        * else if (sg.cs instanceof CovariationColourScheme) {
 452        * covariationColour.setSelected(true); }
 453        */
 454       else
 455       {
 456         noColourmenuItem.setSelected(true);
 457       }
 458
 459       if (sg.cs != null && sg.cs.conservationApplied())
 460       {
 461         conservationMenuItem.setSelected(true);
 462       }
 463       displayNonconserved.setSelected(sg.getShowNonconserved());
 464       showText.setSelected(sg.getDisplayText());
 465       showColourText.setSelected(sg.getColourText());
 466       showBoxes.setSelected(sg.getDisplayBoxes());
 467       // add any groupURLs to the groupURL submenu and make it visible
 468       if (groupLinks != null && groupLinks.size() > 0)
 469       {
 470         buildGroupURLMenu(sg, groupLinks);
 471       }
 472       // Add a 'show all structures' for the current selection
 473       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 474       SequenceI sqass = null;
 475       for (SequenceI sq : ap.av.getSequenceSelection())
 476       {
 477         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 478                 .getPDBId();
 479         if (pes != null)
 480         {
 481           for (PDBEntry pe : pes)
 482           {
 483             pdbe.put(pe.getId(), pe);
 484             if (sqass == null)
 485             {
 486               sqass = sq;
 487             }
 488           }
 489         }
 490       }
 491       if (pdbe.size() > 0)
 492       {
 493         final PDBEntry[] pe = pdbe.values().toArray(
 494                 new PDBEntry[pdbe.size()]);
 495         final JMenuItem gpdbview;
 496         if (pdbe.size() == 1)
 497         {
 498           structureMenu.add(gpdbview = new JMenuItem("View structure for "
 499                   + sqass.getDisplayId(false)));
 500         }
 501         else
 502         {
 503           structureMenu.add(gpdbview = new JMenuItem("View all "
 504                   + pdbe.size() + " structures."));
 505         }
 506         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 507         gpdbview.addActionListener(new ActionListener()
 508         {
 509
 510           @Override
 511           public void actionPerformed(ActionEvent e)
 512           {
 513             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 514           }
 515         });
 516       }
 517     }
 518     else
 519     {
 520       groupMenu.setVisible(false);
 521       editMenu.setVisible(false);
 522     }
 523
 524     if (!isDefinedGroup)
 525     {
 526       createGroupMenuItem.setVisible(true);
 527       unGroupMenuItem.setVisible(false);
 528       jMenu1.setText("Edit New Group");
 529     } else {
 530       createGroupMenuItem.setVisible(false);
 531       unGroupMenuItem.setVisible(true);
 532       jMenu1.setText("Edit Group");
 533     }
 534
 535     if (seq == null)
 536     {
 537       sequenceMenu.setVisible(false);
 538       structureMenu.setVisible(false);
 539     }
 540
 541     if (links != null && links.size() > 0)
 542     {
 543
 544       JMenu linkMenu = new JMenu("Link");
 545       Vector linkset = new Vector();
 546       for (int i = 0; i < links.size(); i++)
 547       {
 548         String link = links.elementAt(i).toString();
 549         UrlLink urlLink = null;
 550         try
 551         {
 552           urlLink = new UrlLink(link);
 553         } catch (Exception foo)
 554         {
 555           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 556                   + "'", foo);
 557           continue;
 558         }
 559         ;
 560         if (!urlLink.isValid())
 561         {
 562           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 563           continue;
 564         }
 565         final String label = urlLink.getLabel();
 566         if (seq != null && urlLink.isDynamic())
 567         {
 568
 569           // collect matching db-refs
 570           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 571                   seq.getDBRef(), new String[]
 572                   { urlLink.getTarget() });
 573           // collect id string too
 574           String id = seq.getName();
 575           String descr = seq.getDescription();
 576           if (descr != null && descr.length() < 1)
 577           {
 578             descr = null;
 579           }
 580
 581           if (dbr != null)
 582           {
 583             for (int r = 0; r < dbr.length; r++)
 584             {
 585               if (id != null && dbr[r].getAccessionId().equals(id))
 586               {
 587                 // suppress duplicate link creation for the bare sequence ID
 588                 // string with this link
 589                 id = null;
 590               }
 591               // create Bare ID link for this RUL
 592               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 593                       true);
 594               if (urls != null)
 595               {
 596                 for (int u = 0; u < urls.length; u += 2)
 597                 {
 598                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 599                   {
 600                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 601                     addshowLink(linkMenu, label + "|" + urls[u],
 602                             urls[u + 1]);
 603                   }
 604                 }
 605               }
 606             }
 607           }
 608           if (id != null)
 609           {
 610             // create Bare ID link for this RUL
 611             String[] urls = urlLink.makeUrls(id, true);
 612             if (urls != null)
 613             {
 614               for (int u = 0; u < urls.length; u += 2)
 615               {
 616                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 617                 {
 618                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 619                   addshowLink(linkMenu, label, urls[u + 1]);
 620                 }
 621               }
 622             }
 623           }
 624           // Create urls from description but only for URL links which are regex
 625           // links
 626           if (descr != null && urlLink.getRegexReplace() != null)
 627           {
 628             // create link for this URL from description where regex matches
 629             String[] urls = urlLink.makeUrls(descr, true);
 630             if (urls != null)
 631             {
 632               for (int u = 0; u < urls.length; u += 2)
 633               {
 634                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 635                 {
 636                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 637                   addshowLink(linkMenu, label, urls[u + 1]);
 638                 }
 639               }
 640             }
 641           }
 642         }
 643         else
 644         {
 645           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 646           {
 647             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 648             // Add a non-dynamic link
 649             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 650           }
 651         }
 652       }
 653       if (sequence != null)
 654       {
 655         sequenceMenu.add(linkMenu);
 656       }
 657       else
 658       {
 659         add(linkMenu);
 660       }
 661     }
 662   }
 663
 664   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 665   {
 666
 667     // TODO: usability: thread off the generation of group url content so root
 668     // menu appears asap
 669     // sequence only URLs
 670     // ID/regex match URLs
 671     groupLinksMenu = new JMenu("Group Link");
 672     JMenu[] linkMenus = new JMenu[]
 673     { null, new JMenu("IDS"), new JMenu("Sequences"),
 674         new JMenu("IDS and Sequences") }; // three types of url that might be
 675                                           // created.
