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   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  74
  75   // protected JRadioButtonMenuItem covariationColour = new
  76   // JRadioButtonMenuItem();
  77
  78   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  79
  80   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  81
  82   AlignmentPanel ap;
  83
  84   JMenu sequenceMenu = new JMenu();
  85
  86   JMenuItem sequenceName = new JMenuItem();
  87
  88   JMenuItem sequenceDetails = new JMenuItem();
  89
  90   JMenuItem sequenceSelDetails = new JMenuItem();
  91
  92   SequenceI sequence;
  93
  94   JMenuItem unGroupMenuItem = new JMenuItem();
  95
  96   JMenuItem outline = new JMenuItem();
  97
  98   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  99
 100   JMenu colourMenu = new JMenu();
 101
 102   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 103
 104   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 105
 106   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 107
 108   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 109
 110   JMenu editMenu = new JMenu();
 111
 112   JMenuItem cut = new JMenuItem();
 113
 114   JMenuItem copy = new JMenuItem();
 115
 116   JMenuItem upperCase = new JMenuItem();
 117
 118   JMenuItem lowerCase = new JMenuItem();
 119
 120   JMenuItem toggle = new JMenuItem();
 121
 122   JMenu pdbMenu = new JMenu();
 123
 124   JMenuItem pdbFromFile = new JMenuItem();
 125     // JBPNote: Commented these out - Should add these services via the web services menu system.
 126     // JMenuItem ContraFold = new JMenuItem();
 127
 128     // JMenuItem RNAFold = new JMenuItem();
 129
 130   JMenuItem enterPDB = new JMenuItem();
 131
 132   JMenuItem discoverPDB = new JMenuItem();
 133
 134   JMenu outputMenu = new JMenu();
 135
 136   JMenuItem sequenceFeature = new JMenuItem();
 137
 138   JMenuItem textColour = new JMenuItem();
 139
 140   JMenu jMenu1 = new JMenu();
 141
 142   JMenu structureMenu = new JMenu();
 143
 144   JMenu viewStructureMenu = new JMenu();
 145
 146   // JMenu colStructureMenu = new JMenu();
 147   JMenuItem editSequence = new JMenuItem();
 148
 149   // JMenuItem annotationMenuItem = new JMenuItem();
 150
 151   JMenu groupLinksMenu;
 152
 153   /**
 154    * Creates a new PopupMenu object.
 155    *
 156    * @param ap
 157    *          DOCUMENT ME!
 158    * @param seq
 159    *          DOCUMENT ME!
 160    */
 161   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 162   {
 163     this(ap, seq, links, null);
 164   }
 165
 166   /**
 167    *
 168    * @param ap
 169    * @param seq
 170    * @param links
 171    * @param groupLinks
 172    */
 173   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 174           Vector links, Vector groupLinks)
 175   {
 176     // /////////////////////////////////////////////////////////
 177     // If this is activated from the sequence panel, the user may want to
 178     // edit or annotate a particular residue. Therefore display the residue menu
 179     //
 180     // If from the IDPanel, we must display the sequence menu
 181     // ////////////////////////////////////////////////////////
 182     this.ap = ap;
 183     sequence = seq;
 184
 185     ButtonGroup colours = new ButtonGroup();
 186     colours.add(noColourmenuItem);
 187     colours.add(clustalColour);
 188     colours.add(zappoColour);
 189     colours.add(taylorColour);
 190     colours.add(hydrophobicityColour);
 191     colours.add(helixColour);
 192     colours.add(strandColour);
 193     colours.add(turnColour);
 194     colours.add(buriedColour);
 195     colours.add(abovePIDColour);
 196     colours.add(userDefinedColour);
 197     colours.add(PIDColour);
 198     colours.add(BLOSUM62Colour);
 199     colours.add(purinePyrimidineColour);
 200     colours.add(RNAInteractionColour);
 201     // colours.add(covariationColour);
 202
 203     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 204     {
 205       JMenuItem item = new JMenuItem(
 206               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 207
 208       item.addActionListener(new java.awt.event.ActionListener()
 209       {
 210         public void actionPerformed(ActionEvent e)
 211         {
 212           outputText_actionPerformed(e);
 213         }
 214       });
 215
 216       outputMenu.add(item);
 217     }
 218
 219     try
 220     {
 221       jbInit();
 222     } catch (Exception e)
 223     {
 224       e.printStackTrace();
 225     }
 226
 227     JMenuItem menuItem;
 228     if (seq != null)
 229     {
 230       sequenceMenu.setText(sequence.getName());
 231
 232       if (seq.getDatasetSequence().getPDBId() != null
 233               && seq.getDatasetSequence().getPDBId().size() > 0)
 234       {
 235         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 236                 .elements();
 237
 238         while (e.hasMoreElements())
 239         {
 240           final PDBEntry pdb = (PDBEntry) e.nextElement();
 241
 242           menuItem = new JMenuItem();
 243           menuItem.setText(pdb.getId());
 244           menuItem.addActionListener(new java.awt.event.ActionListener()
 245           {
 246             public void actionPerformed(ActionEvent e)
 247             {
 248               // TODO re JAL-860: optionally open dialog or provide a menu entry
 249               // allowing user to open just one structure per sequence
 250               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 251               { pdb })[0], null, ap);
 252               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 253             }
 254
 255           });
 256           viewStructureMenu.add(menuItem);
 257
 258           /*
 259            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 260            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 261            * public void actionPerformed(ActionEvent e) {
 262            * colourByStructure(pdb.getId()); } });
 263            * colStructureMenu.add(menuItem);
 264            */
 265         }
 266       }
 267       else
 268       {
 269         if (ap.av.getAlignment().isNucleotide() == false)
 270         {
 271           structureMenu.remove(viewStructureMenu);
 272         }
 273         // structureMenu.remove(colStructureMenu);
 274       }
 275
 276       if (ap.av.getAlignment().isNucleotide() == true)
 277       {
 278         AlignmentAnnotation[] aa = ap.av.getAlignment()
 279                 .getAlignmentAnnotation();
 280         for (int i = 0; i < aa.length; i++)
 281         {
 282           if (aa[i].getRNAStruc() != null)
 283           {
 284             final String rnastruc = aa[i].getRNAStruc();
 285             final String structureLine = aa[i].label;
 286             menuItem = new JMenuItem();
 287             menuItem.setText("2D RNA " + structureLine);
 288             menuItem.addActionListener(new java.awt.event.ActionListener()
 289
 290             {
 291               public void actionPerformed(ActionEvent e)
 292               {
 293                         //System.out.println("1:"+structureLine);
 294                         System.out.println("1:sname"+seq.getName());
 295                         System.out.println("2:seq"+seq);
 296
 297                         //System.out.println("3:"+seq.getSequenceAsString());
 298                         System.out.println("3:strucseq"+rnastruc);
 299                         //System.out.println("4:struc"+seq.getRNA());
 300                         System.out.println("5:name"+seq.getName());
 301                         System.out.println("6:ap"+ap);
 302                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 303                             .getName(), ap);
 304                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 305                         System.out.println("end");
 306               }
 307             });
 308             viewStructureMenu.add(menuItem);
 309           }
 310         }
 311
 312         // SequenceFeatures[] test = seq.getSequenceFeatures();
 313
 314         if (seq.getAnnotation() != null)
 315         {
