src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, 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 MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.GroupUrlLink;
  34 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  35 import jalview.util.UrlLink;
  36
  37 /**
  38  * DOCUMENT ME!
  39  *
  40  * @author $author$
  41  * @version $Revision: 1.118 $
  42  */
  43 public class PopupMenu extends JPopupMenu
  44 {
  45   JMenu groupMenu = new JMenu();
  46
  47   JMenuItem groupName = new JMenuItem();
  48
  49   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  62
  63   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  64
  65   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  66
  67   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  70
  71   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  72
  73   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  74
  75   //protected JRadioButtonMenuItem covariationColour = new 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   Sequence sequence;
  88
  89   JMenuItem unGroupMenuItem = new JMenuItem();
  90
  91   JMenuItem outline = new JMenuItem();
  92
  93   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  94
  95   JMenu colourMenu = new JMenu();
  96
  97   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  98
  99   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 100
 101   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 102
 103   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 104
 105   JMenu editMenu = new JMenu();
 106
 107   JMenuItem cut = new JMenuItem();
 108
 109   JMenuItem copy = new JMenuItem();
 110
 111   JMenuItem upperCase = new JMenuItem();
 112
 113   JMenuItem lowerCase = new JMenuItem();
 114
 115   JMenuItem toggle = new JMenuItem();
 116
 117   JMenu pdbMenu = new JMenu();
 118
 119   JMenuItem pdbFromFile = new JMenuItem();
 120
 121   JMenuItem enterPDB = new JMenuItem();
 122
 123   JMenuItem discoverPDB = new JMenuItem();
 124
 125   JMenu outputMenu = new JMenu();
 126
 127   JMenuItem sequenceFeature = new JMenuItem();
 128
 129   JMenuItem textColour = new JMenuItem();
 130
 131   JMenu jMenu1 = new JMenu();
 132
 133   JMenu structureMenu = new JMenu();
 134
 135   JMenu viewStructureMenu = new JMenu();
 136
 137   // JMenu colStructureMenu = new JMenu();
 138   JMenuItem editSequence = new JMenuItem();
 139
 140   // JMenuItem annotationMenuItem = new JMenuItem();
 141
 142   JMenu groupLinksMenu;
 143
 144   /**
 145    * Creates a new PopupMenu object.
 146    *
 147    * @param ap
 148    *          DOCUMENT ME!
 149    * @param seq
 150    *          DOCUMENT ME!
 151    */
 152   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 153   {
 154     this(ap, seq, links, null);
 155   }
 156
 157   /**
 158    *
 159    * @param ap
 160    * @param seq
 161    * @param links
 162    * @param groupLinks
 163    */
 164   public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
 165           final Vector groupLinks)
 166   {
 167     // /////////////////////////////////////////////////////////
 168     // If this is activated from the sequence panel, the user may want to
 169     // edit or annotate a particular residue. Therefore display the residue menu
 170     //
 171     // If from the IDPanel, we must display the sequence menu
 172     // ////////////////////////////////////////////////////////
 173     this.ap = ap;
 174     sequence = seq;
 175
 176     ButtonGroup colours = new ButtonGroup();
 177     colours.add(noColourmenuItem);
 178     colours.add(clustalColour);
 179     colours.add(zappoColour);
 180     colours.add(taylorColour);
 181     colours.add(hydrophobicityColour);
 182     colours.add(helixColour);
 183     colours.add(strandColour);
 184     colours.add(turnColour);
 185     colours.add(buriedColour);
 186     colours.add(abovePIDColour);
 187     colours.add(userDefinedColour);
 188     colours.add(PIDColour);
 189     colours.add(BLOSUM62Colour);
 190     colours.add(purinePyrimidineColour);
 191     //colours.add(covariationColour);
 192
 193     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 194     {
 195       JMenuItem item = new JMenuItem(
 196               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 197
 198       item.addActionListener(new java.awt.event.ActionListener()
 199       {
 200         public void actionPerformed(ActionEvent e)
 201         {
 202           outputText_actionPerformed(e);
 203         }
 204       });
 205
 206       outputMenu.add(item);
 207     }
 208
 209     try
 210     {
 211       jbInit();
 212     } catch (Exception e)
 213     {
 214       e.printStackTrace();
 215     }
 216
 217     if (seq != null)
 218     {
 219       sequenceMenu.setText(sequence.getName());
 220
 221       JMenuItem menuItem;
 222       if (seq.getDatasetSequence().getPDBId() != null
 223               && seq.getDatasetSequence().getPDBId().size() > 0)
 224       {
 225         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 226                 .elements();
 227
 228         while (e.hasMoreElements())
 229         {
 230           final PDBEntry pdb = (PDBEntry) e.nextElement();
 231
 232           menuItem = new JMenuItem();
 233           menuItem.setText(pdb.getId());
 234           menuItem.addActionListener(new java.awt.event.ActionListener()
 235           {
 236             public void actionPerformed(ActionEvent e)
 237             {
 238                 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