 676     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 677     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 678     Hashtable commonDbrefs = new Hashtable();
 679     for (int sq = 0; sq < seqs.length; sq++)
 680     {
 681
 682       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 683               .findPosition(sg.getEndRes());
 684       // just collect ids from dataset sequence
 685       // TODO: check if IDs collected from selecton group intersects with the
 686       // current selection, too
 687       SequenceI sqi = seqs[sq];
 688       while (sqi.getDatasetSequence() != null)
 689       {
 690         sqi = sqi.getDatasetSequence();
 691       }
 692       DBRefEntry[] dbr = sqi.getDBRef();
 693       if (dbr != null && dbr.length > 0)
 694       {
 695         for (int d = 0; d < dbr.length; d++)
 696         {
 697           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 698           Object[] sarray = (Object[]) commonDbrefs.get(src);
 699           if (sarray == null)
 700           {
 701             sarray = new Object[2];
 702             sarray[0] = new int[]
 703             { 0 };
 704             sarray[1] = new String[seqs.length];
 705
 706             commonDbrefs.put(src, sarray);
 707           }
 708
 709           if (((String[]) sarray[1])[sq] == null)
 710           {
 711             if (!dbr[d].hasMap()
 712                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 713             {
 714               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 715               ((int[]) sarray[0])[0]++;
 716             }
 717           }
 718         }
 719       }
 720     }
 721     // now create group links for all distinct ID/sequence sets.
 722     boolean addMenu = false; // indicates if there are any group links to give
 723                              // to user
 724     for (int i = 0; i < groupLinks.size(); i++)
 725     {
 726       String link = groupLinks.elementAt(i).toString();
 727       GroupUrlLink urlLink = null;
 728       try
 729       {
 730         urlLink = new GroupUrlLink(link);
 731       } catch (Exception foo)
 732       {
 733         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 734                 + "'", foo);
 735         continue;
 736       }
 737       ;
 738       if (!urlLink.isValid())
 739       {
 740         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 741         continue;
 742       }
 743       final String label = urlLink.getLabel();
 744       boolean usingNames = false;
 745       // Now see which parts of the group apply for this URL
 746       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 747       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 748       String[] seqstr, ids; // input to makeUrl
 749       if (idset != null)
 750       {
 751         int numinput = ((int[]) idset[0])[0];
 752         String[] allids = ((String[]) idset[1]);
 753         seqstr = new String[numinput];
 754         ids = new String[numinput];
 755         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 756         {
 757           if (allids[sq] != null)
 758           {
 759             ids[idcount] = allids[sq];
 760             seqstr[idcount++] = idandseqs[1][sq];
 761           }
 762         }
 763       }
 764       else
 765       {
 766         // just use the id/seq set
 767         seqstr = idandseqs[1];
 768         ids = idandseqs[0];
 769         usingNames = true;
 770       }
 771       // and try and make the groupURL!
 772
 773       Object[] urlset = null;
 774       try
 775       {
 776         urlset = urlLink.makeUrlStubs(ids, seqstr,
 777                 "FromJalview" + System.currentTimeMillis(), false);
 778       } catch (UrlStringTooLongException e)
 779       {
 780       }
 781       if (urlset != null)
 782       {
 783         int type = urlLink.getGroupURLType() & 3;
 784         // System.out.println(urlLink.getGroupURLType()
 785         // +" "+((String[])urlset[3])[0]);
 786         // first two bits ofurlLink type bitfield are sequenceids and sequences
 787         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 788         addshowLink(linkMenus[type], label
 789                 + (((type & 1) == 1) ? ("("
 790                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 791                 urlLink, urlset);
 792         addMenu = true;
 793       }
 794     }
 795     if (addMenu)
 796     {
 797       groupLinksMenu = new JMenu("Group Links");
 798       for (int m = 0; m < linkMenus.length; m++)
 799       {
 800         if (linkMenus[m] != null
 801                 && linkMenus[m].getMenuComponentCount() > 0)
 802         {
 803           groupLinksMenu.add(linkMenus[m]);
 804         }
 805       }
 806
 807       groupMenu.add(groupLinksMenu);
 808     }
 809   }
 810
 811   /**
 812    * add a show URL menu item to the given linkMenu
 813    *
 814    * @param linkMenu
 815    * @param label
 816    *          - menu label string
 817    * @param url
 818    *          - url to open
 819    */
 820   private void addshowLink(JMenu linkMenu, String label, final String url)
 821   {
 822     JMenuItem item = new JMenuItem(label);
 823     item.setToolTipText("open URL: " + url);
 824     item.addActionListener(new java.awt.event.ActionListener()
 825     {
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         new Thread(new Runnable()
 829         {
 830
 831           public void run()
 832           {
 833             showLink(url);
 834           }
 835
 836         }).start();
 837       }
 838     });
 839
 840     linkMenu.add(item);
 841   }
 842
 843   /**
 844    * add a late bound groupURL item to the given linkMenu
 845    *
 846    * @param linkMenu
 847    * @param label
 848    *          - menu label string
 849    * @param urlgenerator
 850    *          GroupURLLink used to generate URL
 851    * @param urlstub
 852    *          Object array returned from the makeUrlStubs function.