 316           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 317           for (int i = 0; i < seqAnno.length; i++)
 318           {
 319             if (seqAnno[i].getRNAStruc() != null)
 320             {
 321               final String rnastruc = seqAnno[i].getRNAStruc();
 322
 323               // TODO: make rnastrucF a bit more nice
 324               menuItem = new JMenuItem();
 325               menuItem.setText("2D RNA - " + seq.getName());
 326               menuItem.addActionListener(new java.awt.event.ActionListener()
 327               {
 328                 public void actionPerformed(ActionEvent e)
 329                 {
 330                   // TODO: VARNA does'nt print gaps in the sequence
 331
 332                   new AppVarna(seq.getName() + " structure", seq, seq
 333                           .getSequenceAsString(), rnastruc, seq.getName(),
 334                           ap);
 335                 }
 336               });
 337               viewStructureMenu.add(menuItem);
 338             }
 339           }
 340         }
 341
 342       }
 343
 344       menuItem = new JMenuItem("Hide Sequences");
 345       menuItem.addActionListener(new java.awt.event.ActionListener()
 346       {
 347         public void actionPerformed(ActionEvent e)
 348         {
 349           hideSequences(false);
 350         }
 351       });
 352       add(menuItem);
 353
 354       if (ap.av.getSelectionGroup() != null
 355               && ap.av.getSelectionGroup().getSize() > 1)
 356       {
 357         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 358         menuItem.addActionListener(new java.awt.event.ActionListener()
 359         {
 360           public void actionPerformed(ActionEvent e)
 361           {
 362             hideSequences(true);
 363           }
 364         });
 365         sequenceMenu.add(menuItem);
 366       }
 367
 368       if (ap.av.hasHiddenRows())
 369       {
 370         final int index = ap.av.getAlignment().findIndex(seq);
 371
 372         if (ap.av.adjustForHiddenSeqs(index)
 373                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 374         {
 375           menuItem = new JMenuItem("Reveal Sequences");
 376           menuItem.addActionListener(new ActionListener()
 377           {
 378             public void actionPerformed(ActionEvent e)
 379             {
 380               ap.av.showSequence(index);
 381               if (ap.overviewPanel != null)
 382               {
 383                 ap.overviewPanel.updateOverviewImage();
 384               }
 385             }
 386           });
 387           add(menuItem);
 388         }
 389       }
 390     }
 391     // for the case when no sequences are even visible
 392     if (ap.av.hasHiddenRows())
 393     {
 394       {
 395         menuItem = new JMenuItem("Reveal All");
 396         menuItem.addActionListener(new ActionListener()
 397         {
 398           public void actionPerformed(ActionEvent e)
 399           {
 400             ap.av.showAllHiddenSeqs();
 401             if (ap.overviewPanel != null)
 402             {
 403               ap.overviewPanel.updateOverviewImage();
 404             }
 405           }
 406         });
 407
 408         add(menuItem);
 409       }
 410
 411     }
 412
 413     SequenceGroup sg = ap.av.getSelectionGroup();
 414
 415     if (sg != null && sg.getSize() > 0)
 416     {
 417       groupName.setText("Name: " + sg.getName());
 418       groupName.setText("Edit name and description of current group.");
 419
 420       if (sg.cs instanceof ZappoColourScheme)
 421       {
 422         zappoColour.setSelected(true);
 423       }
 424       else if (sg.cs instanceof TaylorColourScheme)
 425       {
 426         taylorColour.setSelected(true);
 427       }
 428       else if (sg.cs instanceof PIDColourScheme)
 429       {
 430         PIDColour.setSelected(true);
 431       }
 432       else if (sg.cs instanceof Blosum62ColourScheme)
 433       {
 434         BLOSUM62Colour.setSelected(true);
 435       }
 436       else if (sg.cs instanceof UserColourScheme)
 437       {
 438         userDefinedColour.setSelected(true);
 439       }
 440       else if (sg.cs instanceof HydrophobicColourScheme)
 441       {
 442         hydrophobicityColour.setSelected(true);
 443       }
 444       else if (sg.cs instanceof HelixColourScheme)
 445       {
 446         helixColour.setSelected(true);
 447       }
 448       else if (sg.cs instanceof StrandColourScheme)
 449       {
 450         strandColour.setSelected(true);
 451       }
 452       else if (sg.cs instanceof TurnColourScheme)
 453       {
 454         turnColour.setSelected(true);
 455       }
 456       else if (sg.cs instanceof BuriedColourScheme)
 457       {
 458         buriedColour.setSelected(true);
 459       }
 460       else if (sg.cs instanceof ClustalxColourScheme)
 461       {
 462         clustalColour.setSelected(true);
 463       }
 464       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 465       {
 466         purinePyrimidineColour.setSelected(true);
 467       }
 468
 469
 470       /*
 471        * else if (sg.cs instanceof CovariationColourScheme) {
 472        * covariationColour.setSelected(true); }
 473        */
 474       else
 475       {
 476         noColourmenuItem.setSelected(true);
 477       }
 478
 479       if (sg.cs != null && sg.cs.conservationApplied())
 480       {
 481         conservationMenuItem.setSelected(true);
 482       }
 483       displayNonconserved.setSelected(sg.getShowNonconserved());
 484       showText.setSelected(sg.getDisplayText());
 485       showColourText.setSelected(sg.getColourText());
 486       showBoxes.setSelected(sg.getDisplayBoxes());
 487       // add any groupURLs to the groupURL submenu and make it visible
 488       if (groupLinks != null && groupLinks.size() > 0)
 489       {
 490         buildGroupURLMenu(sg, groupLinks);
 491       }
 492       // Add a 'show all structures' for the current selection
 493       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 494       SequenceI sqass = null;
 495       for (SequenceI sq : ap.av.getSequenceSelection())
 496       {
 497         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 498                 .getPDBId();
 499         if (pes != null)
 500         {
 501           for (PDBEntry pe : pes)
 502           {
 503             pdbe.put(pe.getId(), pe);
 504             if (sqass == null)
 505             {
 506               sqass = sq;
 507             }
 508           }
 509         }
 510       }
 511       if (pdbe.size() > 0)
 512       {
 513         final PDBEntry[] pe = pdbe.values().toArray(
 514                 new PDBEntry[pdbe.size()]);
 515         final JMenuItem gpdbview;
 516         if (pdbe.size() == 1)
 517         {
 518           structureMenu.add(gpdbview = new JMenuItem("View structure for "
 519                   + sqass.getDisplayId(false)));
 520         }
 521         else
 522         {
 523           structureMenu.add(gpdbview = new JMenuItem("View all "
 524                   + pdbe.size() + " structures."));
 525         }
 526         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 527         gpdbview.addActionListener(new ActionListener()
 528         {
 529
 530           @Override
 531           public void actionPerformed(ActionEvent e)
 532           {
 533             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 534           }
 535         });
 536       }
 537     }
 538     else
 539     {
 540       groupMenu.setVisible(false);
 541       editMenu.setVisible(false);
 542     }
 543
 544     if (!ap.av.getAlignment().getGroups().contains(sg))
 545     {
 546       unGroupMenuItem.setVisible(false);
 547     }
 548
 549     if (seq == null)
 550     {
 551       sequenceMenu.setVisible(false);
 552       structureMenu.setVisible(false);
 553     }
 554
 555     if (links != null && links.size() > 0)
 556     {
 557
 558       JMenu linkMenu = new JMenu("Link");
 559       Vector linkset = new Vector();
 560       for (int i = 0; i < links.size(); i++)
 561       {
 562         String link = links.elementAt(i).toString();
 563         UrlLink urlLink = null;