 239               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
 240               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 241             }
 242
 243           });
 244           viewStructureMenu.add(menuItem);
 245
 246           /*
 247            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 248            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 249            * public void actionPerformed(ActionEvent e) {
 250            * colourByStructure(pdb.getId()); } });
 251            * colStructureMenu.add(menuItem);
 252            */
 253         }
 254       }
 255       else
 256       {
 257           if(ap.av.alignment.isNucleotide()==false){
 258                   structureMenu.remove(viewStructureMenu);
 259           }
 260         // structureMenu.remove(colStructureMenu);
 261       }
 262
 263       if(ap.av.alignment.isNucleotide()==true){
 264           AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 265           String rnastruc=new String();
 266           for(int i=0; i<aa.length;i++){
 267                   if(aa[i]._rnasecstr != null){
 268                           rnastruc=aa[i].getRNAStruc();
 269                           break;
 270                   }
 271           }
 272           //TODO: make rnastrucF a bit more nice
 273           final String rnastrucF=rnastruc;
 274           menuItem = new JMenuItem();
 275           menuItem.setText("RNA structure");
 276           menuItem.addActionListener(new java.awt.event.ActionListener()
 277           {
 278                   public void actionPerformed(ActionEvent e)
 279                   {
 280                           System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
 281                           //TODO: VARNA does'nt print gaps in the sequence
 282                           new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName());
 283                   }
 284                         });
 285                         viewStructureMenu.add(menuItem);
 286         }
 287
 288       menuItem = new JMenuItem("Hide Sequences");
 289       menuItem.addActionListener(new java.awt.event.ActionListener()
 290       {
 291         public void actionPerformed(ActionEvent e)
 292         {
 293           hideSequences(false);
 294         }
 295       });
 296       add(menuItem);
 297
 298       if (ap.av.getSelectionGroup() != null
 299               && ap.av.getSelectionGroup().getSize() > 1)
 300       {
 301         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 302         menuItem.addActionListener(new java.awt.event.ActionListener()
 303         {
 304           public void actionPerformed(ActionEvent e)
 305           {
 306             hideSequences(true);
 307           }
 308         });
 309         sequenceMenu.add(menuItem);
 310       }
 311
 312       if (ap.av.hasHiddenRows)
 313       {
 314         final int index = ap.av.alignment.findIndex(seq);
 315
 316         if (ap.av.adjustForHiddenSeqs(index)
 317                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 318         {
 319           menuItem = new JMenuItem("Reveal Sequences");
 320           menuItem.addActionListener(new ActionListener()
 321           {
 322             public void actionPerformed(ActionEvent e)
 323             {
 324               ap.av.showSequence(index);
 325               if (ap.overviewPanel != null)
 326               {
 327                 ap.overviewPanel.updateOverviewImage();
 328               }
 329             }
 330           });
 331           add(menuItem);
 332         }
 333
 334         menuItem = new JMenuItem("Reveal All");
 335         menuItem.addActionListener(new ActionListener()
 336         {
 337           public void actionPerformed(ActionEvent e)
 338           {
 339             ap.av.showAllHiddenSeqs();
 340             if (ap.overviewPanel != null)
 341             {
 342               ap.overviewPanel.updateOverviewImage();
 343             }
 344           }
 345         });
 346
 347         add(menuItem);
 348       }
 349
 350     }
 351
 352     SequenceGroup sg = ap.av.getSelectionGroup();
 353
 354     if (sg != null)
 355     {
 356       groupName.setText("Name: "+sg.getName());
 357       groupName.setText("Edit name and description of current group.");
 358
 359       if (sg.cs instanceof ZappoColourScheme)
 360       {
 361         zappoColour.setSelected(true);
 362       }
 363       else if (sg.cs instanceof TaylorColourScheme)
 364       {
 365         taylorColour.setSelected(true);
 366       }
 367       else if (sg.cs instanceof PIDColourScheme)
 368       {
 369         PIDColour.setSelected(true);
 370       }
 371       else if (sg.cs instanceof Blosum62ColourScheme)
 372       {
 373         BLOSUM62Colour.setSelected(true);
 374       }
 375       else if (sg.cs instanceof UserColourScheme)
 376       {
 377         userDefinedColour.setSelected(true);
 378       }
 379       else if (sg.cs instanceof HydrophobicColourScheme)
 380       {
 381         hydrophobicityColour.setSelected(true);
 382       }
 383       else if (sg.cs instanceof HelixColourScheme)
 384       {
 385         helixColour.setSelected(true);
 386       }
 387       else if (sg.cs instanceof StrandColourScheme)
 388       {
 389         strandColour.setSelected(true);
 390       }
 391       else if (sg.cs instanceof TurnColourScheme)
 392       {
 393         turnColour.setSelected(true);
 394       }
 395       else if (sg.cs instanceof BuriedColourScheme)