 853    */
 854   private void addshowLink(JMenu linkMenu, String label,
 855           final GroupUrlLink urlgenerator, final Object[] urlstub)
 856   {
 857     JMenuItem item = new JMenuItem(label);
 858     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 859             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 860                                                                              // put
 861                                                                              // in
 862                                                                              // info
 863                                                                              // about
 864                                                                              // what
 865                                                                              // is
 866                                                                              // being
 867                                                                              // sent.
 868     item.addActionListener(new java.awt.event.ActionListener()
 869     {
 870       public void actionPerformed(ActionEvent e)
 871       {
 872         new Thread(new Runnable()
 873         {
 874
 875           public void run()
 876           {
 877             try
 878             {
 879               showLink(urlgenerator.constructFrom(urlstub));
 880             } catch (UrlStringTooLongException e)
 881             {
 882             }
 883           }
 884
 885         }).start();
 886       }
 887     });
 888
 889     linkMenu.add(item);
 890   }
 891
 892   /**
 893    * DOCUMENT ME!
 894    *
 895    * @throws Exception
 896    *           DOCUMENT ME!
 897    */
 898   private void jbInit() throws Exception
 899   {
 900     groupMenu.setText("Group");
 901     groupMenu.setText("Selection");
 902     groupName.setText("Name");
 903     groupName.addActionListener(new java.awt.event.ActionListener()
 904     {
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         groupName_actionPerformed();
 908       }
 909     });
 910     sequenceMenu.setText("Sequence");
 911     sequenceName.setText("Edit Name/Description");
 912     sequenceName.addActionListener(new java.awt.event.ActionListener()
 913     {
 914       public void actionPerformed(ActionEvent e)
 915       {
 916         sequenceName_actionPerformed();
 917       }
 918     });
 919     sequenceDetails.setText("Sequence Details ...");
 920     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 921     {
 922       public void actionPerformed(ActionEvent e)
 923       {
 924         sequenceDetails_actionPerformed();
 925       }
 926     });
 927     sequenceSelDetails.setText("Sequence Details ...");
 928     sequenceSelDetails
 929             .addActionListener(new java.awt.event.ActionListener()
 930             {
 931               public void actionPerformed(ActionEvent e)
 932               {
 933                 sequenceSelectionDetails_actionPerformed();
 934               }
 935             });
 936     PIDColour.setFocusPainted(false);
 937     unGroupMenuItem.setText("Remove Group");
 938     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 939     {
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         unGroupMenuItem_actionPerformed();
 943       }
 944     });
 945     createGroupMenuItem.setText("Create Group");
 946     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 947     {
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         createGroupMenuItem_actionPerformed();
 951       }
 952     });
 953
 954     outline.setText("Border colour");
 955     outline.addActionListener(new java.awt.event.ActionListener()
 956     {
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         outline_actionPerformed();
 960       }
 961     });
 962     nucleotideMenuItem.setText("Nucleotide");
 963     nucleotideMenuItem.addActionListener(new ActionListener()
 964     {
 965       public void actionPerformed(ActionEvent e)
 966       {
 967         nucleotideMenuItem_actionPerformed();
 968       }
 969     });
 970     colourMenu.setText("Group Colour");
 971     showBoxes.setText("Boxes");
 972     showBoxes.setState(true);
 973     showBoxes.addActionListener(new ActionListener()
 974     {
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         showBoxes_actionPerformed();
 978       }
 979     });
 980     showText.setText("Text");
 981     showText.setState(true);
 982     showText.addActionListener(new ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         showText_actionPerformed();
 987       }
 988     });
 989     showColourText.setText("Colour Text");
 990     showColourText.addActionListener(new ActionListener()
 991     {
 992       public void actionPerformed(ActionEvent e)
 993       {
 994         showColourText_actionPerformed();
 995       }
 996     });
 997     displayNonconserved.setText("Show Nonconserved");
 998     displayNonconserved.setState(true);
 999     displayNonconserved.addActionListener(new ActionListener()
1000     {
1001       public void actionPerformed(ActionEvent e)
1002       {
1003         showNonconserved_actionPerformed();
1004       }
1005     });
1006     editMenu.setText("Edit");
1007     cut.setText("Cut");
1008     cut.addActionListener(new ActionListener()
1009     {
1010       public void actionPerformed(ActionEvent e)
1011       {
1012         cut_actionPerformed();
1013       }
1014     });
1015     upperCase.setText("To Upper Case");
1016     upperCase.addActionListener(new ActionListener()
1017     {
1018       public void actionPerformed(ActionEvent e)
1019       {
1020         changeCase(e);
1021       }
1022     });
1023     copy.setText("Copy");
1024     copy.addActionListener(new ActionListener()
1025     {
1026       public void actionPerformed(ActionEvent e)
1027       {
1028         copy_actionPerformed();
1029       }
1030     });
1031     lowerCase.setText("To Lower Case");
1032     lowerCase.addActionListener(new ActionListener()
1033     {
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         changeCase(e);
1037       }
1038     });
1039     toggle.setText("Toggle Case");
1040     toggle.addActionListener(new ActionListener()
1041     {
1042       public void actionPerformed(ActionEvent e)
1043       {