 564         try
 565         {
 566           urlLink = new UrlLink(link);
 567         } catch (Exception foo)
 568         {
 569           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 570                   + "'", foo);
 571           continue;
 572         }
 573         ;
 574         if (!urlLink.isValid())
 575         {
 576           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 577           continue;
 578         }
 579         final String label = urlLink.getLabel();
 580         if (seq != null && urlLink.isDynamic())
 581         {
 582
 583           // collect matching db-refs
 584           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 585                   seq.getDBRef(), new String[]
 586                   { urlLink.getTarget() });
 587           // collect id string too
 588           String id = seq.getName();
 589           String descr = seq.getDescription();
 590           if (descr != null && descr.length() < 1)
 591           {
 592             descr = null;
 593           }
 594
 595           if (dbr != null)
 596           {
 597             for (int r = 0; r < dbr.length; r++)
 598             {
 599               if (id != null && dbr[r].getAccessionId().equals(id))
 600               {
 601                 // suppress duplicate link creation for the bare sequence ID
 602                 // string with this link
 603                 id = null;
 604               }
 605               // create Bare ID link for this RUL
 606               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 607                       true);
 608               if (urls != null)
 609               {
 610                 for (int u = 0; u < urls.length; u += 2)
 611                 {
 612                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 613                   {
 614                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 615                     addshowLink(linkMenu, label + "|" + urls[u],
 616                             urls[u + 1]);
 617                   }
 618                 }
 619               }
 620             }
 621           }
 622           if (id != null)
 623           {
 624             // create Bare ID link for this RUL
 625             String[] urls = urlLink.makeUrls(id, true);
 626             if (urls != null)
 627             {
 628               for (int u = 0; u < urls.length; u += 2)
 629               {
 630                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 631                 {
 632                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 633                   addshowLink(linkMenu, label, urls[u + 1]);
 634                 }
 635               }
 636             }
 637           }
 638           // Create urls from description but only for URL links which are regex
 639           // links
 640           if (descr != null && urlLink.getRegexReplace() != null)
 641           {
 642             // create link for this URL from description where regex matches
 643             String[] urls = urlLink.makeUrls(descr, true);
 644             if (urls != null)
 645             {
 646               for (int u = 0; u < urls.length; u += 2)
 647               {
 648                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 649                 {
 650                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 651                   addshowLink(linkMenu, label, urls[u + 1]);
 652                 }
 653               }
 654             }
 655           }
 656         }
 657         else
 658         {
 659           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 660           {
 661             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 662             // Add a non-dynamic link
 663             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 664           }
 665         }
 666       }
 667       if (sequence != null)
 668       {
 669         sequenceMenu.add(linkMenu);
 670       }
 671       else
 672       {
 673         add(linkMenu);
 674       }
 675     }
 676   }
 677
 678   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 679   {
 680
 681     // TODO: usability: thread off the generation of group url content so root
 682     // menu appears asap
 683     // sequence only URLs
 684     // ID/regex match URLs
 685     groupLinksMenu = new JMenu("Group Link");
 686     JMenu[] linkMenus = new JMenu[]
 687     { null, new JMenu("IDS"), new JMenu("Sequences"),
 688         new JMenu("IDS and Sequences") }; // three types of url that might be
 689                                           // created.
 690     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 691     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 692     Hashtable commonDbrefs = new Hashtable();
 693     for (int sq = 0; sq < seqs.length; sq++)
 694     {
 695
 696       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 697               .findPosition(sg.getEndRes());
 698       // just collect ids from dataset sequence
 699       // TODO: check if IDs collected from selecton group intersects with the
 700       // current selection, too
 701       SequenceI sqi = seqs[sq];
 702       while (sqi.getDatasetSequence() != null)
 703       {
 704         sqi = sqi.getDatasetSequence();
 705       }
 706       DBRefEntry[] dbr = sqi.getDBRef();
 707       if (dbr != null && dbr.length > 0)
 708       {
 709         for (int d = 0; d < dbr.length; d++)
 710         {
 711           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 712           Object[] sarray = (Object[]) commonDbrefs.get(src);
 713           if (sarray == null)
 714           {
 715             sarray = new Object[2];
 716             sarray[0] = new int[]
 717             { 0 };
 718             sarray[1] = new String[seqs.length];
 719
 720             commonDbrefs.put(src, sarray);
 721           }
 722
 723           if (((String[]) sarray[1])[sq] == null)
 724           {
 725             if (!dbr[d].hasMap()
 726                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 727             {
 728               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 729               ((int[]) sarray[0])[0]++;
 730             }
 731           }
 732         }
 733       }
 734     }
 735     // now create group links for all distinct ID/sequence sets.
 736     boolean addMenu = false; // indicates if there are any group links to give
 737                              // to user
 738     for (int i = 0; i < groupLinks.size(); i++)
 739     {
 740       String link = groupLinks.elementAt(i).toString();
 741       GroupUrlLink urlLink = null;
 742       try
 743       {
 744         urlLink = new GroupUrlLink(link);
 745       } catch (Exception foo)
 746       {
 747         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 748                 + "'", foo);
 749         continue;
 750       }
 751       ;
 752       if (!urlLink.isValid())
 753       {
 754         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 755         continue;
 756       }
 757       final String label = urlLink.getLabel();
 758       boolean usingNames = false;
 759       // Now see which parts of the group apply for this URL
 760       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 761       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 762       String[] seqstr, ids; // input to makeUrl
 763       if (idset != null)
 764       {
 765         int numinput = ((int[]) idset[0])[0];
 766         String[] allids = ((String[]) idset[1]);
 767         seqstr = new String[numinput];
 768         ids = new String[numinput];
 769         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 770         {
 771           if (allids[sq] != null)
 772           {
 773             ids[idcount] = allids[sq];
 774             seqstr[idcount++] = idandseqs[1][sq];
 775           }
 776         }
 777       }
 778       else
 779       {
 780         // just use the id/seq set
 781         seqstr = idandseqs[1];
 782         ids = idandseqs[0];
 783         usingNames = true;
 784       }
 785       // and try and make the groupURL!