 396       {
 397         buriedColour.setSelected(true);
 398       }
 399       else if (sg.cs instanceof ClustalxColourScheme)
 400       {
 401         clustalColour.setSelected(true);
 402       }
 403       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 404       {
 405         purinePyrimidineColour.setSelected(true);
 406       }
 407      /* else if (sg.cs instanceof CovariationColourScheme)
 408       {
 409         covariationColour.setSelected(true);
 410       }*/
 411       else
 412       {
 413         noColourmenuItem.setSelected(true);
 414       }
 415
 416       if (sg.cs != null && sg.cs.conservationApplied())
 417       {
 418         conservationMenuItem.setSelected(true);
 419       }
 420       displayNonconserved.setSelected(sg.getShowNonconserved());
 421       showText.setSelected(sg.getDisplayText());
 422       showColourText.setSelected(sg.getColourText());
 423       showBoxes.setSelected(sg.getDisplayBoxes());
 424       // add any groupURLs to the groupURL submenu and make it visible
 425       if (groupLinks != null && groupLinks.size() > 0)
 426       {
 427         buildGroupURLMenu(sg, groupLinks);
 428       }
 429       // Add a 'show all structures' for the current selection
 430       Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
 431       for (SequenceI sq: ap.av.getSequenceSelection())
 432       {
 433         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
 434         if (pes!=null) {
 435           for (PDBEntry pe: pes)
 436           {
 437             pdbe.put(pe.getId(),  pe);
 438           }
 439         }
 440       }
 441       if (pdbe.size()>0)
 442       {
 443         final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
 444         final JMenuItem gpdbview;
 445         structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
 446         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 447         gpdbview.addActionListener(new ActionListener()
 448         {
 449
 450           @Override
 451           public void actionPerformed(ActionEvent e)
 452           {
 453             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 454           }
 455         });
 456       }
 457     }
 458     else
 459     {
 460       groupMenu.setVisible(false);
 461       editMenu.setVisible(false);
 462     }
 463
 464     if (!ap.av.alignment.getGroups().contains(sg))
 465     {
 466       unGroupMenuItem.setVisible(false);
 467     }
 468
 469     if (seq == null)
 470     {
 471       sequenceMenu.setVisible(false);
 472       structureMenu.setVisible(false);
 473     }
 474
 475     if (links != null && links.size() > 0)
 476     {
 477
 478       JMenu linkMenu = new JMenu("Link");
 479       Vector linkset = new Vector();
 480       for (int i = 0; i < links.size(); i++)
 481       {
 482         String link = links.elementAt(i).toString();
 483         UrlLink urlLink = null;
 484         try
 485         {
 486           urlLink = new UrlLink(link);
 487         } catch (Exception foo)
 488         {
 489           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 490                   + "'", foo);
 491           continue;
 492         }
 493         ;
 494         if (!urlLink.isValid())
 495         {
 496           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 497           continue;
 498         }
 499         final String label = urlLink.getLabel();
 500         if (urlLink.isDynamic())
 501         {
 502
 503           // collect matching db-refs
 504           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 505                   seq.getDBRef(), new String[]
 506                   { urlLink.getTarget() });
 507           // collect id string too
 508           String id = seq.getName();
 509           String descr = seq.getDescription();
 510           if (descr != null && descr.length() < 1)
 511           {
 512             descr = null;
 513           }
 514
 515           if (dbr != null)
 516           {
 517             for (int r = 0; r < dbr.length; r++)
 518             {
 519               if (id != null && dbr[r].getAccessionId().equals(id))
 520               {
 521                 // suppress duplicate link creation for the bare sequence ID
 522                 // string with this link
 523                 id = null;
 524               }
 525               // create Bare ID link for this RUL
 526               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 527                       true);
 528               if (urls != null)
 529               {
 530                 for (int u = 0; u < urls.length; u += 2)
 531                 {
 532                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 533                   {
 534                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 535                     addshowLink(linkMenu, label + "|" + urls[u],
 536                             urls[u + 1]);
 537                   }
 538                 }
 539               }
 540             }
 541           }
 542           if (id != null)
 543           {
 544             // create Bare ID link for this RUL
 545             String[] urls = urlLink.makeUrls(id, true);
 546             if (urls != null)
 547             {
 548               for (int u = 0; u < urls.length; u += 2)
 549               {
 550                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 551                 {
 552                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 553                   addshowLink(linkMenu, label, urls[u + 1]);