1044         changeCase(e);
1045       }
1046     });
1047     pdbMenu.setText("Associate Structure with Sequence");
1048     pdbFromFile.setText("From File");
1049     pdbFromFile.addActionListener(new ActionListener()
1050     {
1051       public void actionPerformed(ActionEvent e)
1052       {
1053         pdbFromFile_actionPerformed();
1054       }
1055     });
1056     enterPDB.setText("Enter PDB Id");
1057     enterPDB.addActionListener(new ActionListener()
1058     {
1059       public void actionPerformed(ActionEvent e)
1060       {
1061         enterPDB_actionPerformed();
1062       }
1063     });
1064     discoverPDB.setText("Discover PDB ids");
1065     discoverPDB.addActionListener(new ActionListener()
1066     {
1067       public void actionPerformed(ActionEvent e)
1068       {
1069         discoverPDB_actionPerformed();
1070       }
1071     });
1072     outputMenu.setText("Output to Textbox...");
1073     sequenceFeature.setText("Create Sequence Feature");
1074     sequenceFeature.addActionListener(new ActionListener()
1075     {
1076       public void actionPerformed(ActionEvent e)
1077       {
1078         sequenceFeature_actionPerformed();
1079       }
1080     });
1081     textColour.setText("Text Colour");
1082     textColour.addActionListener(new ActionListener()
1083     {
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         textColour_actionPerformed();
1087       }
1088     });
1089     jMenu1.setText("Group");
1090     structureMenu.setText("Structure");
1091     viewStructureMenu.setText("View Structure");
1092     // colStructureMenu.setText("Colour By Structure");
1093     editSequence.setText("Edit Sequence...");
1094     editSequence.addActionListener(new ActionListener()
1095     {
1096       public void actionPerformed(ActionEvent actionEvent)
1097       {
1098         editSequence_actionPerformed(actionEvent);
1099       }
1100     });
1101
1102     /*
1103      * annotationMenuItem.setText("By Annotation");
1104      * annotationMenuItem.addActionListener(new ActionListener() { public void
1105      * actionPerformed(ActionEvent actionEvent) {
1106      * annotationMenuItem_actionPerformed(actionEvent); } });
1107      */
1108     groupMenu.add(sequenceSelDetails);
1109     add(groupMenu);
1110     add(sequenceMenu);
1111     this.add(structureMenu);
1112     groupMenu.add(editMenu);
1113     groupMenu.add(outputMenu);
1114     groupMenu.add(sequenceFeature);
1115     groupMenu.add(createGroupMenuItem);
1116     groupMenu.add(unGroupMenuItem);
1117     groupMenu.add(jMenu1);
1118     sequenceMenu.add(sequenceName);
1119     sequenceMenu.add(sequenceDetails);
1120     colourMenu.add(textColour);
1121     colourMenu.add(noColourmenuItem);
1122     colourMenu.add(clustalColour);
1123     colourMenu.add(BLOSUM62Colour);
1124     colourMenu.add(PIDColour);
1125     colourMenu.add(zappoColour);
1126     colourMenu.add(taylorColour);
1127     colourMenu.add(hydrophobicityColour);
1128     colourMenu.add(helixColour);
1129     colourMenu.add(strandColour);
1130     colourMenu.add(turnColour);
1131     colourMenu.add(buriedColour);
1132     colourMenu.add(nucleotideMenuItem);
1133     if (ap.getAlignment().isNucleotide())
1134     {
1135       colourMenu.add(purinePyrimidineColour);
1136     }
1137     // colourMenu.add(covariationColour);
1138     colourMenu.add(userDefinedColour);
1139
1140     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1141     {
1142       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1143               .getUserColourSchemes().keys();
1144
1145       while (userColours.hasMoreElements())
1146       {
1147         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1148         item.addActionListener(new ActionListener()
1149         {
1150           public void actionPerformed(ActionEvent evt)
1151           {
1152             userDefinedColour_actionPerformed(evt);
1153           }
1154         });
1155         colourMenu.add(item);
1156       }
1157     }
1158
1159     colourMenu.addSeparator();
1160     colourMenu.add(abovePIDColour);
1161     colourMenu.add(conservationMenuItem);
1162     // colourMenu.add(annotationMenuItem);
1163     editMenu.add(copy);
1164     editMenu.add(cut);
1165     editMenu.add(editSequence);
1166     editMenu.add(upperCase);
1167     editMenu.add(lowerCase);
1168     editMenu.add(toggle);
1169     pdbMenu.add(pdbFromFile);
1170     pdbMenu.add(enterPDB);
1171     pdbMenu.add(discoverPDB);
1172     jMenu1.add(groupName);
1173     jMenu1.add(colourMenu);
1174     jMenu1.add(showBoxes);
1175     jMenu1.add(showText);
1176     jMenu1.add(showColourText);
1177     jMenu1.add(outline);
1178     jMenu1.add(displayNonconserved);
1179     structureMenu.add(pdbMenu);
1180     structureMenu.add(viewStructureMenu);
1181     // structureMenu.add(colStructureMenu);
1182     noColourmenuItem.setText("None");
1183     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1184     {
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         noColourmenuItem_actionPerformed();
1188       }
1189     });
1190
1191     clustalColour.setText("Clustalx colours");
1192     clustalColour.addActionListener(new java.awt.event.ActionListener()
1193     {
1194       public void actionPerformed(ActionEvent e)
1195       {
1196         clustalColour_actionPerformed();
1197       }
1198     });
1199     zappoColour.setText("Zappo");
1200     zappoColour.addActionListener(new java.awt.event.ActionListener()
1201     {
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         zappoColour_actionPerformed();
1205       }
1206     });
1207     taylorColour.setText("Taylor");
1208     taylorColour.addActionListener(new java.awt.event.ActionListener()
1209     {
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         taylorColour_actionPerformed();
1213       }
1214     });
1215     hydrophobicityColour.setText("Hydrophobicity");
1216     hydrophobicityColour
1217             .addActionListener(new java.awt.event.ActionListener()
1218             {
1219               public void actionPerformed(ActionEvent e)
1220               {
1221                 hydrophobicityColour_actionPerformed();
1222               }
1223             });
1224     helixColour.setText("Helix propensity");
1225     helixColour.addActionListener(new java.awt.event.ActionListener()
1226     {