 786
 787       Object[] urlset = null;
 788       try
 789       {
 790         urlset = urlLink.makeUrlStubs(ids, seqstr,
 791                 "FromJalview" + System.currentTimeMillis(), false);
 792       } catch (UrlStringTooLongException e)
 793       {
 794       }
 795       if (urlset != null)
 796       {
 797         int type = urlLink.getGroupURLType() & 3;
 798         // System.out.println(urlLink.getGroupURLType()
 799         // +" "+((String[])urlset[3])[0]);
 800         // first two bits ofurlLink type bitfield are sequenceids and sequences
 801         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 802         addshowLink(linkMenus[type], label
 803                 + (((type & 1) == 1) ? ("("
 804                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 805                 urlLink, urlset);
 806         addMenu = true;
 807       }
 808     }
 809     if (addMenu)
 810     {
 811       groupLinksMenu = new JMenu("Group Links");
 812       for (int m = 0; m < linkMenus.length; m++)
 813       {
 814         if (linkMenus[m] != null
 815                 && linkMenus[m].getMenuComponentCount() > 0)
 816         {
 817           groupLinksMenu.add(linkMenus[m]);
 818         }
 819       }
 820
 821       groupMenu.add(groupLinksMenu);
 822     }
 823   }
 824
 825   /**
 826    * add a show URL menu item to the given linkMenu
 827    *
 828    * @param linkMenu
 829    * @param label
 830    *          - menu label string
 831    * @param url
 832    *          - url to open
 833    */
 834   private void addshowLink(JMenu linkMenu, String label, final String url)
 835   {
 836     JMenuItem item = new JMenuItem(label);
 837     item.setToolTipText("open URL: " + url);
 838     item.addActionListener(new java.awt.event.ActionListener()
 839     {
 840       public void actionPerformed(ActionEvent e)
 841       {
 842         new Thread(new Runnable()
 843         {
 844
 845           public void run()
 846           {
 847             showLink(url);
 848           }
 849
 850         }).start();
 851       }
 852     });
 853
 854     linkMenu.add(item);
 855   }
 856
 857   /**
 858    * add a late bound groupURL item to the given linkMenu
 859    *
 860    * @param linkMenu
 861    * @param label
 862    *          - menu label string
 863    * @param urlgenerator
 864    *          GroupURLLink used to generate URL
 865    * @param urlstub
 866    *          Object array returned from the makeUrlStubs function.
 867    */
 868   private void addshowLink(JMenu linkMenu, String label,
 869           final GroupUrlLink urlgenerator, final Object[] urlstub)
 870   {
 871     JMenuItem item = new JMenuItem(label);
 872     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 873             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 874                                                                              // put
 875                                                                              // in
 876                                                                              // info
 877                                                                              // about
 878                                                                              // what
 879                                                                              // is
 880                                                                              // being
 881                                                                              // sent.
 882     item.addActionListener(new java.awt.event.ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         new Thread(new Runnable()
 887         {
 888
 889           public void run()
 890           {
 891             try
 892             {
 893               showLink(urlgenerator.constructFrom(urlstub));
 894             } catch (UrlStringTooLongException e)
 895             {
 896             }
 897           }
 898
 899         }).start();
 900       }
 901     });
 902
 903     linkMenu.add(item);
 904   }
 905
 906   /**
 907    * DOCUMENT ME!
 908    *
 909    * @throws Exception
 910    *           DOCUMENT ME!
 911    */
 912   private void jbInit() throws Exception
 913   {
 914     groupMenu.setText("Group");
 915     groupMenu.setText("Selection");
 916     groupName.setText("Name");
 917     groupName.addActionListener(new java.awt.event.ActionListener()
 918     {
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         groupName_actionPerformed();
 922       }
 923     });
 924     sequenceMenu.setText("Sequence");
 925     sequenceName.setText("Edit Name/Description");
 926     sequenceName.addActionListener(new java.awt.event.ActionListener()
 927     {
 928       public void actionPerformed(ActionEvent e)
 929       {
 930         sequenceName_actionPerformed();
 931       }
 932     });
 933     sequenceDetails.setText("Sequence Details ...");
 934     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 935     {
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         sequenceDetails_actionPerformed();
 939       }
 940     });
 941     sequenceSelDetails.setText("Sequence Details ...");
 942     sequenceSelDetails
 943             .addActionListener(new java.awt.event.ActionListener()
 944             {
 945               public void actionPerformed(ActionEvent e)
 946               {
 947                 sequenceSelectionDetails_actionPerformed();
 948               }
 949             });
 950     PIDColour.setFocusPainted(false);
 951     unGroupMenuItem.setText("Remove Group");
 952     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 953     {
 954       public void actionPerformed(ActionEvent e)
 955       {
 956         unGroupMenuItem_actionPerformed();
 957       }
 958     });
 959
 960     outline.setText("Border colour");
 961     outline.addActionListener(new java.awt.event.ActionListener()
 962     {
 963       public void actionPerformed(ActionEvent e)
 964       {
 965         outline_actionPerformed();
 966       }
 967     });
 968     nucleotideMenuItem.setText("Nucleotide");
 969     nucleotideMenuItem.addActionListener(new ActionListener()
 970     {
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         nucleotideMenuItem_actionPerformed();
 974       }
 975     });
 976     colourMenu.setText("Group Colour");
 977     showBoxes.setText("Boxes");
 978     showBoxes.setState(true);
 979     showBoxes.addActionListener(new ActionListener()
 980     {
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         showBoxes_actionPerformed();
 984       }
 985     });
 986     showText.setText("Text");
 987     showText.setState(true);
 988     showText.addActionListener(new ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         showText_actionPerformed();
 993       }
 994     });
 995     showColourText.setText("Colour Text");
 996     showColourText.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         showColourText_actionPerformed();
1001       }
1002     });
1003     displayNonconserved.setText("Show Nonconserved");
1004     displayNonconserved.setState(true);
1005     displayNonconserved.addActionListener(new ActionListener()
1006     {
1007       public void actionPerformed(ActionEvent e)
1008       {
1009         showNonconserved_actionPerformed();
1010       }
1011     });
1012     editMenu.setText("Edit");
1013     cut.setText("Cut");
1014     cut.addActionListener(new ActionListener()
1015     {
1016       public void actionPerformed(ActionEvent e)
1017       {
1018         cut_actionPerformed();
1019       }
1020     });
1021     upperCase.setText("To Upper Case");
1022     upperCase.addActionListener(new ActionListener()
1023     {
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         changeCase(e);
1027       }
1028     });
1029     copy.setText("Copy");
1030     copy.addActionListener(new ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         copy_actionPerformed();
1035       }
1036     });
1037     lowerCase.setText("To Lower Case");
1038     lowerCase.addActionListener(new ActionListener()
1039     {
1040       public void actionPerformed(ActionEvent e)
1041       {
1042         changeCase(e);
1043       }
1044     });
1045     toggle.setText("Toggle Case");
1046     toggle.addActionListener(new ActionListener()