 554                 }
 555               }
 556             }
 557           }
 558           // Create urls from description but only for URL links which are regex
 559           // links
 560           if (descr != null && urlLink.getRegexReplace() != null)
 561           {
 562             // create link for this URL from description where regex matches
 563             String[] urls = urlLink.makeUrls(descr, true);
 564             if (urls != null)
 565             {
 566               for (int u = 0; u < urls.length; u += 2)
 567               {
 568                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 569                 {
 570                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 571                   addshowLink(linkMenu, label, urls[u + 1]);
 572                 }
 573               }
 574             }
 575           }
 576         }
 577         else
 578         {
 579           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 580           {
 581             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 582             // Add a non-dynamic link
 583             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 584           }
 585         }
 586       }
 587       if (sequence != null)
 588       {
 589         sequenceMenu.add(linkMenu);
 590       }
 591       else
 592       {
 593         add(linkMenu);
 594       }
 595     }
 596   }
 597
 598   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 599   {
 600
 601     // TODO: usability: thread off the generation of group url content so root
 602     // menu appears asap
 603     // sequence only URLs
 604     // ID/regex match URLs
 605     groupLinksMenu = new JMenu("Group Link");
 606     JMenu[] linkMenus = new JMenu[]
 607     { null, new JMenu("IDS"), new JMenu("Sequences"),
 608         new JMenu("IDS and Sequences") }; // three types of url that might be
 609                                           // created.
 610     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 611     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 612     Hashtable commonDbrefs = new Hashtable();
 613     for (int sq = 0; sq < seqs.length; sq++)
 614     {
 615
 616       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 617               .findPosition(sg.getEndRes());
 618       // just collect ids from dataset sequence
 619       // TODO: check if IDs collected from selecton group intersects with the
 620       // current selection, too
 621       SequenceI sqi = seqs[sq];
 622       while (sqi.getDatasetSequence() != null)
 623       {
 624         sqi = sqi.getDatasetSequence();
 625       }
 626       DBRefEntry[] dbr = sqi.getDBRef();
 627       if (dbr != null && dbr.length > 0)
 628       {
 629         for (int d = 0; d < dbr.length; d++)
 630         {
 631           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 632           Object[] sarray = (Object[]) commonDbrefs.get(src);
 633           if (sarray == null)
 634           {
 635             sarray = new Object[2];
 636             sarray[0] = new int[]
 637             { 0 };
 638             sarray[1] = new String[seqs.length];
 639
 640             commonDbrefs.put(src, sarray);
 641           }
 642
 643           if (((String[]) sarray[1])[sq] == null)
 644           {
 645             if (!dbr[d].hasMap()
 646                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 647             {
 648               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 649               ((int[]) sarray[0])[0]++;
 650             }
 651           }
 652         }
 653       }
 654     }
 655     // now create group links for all distinct ID/sequence sets.
 656     boolean addMenu = false; // indicates if there are any group links to give
 657                              // to user
 658     for (int i = 0; i < groupLinks.size(); i++)
 659     {
 660       String link = groupLinks.elementAt(i).toString();
 661       GroupUrlLink urlLink = null;
 662       try
 663       {
 664         urlLink = new GroupUrlLink(link);
 665       } catch (Exception foo)
 666       {
 667         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 668                 + "'", foo);
 669         continue;
 670       }
 671       ;
 672       if (!urlLink.isValid())
 673       {
 674         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 675         continue;
 676       }
 677       final String label = urlLink.getLabel();
 678       boolean usingNames = false;
 679       // Now see which parts of the group apply for this URL
 680       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 681       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 682       String[] seqstr, ids; // input to makeUrl
 683       if (idset != null)
 684       {
 685         int numinput = ((int[]) idset[0])[0];
 686         String[] allids = ((String[]) idset[1]);
 687         seqstr = new String[numinput];
 688         ids = new String[numinput];
 689         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 690         {
 691           if (allids[sq] != null)
 692           {
 693             ids[idcount] = allids[sq];
 694             seqstr[idcount++] = idandseqs[1][sq];
 695           }
 696         }
 697       }
 698       else
 699       {
 700         // just use the id/seq set
 701         seqstr = idandseqs[1];
 702         ids = idandseqs[0];
 703         usingNames = true;
 704       }
 705       // and try and make the groupURL!