1227       public void actionPerformed(ActionEvent e)
1228       {
1229         helixColour_actionPerformed();
1230       }
1231     });
1232     strandColour.setText("Strand propensity");
1233     strandColour.addActionListener(new java.awt.event.ActionListener()
1234     {
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         strandColour_actionPerformed();
1238       }
1239     });
1240     turnColour.setText("Turn propensity");
1241     turnColour.addActionListener(new java.awt.event.ActionListener()
1242     {
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         turnColour_actionPerformed();
1246       }
1247     });
1248     buriedColour.setText("Buried Index");
1249     buriedColour.addActionListener(new java.awt.event.ActionListener()
1250     {
1251       public void actionPerformed(ActionEvent e)
1252       {
1253         buriedColour_actionPerformed();
1254       }
1255     });
1256     abovePIDColour.setText("Above % Identity");
1257     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1258     {
1259       public void actionPerformed(ActionEvent e)
1260       {
1261         abovePIDColour_actionPerformed();
1262       }
1263     });
1264     userDefinedColour.setText("User Defined...");
1265     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1266     {
1267       public void actionPerformed(ActionEvent e)
1268       {
1269         userDefinedColour_actionPerformed(e);
1270       }
1271     });
1272     PIDColour.setText("Percentage Identity");
1273     PIDColour.addActionListener(new java.awt.event.ActionListener()
1274     {
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         PIDColour_actionPerformed();
1278       }
1279     });
1280     BLOSUM62Colour.setText("BLOSUM62");
1281     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1282     {
1283       public void actionPerformed(ActionEvent e)
1284       {
1285         BLOSUM62Colour_actionPerformed();
1286       }
1287     });
1288     purinePyrimidineColour.setText("Purine/Pyrimidine");
1289     purinePyrimidineColour
1290             .addActionListener(new java.awt.event.ActionListener()
1291             {
1292               public void actionPerformed(ActionEvent e)
1293               {
1294                 purinePyrimidineColour_actionPerformed();
1295               }
1296             });
1297     /*
1298      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1299      * public void actionPerformed(ActionEvent e) {
1300      * covariationColour_actionPerformed(); } });
1301      */
1302
1303     conservationMenuItem.setText("Conservation");
1304     conservationMenuItem
1305             .addActionListener(new java.awt.event.ActionListener()
1306             {
1307               public void actionPerformed(ActionEvent e)
1308               {
1309                 conservationMenuItem_actionPerformed();
1310               }
1311             });
1312   }
1313
1314   protected void sequenceSelectionDetails_actionPerformed()
1315   {
1316     createSequenceDetailsReport(ap.av.getSequenceSelection());
1317   }
1318
1319   protected void sequenceDetails_actionPerformed()
1320   {
1321     createSequenceDetailsReport(new SequenceI[]
1322     { sequence });
1323   }
1324
1325   public void createSequenceDetailsReport(SequenceI[] sequences)
1326   {
1327     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1328     StringBuffer contents = new StringBuffer();
1329     for (SequenceI seq : sequences)
1330     {
1331       contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1332               + "</h2></p><p>");
1333       new SequenceAnnotationReport(null)
1334               .createSequenceAnnotationReport(
1335                       contents,
1336                       seq,
1337                       true,
1338                       true,
1339                       false,
1340                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1341                               : null);
1342       contents.append("</p>");
1343     }
1344     cap.setText("<html>" + contents.toString() + "</html>");
1345
1346     Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1347             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1348                     : "Selection"), 500, 400);
1349
1350   }
1351
1352   protected void showNonconserved_actionPerformed()
1353   {
1354     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1355     refresh();
1356   }
1357
1358   /**
1359    * call to refresh view after settings change
1360    */
1361   void refresh()
1362   {
1363     ap.updateAnnotation();
1364     ap.paintAlignment(true);
1365
1366     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1367   }
1368
1369   /**
1370    * DOCUMENT ME!
1371    *
1372    * @param e
1373    *          DOCUMENT ME!
1374    */
1375   protected void clustalColour_actionPerformed()
1376   {
1377     SequenceGroup sg = getGroup();
1378     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1379     refresh();
1380   }
1381
1382   /**
1383    * DOCUMENT ME!
1384    *
1385    * @param e
1386    *          DOCUMENT ME!
1387    */
1388   protected void zappoColour_actionPerformed()
1389   {
1390     getGroup().cs = new ZappoColourScheme();
1391     refresh();
1392   }
1393
1394   /**
1395    * DOCUMENT ME!
1396    *
1397    * @param e
1398    *          DOCUMENT ME!
1399    */
1400   protected void taylorColour_actionPerformed()
1401   {
1402     getGroup().cs = new TaylorColourScheme();
1403     refresh();
1404   }
1405
1406   /**
1407    * DOCUMENT ME!
1408    *
1409    * @param e
1410    *          DOCUMENT ME!
1411    */
1412   protected void hydrophobicityColour_actionPerformed()
1413   {
1414     getGroup().cs = new HydrophobicColourScheme();
1415     refresh();
1416   }
1417
1418   /**
1419    * DOCUMENT ME!
1420    *
1421    * @param e
1422    *          DOCUMENT ME!
1423    */
1424   protected void helixColour_actionPerformed()
1425   {
1426     getGroup().cs = new HelixColourScheme();
1427     refresh();
1428   }
1429
1430   /**
1431    * DOCUMENT ME!
1432    *
1433    * @param e
1434    *          DOCUMENT ME!
1435    */
1436   protected void strandColour_actionPerformed()
1437   {
1438     getGroup().cs = new StrandColourScheme();
1439     refresh();
1440   }
1441
1442   /**
1443    * DOCUMENT ME!
1444    *
1445    * @param e
1446    *          DOCUMENT ME!