1047     {
1048       public void actionPerformed(ActionEvent e)
1049       {
1050         changeCase(e);
1051       }
1052     });
1053     pdbMenu.setText("Associate Structure with Sequence");
1054     pdbFromFile.setText("From File");
1055     pdbFromFile.addActionListener(new ActionListener()
1056     {
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         pdbFromFile_actionPerformed();
1060       }
1061     });
1062 //    RNAFold.setText("From RNA Fold with predict2D");
1063 //    RNAFold.addActionListener(new ActionListener()
1064 //    {
1065 //      public void actionPerformed(ActionEvent e)
1066 //      {
1067 //        try {
1068 //                      RNAFold_actionPerformed();
1069 //              } catch (Exception e1) {
1070 //                      // TODO Auto-generated catch block
1071 //                      e1.printStackTrace();
1072 //              }
1073 //      }
1074 //    });
1075 //    ContraFold.setText("From Contra Fold with predict2D");
1076 //    ContraFold.addActionListener(new ActionListener()
1077 //    {
1078 //      public void actionPerformed(ActionEvent e)
1079 //      {
1080 //        try {
1081 //                      ContraFold_actionPerformed();
1082 //              } catch (Exception e1) {
1083 //                      // TODO Auto-generated catch block
1084 //                      e1.printStackTrace();
1085 //              }
1086 //      }
1087 //    });
1088     enterPDB.setText("Enter PDB Id");
1089     enterPDB.addActionListener(new ActionListener()
1090     {
1091       public void actionPerformed(ActionEvent e)
1092       {
1093         enterPDB_actionPerformed();
1094       }
1095     });
1096     discoverPDB.setText("Discover PDB ids");
1097     discoverPDB.addActionListener(new ActionListener()
1098     {
1099       public void actionPerformed(ActionEvent e)
1100       {
1101         discoverPDB_actionPerformed();
1102       }
1103     });
1104     outputMenu.setText("Output to Textbox...");
1105     sequenceFeature.setText("Create Sequence Feature");
1106     sequenceFeature.addActionListener(new ActionListener()
1107     {
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         sequenceFeature_actionPerformed();
1111       }
1112     });
1113     textColour.setText("Text Colour");
1114     textColour.addActionListener(new ActionListener()
1115     {
1116       public void actionPerformed(ActionEvent e)
1117       {
1118         textColour_actionPerformed();
1119       }
1120     });
1121     jMenu1.setText("Group");
1122     structureMenu.setText("Structure");
1123     viewStructureMenu.setText("View Structure");
1124     // colStructureMenu.setText("Colour By Structure");
1125     editSequence.setText("Edit Sequence...");
1126     editSequence.addActionListener(new ActionListener()
1127     {
1128       public void actionPerformed(ActionEvent actionEvent)
1129       {
1130         editSequence_actionPerformed(actionEvent);
1131       }
1132     });
1133
1134     /*
1135      * annotationMenuItem.setText("By Annotation");
1136      * annotationMenuItem.addActionListener(new ActionListener() { public void
1137      * actionPerformed(ActionEvent actionEvent) {
1138      * annotationMenuItem_actionPerformed(actionEvent); } });
1139      */
1140     groupMenu.add(sequenceSelDetails);
1141     add(groupMenu);
1142     add(sequenceMenu);
1143     this.add(structureMenu);
1144     groupMenu.add(editMenu);
1145     groupMenu.add(outputMenu);
1146     groupMenu.add(sequenceFeature);
1147     groupMenu.add(jMenu1);
1148     sequenceMenu.add(sequenceName);
1149     sequenceMenu.add(sequenceDetails);
1150     colourMenu.add(textColour);
1151     colourMenu.add(noColourmenuItem);
1152     colourMenu.add(clustalColour);
1153     colourMenu.add(BLOSUM62Colour);
1154     colourMenu.add(PIDColour);
1155     colourMenu.add(zappoColour);
1156     colourMenu.add(taylorColour);
1157     colourMenu.add(hydrophobicityColour);
1158     colourMenu.add(helixColour);
1159     colourMenu.add(strandColour);
1160     colourMenu.add(turnColour);
1161     colourMenu.add(buriedColour);
1162     colourMenu.add(nucleotideMenuItem);
1163     if (ap.getAlignment().isNucleotide()) {
1164         // JBPNote - commented since the colourscheme isn't functional
1165         //  colourMenu.add(RNAInteractionColour);
1166         colourMenu.add(purinePyrimidineColour);
1167     }
1168     // colourMenu.add(covariationColour);
1169     colourMenu.add(userDefinedColour);
1170
1171     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1172     {
1173       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1174               .getUserColourSchemes().keys();
1175
1176       while (userColours.hasMoreElements())
1177       {
1178         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1179         item.addActionListener(new ActionListener()
1180         {
1181           public void actionPerformed(ActionEvent evt)
1182           {
1183             userDefinedColour_actionPerformed(evt);
1184           }
1185         });
1186         colourMenu.add(item);
1187       }
1188     }
1189
1190     colourMenu.addSeparator();
1191     colourMenu.add(abovePIDColour);
1192     colourMenu.add(conservationMenuItem);
1193     // colourMenu.add(annotationMenuItem);
1194     editMenu.add(copy);
1195     editMenu.add(cut);
1196     editMenu.add(editSequence);
1197     editMenu.add(upperCase);
1198     editMenu.add(lowerCase);
1199     editMenu.add(toggle);
1200     pdbMenu.add(pdbFromFile);
1201     // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1202     //    pdbMenu.add(RNAFold);
1203     //    pdbMenu.add(ContraFold);
1204     pdbMenu.add(enterPDB);
1205     pdbMenu.add(discoverPDB);
1206     jMenu1.add(groupName);
1207     jMenu1.add(unGroupMenuItem);
1208     jMenu1.add(colourMenu);
1209     jMenu1.add(showBoxes);
1210     jMenu1.add(showText);
1211     jMenu1.add(showColourText);
1212     jMenu1.add(outline);
1213     jMenu1.add(displayNonconserved);
1214     structureMenu.add(pdbMenu);
1215     structureMenu.add(viewStructureMenu);
1216     // structureMenu.add(colStructureMenu);
1217     noColourmenuItem.setText("None");
1218     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1219     {
1220       public void actionPerformed(ActionEvent e)
1221       {
1222         noColourmenuItem_actionPerformed();
1223       }
1224     });
1225
1226     clustalColour.setText("Clustalx colours");
1227     clustalColour.addActionListener(new java.awt.event.ActionListener()
1228     {
1229       public void actionPerformed(ActionEvent e)
1230       {
1231         clustalColour_actionPerformed();
1232       }
1233     });
1234     zappoColour.setText("Zappo");
1235     zappoColour.addActionListener(new java.awt.event.ActionListener()
1236     {
1237       public void actionPerformed(ActionEvent e)
1238       {
1239         zappoColour_actionPerformed();
1240       }
1241     });
1242     taylorColour.setText("Taylor");
1243     taylorColour.addActionListener(new java.awt.event.ActionListener()
1244     {
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         taylorColour_actionPerformed();
1248       }
1249     });
1250     hydrophobicityColour.setText("Hydrophobicity");
1251     hydrophobicityColour
1252             .addActionListener(new java.awt.event.ActionListener()
1253             {
1254               public void actionPerformed(ActionEvent e)
1255               {
1256                 hydrophobicityColour_actionPerformed();
1257               }
1258             });
1259     helixColour.setText("Helix propensity");
1260     helixColour.addActionListener(new java.awt.event.ActionListener()
1261     {
1262       public void actionPerformed(ActionEvent e)
1263       {
1264         helixColour_actionPerformed();
1265       }
1266     });
1267     strandColour.setText("Strand propensity");
1268     strandColour.addActionListener(new java.awt.event.ActionListener()
1269     {
1270       public void actionPerformed(ActionEvent e)
1271       {
1272         strandColour_actionPerformed();
1273       }
1274     });
1275     turnColour.setText("Turn propensity");
1276     turnColour.addActionListener(new java.awt.event.ActionListener()
1277     {
1278       public void actionPerformed(ActionEvent e)
1279       {
1280         turnColour_actionPerformed();