1447    */
1448   protected void turnColour_actionPerformed()
1449   {
1450     getGroup().cs = new TurnColourScheme();
1451     refresh();
1452   }
1453
1454   /**
1455    * DOCUMENT ME!
1456    *
1457    * @param e
1458    *          DOCUMENT ME!
1459    */
1460   protected void buriedColour_actionPerformed()
1461   {
1462     getGroup().cs = new BuriedColourScheme();
1463     refresh();
1464   }
1465
1466   /**
1467    * DOCUMENT ME!
1468    *
1469    * @param e
1470    *          DOCUMENT ME!
1471    */
1472   public void nucleotideMenuItem_actionPerformed()
1473   {
1474     getGroup().cs = new NucleotideColourScheme();
1475     refresh();
1476   }
1477
1478   protected void purinePyrimidineColour_actionPerformed()
1479   {
1480     getGroup().cs = new PurinePyrimidineColourScheme();
1481     refresh();
1482   }
1483
1484   /*
1485    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1486    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1487    */
1488   /**
1489    * DOCUMENT ME!
1490    *
1491    * @param e
1492    *          DOCUMENT ME!
1493    */
1494   protected void abovePIDColour_actionPerformed()
1495   {
1496     SequenceGroup sg = getGroup();
1497     if (sg.cs == null)
1498     {
1499       return;
1500     }
1501
1502     if (abovePIDColour.isSelected())
1503     {
1504       sg.cs.setConsensus(AAFrequency.calculate(
1505               sg.getSequences(ap.av.getHiddenRepSequences()),
1506               sg.getStartRes(), sg.getEndRes() + 1));
1507
1508       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1509               .getName());
1510
1511       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1512
1513       SliderPanel.showPIDSlider();
1514     }
1515     else
1516     // remove PIDColouring
1517     {
1518       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1519     }
1520
1521     refresh();
1522   }
1523
1524   /**
1525    * DOCUMENT ME!
1526    *
1527    * @param e
1528    *          DOCUMENT ME!
1529    */
1530   protected void userDefinedColour_actionPerformed(ActionEvent e)
1531   {
1532     SequenceGroup sg = getGroup();
1533
1534     if (e.getActionCommand().equals("User Defined..."))
1535     {
1536       new UserDefinedColours(ap, sg);
1537     }
1538     else
1539     {
1540       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1541               .getUserColourSchemes().get(e.getActionCommand());
1542
1543       sg.cs = udc;
1544     }
1545     refresh();
1546   }
1547
1548   /**
1549    * DOCUMENT ME!
1550    *
1551    * @param e
1552    *          DOCUMENT ME!
1553    */
1554   protected void PIDColour_actionPerformed()
1555   {
1556     SequenceGroup sg = getGroup();
1557     sg.cs = new PIDColourScheme();
1558     sg.cs.setConsensus(AAFrequency.calculate(
1559             sg.getSequences(ap.av.getHiddenRepSequences()),
1560             sg.getStartRes(), sg.getEndRes() + 1));
1561     refresh();
1562   }
1563
1564   /**
1565    * DOCUMENT ME!
1566    *
1567    * @param e
1568    *          DOCUMENT ME!
1569    */
1570   protected void BLOSUM62Colour_actionPerformed()
1571   {
1572     SequenceGroup sg = getGroup();
1573
1574     sg.cs = new Blosum62ColourScheme();
1575
1576     sg.cs.setConsensus(AAFrequency.calculate(
1577             sg.getSequences(ap.av.getHiddenRepSequences()),
1578             sg.getStartRes(), sg.getEndRes() + 1));
1579
1580     refresh();
1581   }
1582
1583   /**
1584    * DOCUMENT ME!
1585    *
1586    * @param e
1587    *          DOCUMENT ME!
1588    */
1589   protected void noColourmenuItem_actionPerformed()
1590   {
1591     getGroup().cs = null;
1592     refresh();
1593   }
1594
1595   /**
1596    * DOCUMENT ME!
1597    *
1598    * @param e
1599    *          DOCUMENT ME!
1600    */
1601   protected void conservationMenuItem_actionPerformed()
1602   {
1603     SequenceGroup sg = getGroup();
1604     if (sg.cs == null)
1605     {
1606       return;
1607     }
1608
1609     if (conservationMenuItem.isSelected())
1610     {
1611       Conservation c = new Conservation("Group",
1612               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1613                       .getHiddenRepSequences()), sg.getStartRes(),
1614               sg.getEndRes() + 1);
1615
1616       c.calculate();
1617       c.verdict(false, ap.av.getConsPercGaps());
1618
1619       sg.cs.setConservation(c);
1620
1621       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1622       SliderPanel.showConservationSlider();
1623     }
1624     else
1625     // remove ConservationColouring
1626     {
1627       sg.cs.setConservation(null);
1628     }
1629
1630     refresh();
1631   }
1632
1633   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1634   {
1635     SequenceGroup sg = getGroup();
1636     if (sg == null)
1637     {
1638       return;
1639     }
1640
1641     AnnotationColourGradient acg = new AnnotationColourGradient(
1642             sequence.getAnnotation()[0], null,
1643             AnnotationColourGradient.NO_THRESHOLD);
1644
1645     acg.setPredefinedColours(true);
1646     sg.cs = acg;
1647
1648     refresh();
1649   }
1650
1651   /**
1652    * DOCUMENT ME!
1653    *
1654    * @param e
1655    *          DOCUMENT ME!
1656    */
1657   protected void groupName_actionPerformed()
1658   {
1659
1660     SequenceGroup sg = getGroup();
1661     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1662             sg.getDescription(), "       Group Name ",
1663             "Group Description ", "Edit Group Name/Description",
1664             ap.alignFrame);
1665
1666     if (!dialog.accept)
1667     {
1668       return;
1669     }
1670
1671     sg.setName(dialog.getName());
1672     sg.setDescription(dialog.getDescription());
1673     refresh();
1674   }
1675
1676   /**
1677    * Get selection group - adding it to the alignment if necessary.
1678    *
1679    * @return sequence group to operate on
1680    */
1681   SequenceGroup getGroup()
1682   {
1683     SequenceGroup sg = ap.av.getSelectionGroup();
1684     // this method won't add a new group if it already exists
1685     if (sg != null)
1686     {
1687       ap.av.getAlignment().addGroup(sg);
1688     }
1689
1690     return sg;
1691   }
1692
1693   /**
1694    * DOCUMENT ME!
1695    *
1696    * @param e
1697    *          DOCUMENT ME!
1698    */
1699   void sequenceName_actionPerformed()
1700   {
1701     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1702             sequence.getDescription(), "       Sequence Name ",
1703             "Sequence Description ", "Edit Sequence Name/Description",
1704             ap.alignFrame);
1705
1706     if (!dialog.accept)
1707     {
1708       return;
1709     }
1710
1711     if (dialog.getName() != null)
1712     {
1713       if (dialog.getName().indexOf(" ") > -1)
1714       {
1715         JOptionPane.showMessageDialog(ap,
1716                 "Spaces have been converted to \"_\"",
1717                 "No spaces allowed in Sequence Name",
1718                 JOptionPane.WARNING_MESSAGE);
1719       }
1720
1721       sequence.setName(dialog.getName().replace(' ', '_'));
1722       ap.paintAlignment(false);
1723     }
1724
1725     sequence.setDescription(dialog.getDescription());
1726
1727     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1728             .getSequences());
1729
1730   }
1731
1732   /**
1733    * DOCUMENT ME!
1734    *
1735    * @param e
1736    *          DOCUMENT ME!
1737    */
1738   void unGroupMenuItem_actionPerformed()
1739   {
1740     SequenceGroup sg = ap.av.getSelectionGroup();
1741     ap.av.getAlignment().deleteGroup(sg);
1742     ap.av.setSelectionGroup(null);
1743     refresh();
1744   }
1745   void createGroupMenuItem_actionPerformed()
1746   {
1747     getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
1748     refresh();
1749   }
1750
1751   /**
1752    * DOCUMENT ME!
1753    *
1754    * @param e
1755    *          DOCUMENT ME!
1756    */
1757   protected void outline_actionPerformed()
1758   {
1759     SequenceGroup sg = getGroup();
1760     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1761             Color.BLUE);
1762
1763     if (col != null)
1764     {
1765       sg.setOutlineColour(col);
1766     }
1767
1768     refresh();
1769   }
1770
1771   /**
1772    * DOCUMENT ME!
1773    *
1774    * @param e
1775    *          DOCUMENT ME!
1776    */
1777   public void showBoxes_actionPerformed()
1778   {
1779     getGroup().setDisplayBoxes(showBoxes.isSelected());
1780     refresh();
1781   }
1782
1783   /**
1784    * DOCUMENT ME!
1785    *
1786    * @param e
1787    *          DOCUMENT ME!
1788    */
1789   public void showText_actionPerformed()
1790   {
1791     getGroup().setDisplayText(showText.isSelected());
1792     refresh();
1793   }
1794
1795   /**
1796    * DOCUMENT ME!
1797    *
1798    * @param e
1799    *          DOCUMENT ME!
1800    */
1801   public void showColourText_actionPerformed()
1802   {
1803     getGroup().setColourText(showColourText.isSelected());
1804     refresh();
1805   }
1806
1807   public void showLink(String url)
1808   {
1809     try
1810     {
1811       jalview.util.BrowserLauncher.openURL(url);
1812     } catch (Exception ex)
1813     {
1814       JOptionPane
1815               .showInternalMessageDialog(
1816                       Desktop.desktop,
1817                       "Unixers: Couldn't find default web browser."
1818                               + "\nAdd the full path to your browser in Preferences.",
1819                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1820
1821       ex.printStackTrace();
1822     }
1823   }
1824
1825   void hideSequences(boolean representGroup)
1826   {
1827     SequenceGroup sg = ap.av.getSelectionGroup();
1828     if (sg == null || sg.getSize() < 1)
1829     {
1830       ap.av.hideSequence(new SequenceI[]
1831       { sequence });
1832       return;
1833     }
1834
1835     ap.av.setSelectionGroup(null);
1836
1837     if (representGroup)
1838     {
1839       ap.av.hideRepSequences(sequence, sg);
1840
1841       return;
1842     }
1843
1844     int gsize = sg.getSize();
1845     SequenceI[] hseqs;
1846
1847     hseqs = new SequenceI[gsize];
1848
1849     int index = 0;
1850     for (int i = 0; i < gsize; i++)
1851     {
1852       hseqs[index++] = sg.getSequenceAt(i);
1853     }
1854
1855     ap.av.hideSequence(hseqs);
1856     // refresh(); TODO: ? needed ?