1281       }
1282     });
1283     buriedColour.setText("Buried Index");
1284     buriedColour.addActionListener(new java.awt.event.ActionListener()
1285     {
1286       public void actionPerformed(ActionEvent e)
1287       {
1288         buriedColour_actionPerformed();
1289       }
1290     });
1291     abovePIDColour.setText("Above % Identity");
1292     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1293     {
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         abovePIDColour_actionPerformed();
1297       }
1298     });
1299     userDefinedColour.setText("User Defined...");
1300     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1301     {
1302       public void actionPerformed(ActionEvent e)
1303       {
1304         userDefinedColour_actionPerformed(e);
1305       }
1306     });
1307     PIDColour.setText("Percentage Identity");
1308     PIDColour.addActionListener(new java.awt.event.ActionListener()
1309     {
1310       public void actionPerformed(ActionEvent e)
1311       {
1312         PIDColour_actionPerformed();
1313       }
1314     });
1315     BLOSUM62Colour.setText("BLOSUM62");
1316     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1317     {
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         BLOSUM62Colour_actionPerformed();
1321       }
1322     });
1323     purinePyrimidineColour.setText("Purine/Pyrimidine");
1324     purinePyrimidineColour
1325             .addActionListener(new java.awt.event.ActionListener()
1326             {
1327               public void actionPerformed(ActionEvent e)
1328               {
1329                 purinePyrimidineColour_actionPerformed();
1330               }
1331             });
1332
1333
1334     /*
1335      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1336      * public void actionPerformed(ActionEvent e) {
1337      * covariationColour_actionPerformed(); } });
1338      */
1339
1340     conservationMenuItem.setText("Conservation");
1341     conservationMenuItem
1342             .addActionListener(new java.awt.event.ActionListener()
1343             {
1344               public void actionPerformed(ActionEvent e)
1345               {
1346                 conservationMenuItem_actionPerformed();
1347               }
1348             });
1349   }
1350
1351   protected void sequenceSelectionDetails_actionPerformed()
1352   {
1353     createSequenceDetailsReport(ap.av.getSequenceSelection());
1354   }
1355
1356   protected void sequenceDetails_actionPerformed()
1357   {
1358     createSequenceDetailsReport(new SequenceI[]
1359     { sequence });
1360   }
1361
1362   public void createSequenceDetailsReport(SequenceI[] sequences)
1363   {
1364     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1365     StringBuffer contents = new StringBuffer();
1366     for (SequenceI seq : sequences)
1367     {
1368       contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1369               + "</h2></p><p>");
1370       new SequenceAnnotationReport(null)
1371               .createSequenceAnnotationReport(
1372                       contents,
1373                       seq,
1374                       true,
1375                       true,
1376                       false,
1377                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1378                               : null);
1379       contents.append("</p>");
1380     }
1381     cap.setText("<html>" + contents.toString() + "</html>");
1382
1383     Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1384             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1385                     : "Selection"), 500, 400);
1386
1387   }
1388
1389   protected void showNonconserved_actionPerformed()
1390   {
1391     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1392     refresh();
1393   }
1394
1395   /**
1396    * call to refresh view after settings change
1397    */
1398   void refresh()
1399   {
1400     ap.updateAnnotation();
1401     ap.paintAlignment(true);
1402
1403     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1404   }
1405
1406   /**
1407    * DOCUMENT ME!
1408    *
1409    * @param e
1410    *          DOCUMENT ME!
1411    */
1412   protected void clustalColour_actionPerformed()
1413   {
1414     SequenceGroup sg = getGroup();
1415     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1416     refresh();
1417   }
1418
1419   /**
1420    * DOCUMENT ME!
1421    *
1422    * @param e
1423    *          DOCUMENT ME!
1424    */
1425   protected void zappoColour_actionPerformed()
1426   {
1427     getGroup().cs = new ZappoColourScheme();
1428     refresh();
1429   }
1430
1431   /**
1432    * DOCUMENT ME!
1433    *
1434    * @param e
1435    *          DOCUMENT ME!
1436    */
1437   protected void taylorColour_actionPerformed()
1438   {
1439     getGroup().cs = new TaylorColourScheme();
1440     refresh();
1441   }
1442
1443   /**
1444    * DOCUMENT ME!
1445    *
1446    * @param e
1447    *          DOCUMENT ME!
1448    */
1449   protected void hydrophobicityColour_actionPerformed()
1450   {
1451     getGroup().cs = new HydrophobicColourScheme();
1452     refresh();
1453   }
1454
1455   /**
1456    * DOCUMENT ME!
1457    *
1458    * @param e
1459    *          DOCUMENT ME!
1460    */
1461   protected void helixColour_actionPerformed()
1462   {
1463     getGroup().cs = new HelixColourScheme();
1464     refresh();
1465   }
1466
1467   /**
1468    * DOCUMENT ME!
1469    *
1470    * @param e
1471    *          DOCUMENT ME!
1472    */
1473   protected void strandColour_actionPerformed()
1474   {
1475     getGroup().cs = new StrandColourScheme();
1476     refresh();
1477   }
1478
1479   /**
1480    * DOCUMENT ME!
1481    *
1482    * @param e
1483    *          DOCUMENT ME!
1484    */
1485   protected void turnColour_actionPerformed()
1486   {
1487     getGroup().cs = new TurnColourScheme();
1488     refresh();
1489   }
1490
1491   /**
1492    * DOCUMENT ME!
1493    *
1494    * @param e
1495    *          DOCUMENT ME!
1496    */
1497   protected void buriedColour_actionPerformed()
1498   {
1499     getGroup().cs = new BuriedColourScheme();
1500     refresh();
1501   }
1502
1503   /**
1504    * DOCUMENT ME!
1505    *
1506    * @param e
1507    *          DOCUMENT ME!
1508    */
1509   public void nucleotideMenuItem_actionPerformed()
1510   {
1511     getGroup().cs = new NucleotideColourScheme();
1512     refresh();
1513   }
1514
1515   protected void purinePyrimidineColour_actionPerformed()
1516   {
1517     getGroup().cs = new PurinePyrimidineColourScheme();
1518     refresh();
1519   }
1520
1521
1522   /*
1523    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1524    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1525    */
1526   /**
1527    * DOCUMENT ME!
1528    *
1529    * @param e
1530    *          DOCUMENT ME!
1531    */
1532   protected void abovePIDColour_actionPerformed()
1533   {
1534     SequenceGroup sg = getGroup();
1535     if (sg.cs == null)
1536     {
1537       return;
1538     }
1539
1540     if (abovePIDColour.isSelected())
1541     {
1542       sg.cs.setConsensus(AAFrequency.calculate(
1543               sg.getSequences(ap.av.getHiddenRepSequences()),
1544               sg.getStartRes(), sg.getEndRes() + 1));
1545
1546       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1547               .getName());
1548
1549       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1550
1551       SliderPanel.showPIDSlider();
1552     }
1553     else
1554     // remove PIDColouring
1555     {
1556       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1557     }
1558
1559     refresh();
1560   }
1561
1562   /**
1563    * DOCUMENT ME!
1564    *
1565    * @param e
1566    *          DOCUMENT ME!
1567    */
1568   protected void userDefinedColour_actionPerformed(ActionEvent e)
1569   {
1570     SequenceGroup sg = getGroup();
1571
1572     if (e.getActionCommand().equals("User Defined..."))
1573     {
1574       new UserDefinedColours(ap, sg);
1575     }
1576     else
1577     {
1578       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1579               .getUserColourSchemes().get(e.getActionCommand());
1580
1581       sg.cs = udc;
1582     }
1583     refresh();
1584   }
1585
1586   /**
1587    * DOCUMENT ME!
1588    *
1589    * @param e
1590    *          DOCUMENT ME!
1591    */
1592   protected void PIDColour_actionPerformed()
1593   {
1594     SequenceGroup sg = getGroup();
1595     sg.cs = new PIDColourScheme();
1596     sg.cs.setConsensus(AAFrequency.calculate(
1597             sg.getSequences(ap.av.getHiddenRepSequences()),
1598             sg.getStartRes(), sg.getEndRes() + 1));
1599     refresh();
1600   }
1601
1602   /**
1603    * DOCUMENT ME!
1604    *
1605    * @param e
1606    *          DOCUMENT ME!
1607    */
1608   protected void BLOSUM62Colour_actionPerformed()
1609   {
1610     SequenceGroup sg = getGroup();
1611
1612     sg.cs = new Blosum62ColourScheme();
1613
1614     sg.cs.setConsensus(AAFrequency.calculate(
1615             sg.getSequences(ap.av.getHiddenRepSequences()),
1616             sg.getStartRes(), sg.getEndRes() + 1));
1617
1618     refresh();
1619   }
1620
1621   /**
1622    * DOCUMENT ME!
1623    *
1624    * @param e
1625    *          DOCUMENT ME!
1626    */
1627   protected void noColourmenuItem_actionPerformed()
1628   {
1629     getGroup().cs = null;
1630     refresh();
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   protected void conservationMenuItem_actionPerformed()
1640   {
1641     SequenceGroup sg = getGroup();
1642     if (sg.cs == null)
1643     {
1644       return;
1645     }
1646
1647     if (conservationMenuItem.isSelected())
1648     {
1649       Conservation c = new Conservation("Group",
1650               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1651                       .getHiddenRepSequences()), sg.getStartRes(),
1652               sg.getEndRes() + 1);
1653
1654       c.calculate();
1655       c.verdict(false, ap.av.getConsPercGaps());
1656
1657       sg.cs.setConservation(c);
1658
1659       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1660       SliderPanel.showConservationSlider();
1661     }
1662     else
1663     // remove ConservationColouring
1664     {
1665       sg.cs.setConservation(null);
1666     }
1667
1668     refresh();
1669   }
1670
1671   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1672   {
1673     SequenceGroup sg = getGroup();
1674     if (sg == null)
1675     {
1676       return;
1677     }
1678
1679     AnnotationColourGradient acg = new AnnotationColourGradient(
1680             sequence.getAnnotation()[0], null,
1681             AnnotationColourGradient.NO_THRESHOLD);
1682
1683     acg.predefinedColours = true;
1684     sg.cs = acg;
1685
1686     refresh();
1687   }
1688
1689   /**
1690    * DOCUMENT ME!
1691    *
1692    * @param e
1693    *          DOCUMENT ME!
1694    */
1695   protected void groupName_actionPerformed()
1696   {
1697
1698     SequenceGroup sg = getGroup();
1699     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1700             sg.getDescription(), "       Group Name ",
1701             "Group Description ", "Edit Group Name/Description",
1702             ap.alignFrame);
1703
1704     if (!dialog.accept)
1705     {
1706       return;
1707     }
1708
1709     sg.setName(dialog.getName());
1710     sg.setDescription(dialog.getDescription());
1711     refresh();
1712   }
1713
1714   /**
1715    * Get selection group - adding it to the alignment if necessary.
1716    *
1717    * @return sequence group to operate on
1718    */
1719   SequenceGroup getGroup()
1720   {
1721     SequenceGroup sg = ap.av.getSelectionGroup();
1722     // this method won't add a new group if it already exists
1723     if (sg != null)
1724     {
1725       ap.av.getAlignment().addGroup(sg);
1726     }
1727
1728     return sg;
1729   }
1730
1731   /**
1732    * DOCUMENT ME!
1733    *
1734    * @param e
1735    *          DOCUMENT ME!
1736    */
1737   void sequenceName_actionPerformed()
1738   {
1739     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1740             sequence.getDescription(), "       Sequence Name ",
1741             "Sequence Description ", "Edit Sequence Name/Description",
1742             ap.alignFrame);
1743
1744     if (!dialog.accept)
1745     {
1746       return;
1747     }
1748
1749     if (dialog.getName() != null)
1750     {
1751       if (dialog.getName().indexOf(" ") > -1)
1752       {
1753         JOptionPane.showMessageDialog(ap,
1754                 "Spaces have been converted to \"_\"",
1755                 "No spaces allowed in Sequence Name",
1756                 JOptionPane.WARNING_MESSAGE);
1757       }
1758
1759       sequence.setName(dialog.getName().replace(' ', '_'));
1760       ap.paintAlignment(false);
1761     }
1762
1763     sequence.setDescription(dialog.getDescription());
1764
1765     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1766             .getSequences());
1767
1768   }
1769
1770   /**
1771    * DOCUMENT ME!
1772    *
1773    * @param e
1774    *          DOCUMENT ME!
1775    */
1776   void unGroupMenuItem_actionPerformed()
1777   {
1778     SequenceGroup sg = ap.av.getSelectionGroup();
1779     ap.av.getAlignment().deleteGroup(sg);
1780     ap.av.setSelectionGroup(null);
1781     refresh();
1782   }
1783
1784   /**
1785    * DOCUMENT ME!
1786    *
1787    * @param e
1788    *          DOCUMENT ME!
1789    */
1790   protected void outline_actionPerformed()
1791   {
1792     SequenceGroup sg = getGroup();
1793     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1794             Color.BLUE);
1795
1796     if (col != null)
1797     {
1798       sg.setOutlineColour(col);
1799     }
1800
1801     refresh();
1802   }
1803
1804   /**
1805    * DOCUMENT ME!
1806    *
1807    * @param e
1808    *          DOCUMENT ME!
1809    */
1810   public void showBoxes_actionPerformed()
1811   {
1812     getGroup().setDisplayBoxes(showBoxes.isSelected());
1813     refresh();
1814   }
1815
1816   /**
1817    * DOCUMENT ME!
1818    *
1819    * @param e
1820    *          DOCUMENT ME!
1821    */
1822   public void showText_actionPerformed()
1823   {
1824     getGroup().setDisplayText(showText.isSelected());
1825     refresh();
1826   }
1827
1828   /**
1829    * DOCUMENT ME!
1830    *
1831    * @param e
1832    *          DOCUMENT ME!
1833    */
1834   public void showColourText_actionPerformed()
1835   {
1836     getGroup().setColourText(showColourText.isSelected());
1837     refresh();
1838   }
1839
1840   public void showLink(String url)
1841   {
1842     try
1843     {
1844       jalview.util.BrowserLauncher.openURL(url);
1845     } catch (Exception ex)
1846     {
1847       JOptionPane
1848               .showInternalMessageDialog(
1849                       Desktop.desktop,
1850                       "Unixers: Couldn't find default web browser."
1851                               + "\nAdd the full path to your browser in Preferences.",
1852                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1853
1854       ex.printStackTrace();
1855     }
1856   }
1857
1858   void hideSequences(boolean representGroup)
1859   {
1860     SequenceGroup sg = ap.av.getSelectionGroup();
1861     if (sg == null || sg.getSize() < 1)
1862     {
1863       ap.av.hideSequence(new SequenceI[]
1864       { sequence });
1865       return;
1866     }
1867
1868     ap.av.setSelectionGroup(null);
1869
1870     if (representGroup)
1871     {
1872       ap.av.hideRepSequences(sequence, sg);
1873
1874       return;
1875     }
1876
1877     int gsize = sg.getSize();
1878     SequenceI[] hseqs;
1879
1880     hseqs = new SequenceI[gsize];
1881
1882     int index = 0;
1883     for (int i = 0; i < gsize; i++)
1884     {
1885       hseqs[index++] = sg.getSequenceAt(i);
1886     }
1887
1888     ap.av.hideSequence(hseqs);
1889     // refresh(); TODO: ? needed ?