1857     ap.av.sendSelection();
1858   }
1859
1860   public void copy_actionPerformed()
1861   {
1862     ap.alignFrame.copy_actionPerformed(null);
1863   }
1864
1865   public void cut_actionPerformed()
1866   {
1867     ap.alignFrame.cut_actionPerformed(null);
1868   }
1869
1870   void changeCase(ActionEvent e)
1871   {
1872     Object source = e.getSource();
1873     SequenceGroup sg = ap.av.getSelectionGroup();
1874
1875     if (sg != null)
1876     {
1877       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1878               sg.getEndRes() + 1);
1879
1880       String description;
1881       int caseChange;
1882
1883       if (source == toggle)
1884       {
1885         description = "Toggle Case";
1886         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1887       }
1888       else if (source == upperCase)
1889       {
1890         description = "To Upper Case";
1891         caseChange = ChangeCaseCommand.TO_UPPER;
1892       }
1893       else
1894       {
1895         description = "To Lower Case";
1896         caseChange = ChangeCaseCommand.TO_LOWER;
1897       }
1898
1899       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1900               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1901               startEnd, caseChange);
1902
1903       ap.alignFrame.addHistoryItem(caseCommand);
1904
1905       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1906               .getSequences());
1907
1908     }
1909   }
1910
1911   public void outputText_actionPerformed(ActionEvent e)
1912   {
1913     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1914     cap.setForInput(null);
1915     Desktop.addInternalFrame(cap,
1916             "Alignment output - " + e.getActionCommand(), 600, 500);
1917
1918     String[] omitHidden = null;
1919
1920     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1921     // or we simply trust the user wants
1922     // wysiwig behaviour
1923     SequenceGroup sg = ap.av.getSelectionGroup();
1924     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1925     omitHidden = ap.av.getViewAsString(true);
1926     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1927     AlignmentAnnotation[] nala = ap.av.getAlignment()
1928             .getAlignmentAnnotation();
1929     if (nala != null)
1930     {
1931       for (int i = 0; i < nala.length; i++)
1932       {
1933         AlignmentAnnotation na = nala[i];
1934         oal.addAnnotation(na);
1935       }
1936     }
1937     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1938             oal, omitHidden, csel, sg));
1939     oal = null;
1940   }
1941
1942   public void pdbFromFile_actionPerformed()
1943   {
1944     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1945             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1946     chooser.setFileView(new jalview.io.JalviewFileView());
1947     chooser.setDialogTitle("Select a PDB file for "
1948             + sequence.getDisplayId(false));
1949     chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1950             + sequence.getDisplayId(false) + "'");
1951
1952     int value = chooser.showOpenDialog(null);
1953
1954     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1955     {
1956       String choice = chooser.getSelectedFile().getPath();
1957       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1958       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1959               jalview.io.AppletFormatAdapter.FILE, sequence, true);
1960     }
1961
1962   }
1963
1964   public void enterPDB_actionPerformed()
1965   {
1966     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1967             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1968
1969     if (id != null && id.length() > 0)
1970     {
1971       PDBEntry entry = new PDBEntry();
1972       entry.setId(id.toUpperCase());
1973       sequence.getDatasetSequence().addPDBId(entry);
1974     }
1975   }
1976
1977   public void discoverPDB_actionPerformed()
1978   {
1979
1980     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
1981     { sequence }
1982             : ap.av.getSequenceSelection());
1983     Thread discpdb = new Thread(new Runnable()
1984     {
1985       public void run()
1986       {
1987
1988         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1989                 .fetchDBRefs(false);
1990       }
1991
1992     });
1993     discpdb.start();
1994   }
1995
1996   public void sequenceFeature_actionPerformed()
1997   {
1998     SequenceGroup sg = ap.av.getSelectionGroup();
1999     if (sg == null)
2000     {
2001       return;
2002     }
2003
2004     int rsize = 0, gSize = sg.getSize();
2005     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2006     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2007
2008     for (int i = 0; i < gSize; i++)
2009     {
2010       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2011       int end = sg.findEndRes(sg.getSequenceAt(i));
2012       if (start <= end)
2013       {
2014         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2015         features[rsize] = new SequenceFeature(null, null, null, start, end,
2016                 "Jalview");
2017         rsize++;
2018       }
2019     }
2020     rseqs = new SequenceI[rsize];
2021     tfeatures = new SequenceFeature[rsize];
2022     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2023     System.arraycopy(features, 0, tfeatures, 0, rsize);
2024     features = tfeatures;
2025     seqs = rseqs;
2026     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2027             features, true, ap))
2028     {
2029       ap.alignFrame.setShowSeqFeatures(true);
2030       ap.highlightSearchResults(null);
2031     }
2032   }
2033
2034   public void textColour_actionPerformed()
2035   {
2036     SequenceGroup sg = getGroup();
2037     if (sg != null)
2038     {
2039       new TextColourChooser().chooseColour(ap, sg);
2040     }
2041   }
2042
2043   public void colourByStructure(String pdbid)
2044   {
2045     Annotation[] anots = ap.av.getStructureSelectionManager()
2046             .colourSequenceFromStructure(sequence, pdbid);
2047
2048     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2049             "Coloured by " + pdbid, anots);
2050
2051     ap.av.getAlignment().addAnnotation(an);
2052     an.createSequenceMapping(sequence, 0, true);
2053     // an.adjustForAlignment();
2054     ap.av.getAlignment().setAnnotationIndex(an, 0);
2055
2056     ap.adjustAnnotationHeight();
2057
2058     sequence.addAlignmentAnnotation(an);
2059
2060   }
2061
2062   public void editSequence_actionPerformed(ActionEvent actionEvent)
2063   {
2064     SequenceGroup sg = ap.av.getSelectionGroup();
2065
2066     if (sg != null)
2067     {
2068       if (sequence == null)
2069         sequence = (Sequence) sg.getSequenceAt(0);
2070
2071       EditNameDialog dialog = new EditNameDialog(
2072               sequence.getSequenceAsString(sg.getStartRes(),
2073                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2074               "Edit Sequence", ap.alignFrame);
2075
2076       if (dialog.accept)
2077       {
2078         EditCommand editCommand = new EditCommand("Edit Sequences",
2079                 EditCommand.REPLACE, dialog.getName().replace(' ',
2080                         ap.av.getGapCharacter()),
2081                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2082                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2083
2084         ap.alignFrame.addHistoryItem(editCommand);
2085
2086         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2087                 .getSequences());
2088       }
2089     }
2090   }
2091
2092 }