1890     ap.av.sendSelection();
1891   }
1892
1893   public void copy_actionPerformed()
1894   {
1895     ap.alignFrame.copy_actionPerformed(null);
1896   }
1897
1898   public void cut_actionPerformed()
1899   {
1900     ap.alignFrame.cut_actionPerformed(null);
1901   }
1902
1903   void changeCase(ActionEvent e)
1904   {
1905     Object source = e.getSource();
1906     SequenceGroup sg = ap.av.getSelectionGroup();
1907
1908     if (sg != null)
1909     {
1910       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1911               sg.getEndRes() + 1);
1912
1913       String description;
1914       int caseChange;
1915
1916       if (source == toggle)
1917       {
1918         description = "Toggle Case";
1919         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1920       }
1921       else if (source == upperCase)
1922       {
1923         description = "To Upper Case";
1924         caseChange = ChangeCaseCommand.TO_UPPER;
1925       }
1926       else
1927       {
1928         description = "To Lower Case";
1929         caseChange = ChangeCaseCommand.TO_LOWER;
1930       }
1931
1932       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1933               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1934               startEnd, caseChange);
1935
1936       ap.alignFrame.addHistoryItem(caseCommand);
1937
1938       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1939               .getSequences());
1940
1941     }
1942   }
1943
1944   public void outputText_actionPerformed(ActionEvent e)
1945   {
1946     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1947     cap.setForInput(null);
1948     Desktop.addInternalFrame(cap,
1949             "Alignment output - " + e.getActionCommand(), 600, 500);
1950
1951     String[] omitHidden = null;
1952
1953     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1954     // or we simply trust the user wants
1955     // wysiwig behaviour
1956     SequenceGroup sg = ap.av.getSelectionGroup();
1957     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1958     omitHidden = ap.av.getViewAsString(true);
1959     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1960     AlignmentAnnotation[] nala = ap.av.getAlignment()
1961             .getAlignmentAnnotation();
1962     if (nala != null)
1963     {
1964       for (int i = 0; i < nala.length; i++)
1965       {
1966         AlignmentAnnotation na = nala[i];
1967         oal.addAnnotation(na);
1968       }
1969     }
1970     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1971             oal, omitHidden, csel, sg));
1972     oal = null;
1973   }
1974
1975   public void pdbFromFile_actionPerformed()
1976   {
1977     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1978             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1979     chooser.setFileView(new jalview.io.JalviewFileView());
1980     chooser.setDialogTitle("Select a PDB file for "
1981             + sequence.getDisplayId(false));
1982     chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1983             + sequence.getDisplayId(false) + "'");
1984
1985     int value = chooser.showOpenDialog(null);
1986
1987     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1988     {
1989       String choice = chooser.getSelectedFile().getPath();
1990       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1991       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1992               jalview.io.AppletFormatAdapter.FILE, sequence, true);
1993     }
1994
1995   }
1996     // JBNote: commented out - these won't be instantiated here...!
1997 //  public void RNAFold_actionPerformed() throws Exception
1998 //  {
1999 //        Predict2D P2D = new Predict2D();
2000 //        P2D.getStructure2DFromRNAFold("toto");
2001 //  }
2002 //
2003 //  public void ContraFold_actionPerformed() throws Exception
2004 //  {
2005 //        Predict2D P2D = new Predict2D();
2006 //        P2D.getStructure2DFromContraFold("toto");
2007 //  }
2008   public void enterPDB_actionPerformed()
2009   {
2010     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2011             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
2012
2013     if (id != null && id.length() > 0)
2014     {
2015       PDBEntry entry = new PDBEntry();
2016       entry.setId(id.toUpperCase());
2017       sequence.getDatasetSequence().addPDBId(entry);
2018     }
2019   }
2020
2021   public void discoverPDB_actionPerformed()
2022   {
2023
2024     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2025     { sequence }
2026             : ap.av.getSequenceSelection());
2027     Thread discpdb = new Thread(new Runnable()
2028     {
2029       public void run()
2030       {
2031
2032         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2033                 .fetchDBRefs(false);
2034       }
2035
2036     });
2037     discpdb.start();
2038   }
2039
2040   public void sequenceFeature_actionPerformed()
2041   {
2042     SequenceGroup sg = ap.av.getSelectionGroup();
2043     if (sg == null)
2044     {
2045       return;
2046     }
2047
2048     int rsize = 0, gSize = sg.getSize();
2049     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2050     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2051
2052     for (int i = 0; i < gSize; i++)
2053     {
2054       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2055       int end = sg.findEndRes(sg.getSequenceAt(i));
2056       if (start <= end)
2057       {
2058         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2059         features[rsize] = new SequenceFeature(null, null, null, start, end,
2060                 "Jalview");
2061         rsize++;
2062       }
2063     }
2064     rseqs = new SequenceI[rsize];
2065     tfeatures = new SequenceFeature[rsize];
2066     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2067     System.arraycopy(features, 0, tfeatures, 0, rsize);
2068     features = tfeatures;
2069     seqs = rseqs;
2070     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2071             features, true, ap))
2072     {
2073       ap.alignFrame.setShowSeqFeatures(true);
2074       ap.highlightSearchResults(null);
2075     }
2076   }
2077
2078   public void textColour_actionPerformed()
2079   {
2080     SequenceGroup sg = getGroup();
2081     if (sg != null)
2082     {
2083       new TextColourChooser().chooseColour(ap, sg);
2084     }
2085   }
2086
2087   public void colourByStructure(String pdbid)
2088   {
2089     Annotation[] anots = ap.av.getStructureSelectionManager()
2090             .colourSequenceFromStructure(sequence, pdbid);
2091
2092     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2093             "Coloured by " + pdbid, anots);
2094
2095     ap.av.getAlignment().addAnnotation(an);
2096     an.createSequenceMapping(sequence, 0, true);
2097     // an.adjustForAlignment();
2098     ap.av.getAlignment().setAnnotationIndex(an, 0);
2099
2100     ap.adjustAnnotationHeight();
2101
2102     sequence.addAlignmentAnnotation(an);
2103
2104   }
2105
2106   public void editSequence_actionPerformed(ActionEvent actionEvent)
2107   {
2108     SequenceGroup sg = ap.av.getSelectionGroup();
2109
2110     if (sg != null)
2111     {
2112       if (sequence == null)
2113         sequence = (Sequence) sg.getSequenceAt(0);
2114
2115       EditNameDialog dialog = new EditNameDialog(
2116               sequence.getSequenceAsString(sg.getStartRes(),
2117                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2118               "Edit Sequence", ap.alignFrame);
2119
2120       if (dialog.accept)
2121       {
2122         EditCommand editCommand = new EditCommand("Edit Sequences",
2123                 EditCommand.REPLACE, dialog.getName().replace(' ',
2124                         ap.av.getGapCharacter()),
2125                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2126                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2127
2128         ap.alignFrame.addHistoryItem(editCommand);
2129
2130         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2131                 .getSequences());
2132       }
2133     }
2134   }
2135
2136 }