 706
 707       Object[] urlset = null;
 708       try
 709       {
 710         urlset = urlLink.makeUrlStubs(ids, seqstr,
 711                 "FromJalview" + System.currentTimeMillis(), false);
 712       } catch (UrlStringTooLongException e)
 713       {
 714       }
 715       if (urlset != null)
 716       {
 717         int type = urlLink.getGroupURLType() & 3;
 718         // System.out.println(urlLink.getGroupURLType()
 719         // +" "+((String[])urlset[3])[0]);
 720         // first two bits ofurlLink type bitfield are sequenceids and sequences
 721         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 722         addshowLink(linkMenus[type], label
 723                 + (((type & 1) == 1) ? ("("
 724                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 725                 urlLink, urlset);
 726         addMenu = true;
 727       }
 728     }
 729     if (addMenu)
 730     {
 731       groupLinksMenu = new JMenu("Group Links");
 732       for (int m = 0; m < linkMenus.length; m++)
 733       {
 734         if (linkMenus[m] != null
 735                 && linkMenus[m].getMenuComponentCount() > 0)
 736         {
 737           groupLinksMenu.add(linkMenus[m]);
 738         }
 739       }
 740
 741       groupMenu.add(groupLinksMenu);
 742     }
 743   }
 744
 745   /**
 746    * add a show URL menu item to the given linkMenu
 747    *
 748    * @param linkMenu
 749    * @param label
 750    *          - menu label string
 751    * @param url
 752    *          - url to open
 753    */
 754   private void addshowLink(JMenu linkMenu, String label, final String url)
 755   {
 756     JMenuItem item = new JMenuItem(label);
 757     item.setToolTipText("open URL: " + url);
 758     item.addActionListener(new java.awt.event.ActionListener()
 759     {
 760       public void actionPerformed(ActionEvent e)
 761       {
 762         new Thread(new Runnable()
 763         {
 764
 765           public void run()
 766           {
 767             showLink(url);
 768           }
 769
 770         }).start();
 771       }
 772     });
 773
 774     linkMenu.add(item);
 775   }
 776
 777   /**
 778    * add a late bound groupURL item to the given linkMenu
 779    *
 780    * @param linkMenu
 781    * @param label
 782    *          - menu label string
 783    * @param urlgenerator
 784    *          GroupURLLink used to generate URL
 785    * @param urlstub
 786    *          Object array returned from the makeUrlStubs function.
 787    */
 788   private void addshowLink(JMenu linkMenu, String label,
 789           final GroupUrlLink urlgenerator, final Object[] urlstub)
 790   {
 791     JMenuItem item = new JMenuItem(label);
 792     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 793             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 794                                                                              // put
 795                                                                              // in
 796                                                                              // info
 797                                                                              // about
 798                                                                              // what
 799                                                                              // is
 800                                                                              // being
 801                                                                              // sent.
 802     item.addActionListener(new java.awt.event.ActionListener()
 803     {
 804       public void actionPerformed(ActionEvent e)
 805       {
 806         new Thread(new Runnable()
 807         {
 808
 809           public void run()
 810           {
 811             try
 812             {
 813               showLink(urlgenerator.constructFrom(urlstub));
 814             } catch (UrlStringTooLongException e)
 815             {
 816             }
 817           }
 818
 819         }).start();
 820       }
 821     });
 822
 823     linkMenu.add(item);
 824   }
 825
 826   /**
 827    * DOCUMENT ME!
 828    *
 829    * @throws Exception
 830    *           DOCUMENT ME!
 831    */
 832   private void jbInit() throws Exception
 833   {
 834     groupMenu.setText("Group");
 835     groupMenu.setText("Selection");
 836     groupName.setText("Name");
 837     groupName.addActionListener(new java.awt.event.ActionListener()
 838     {
 839       public void actionPerformed(ActionEvent e)
 840       {
 841         groupName_actionPerformed();
 842       }
 843     });
 844     sequenceMenu.setText("Sequence");
 845     sequenceName.setText("Edit Name/Description");
 846     sequenceName.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         sequenceName_actionPerformed();
 851       }
 852     });
 853     PIDColour.setFocusPainted(false);
 854     unGroupMenuItem.setText("Remove Group");
 855     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 856     {
 857       public void actionPerformed(ActionEvent e)
 858       {
 859         unGroupMenuItem_actionPerformed();
 860       }
 861     });
 862
 863     outline.setText("Border colour");
 864     outline.addActionListener(new java.awt.event.ActionListener()
 865     {
 866       public void actionPerformed(ActionEvent e)
 867       {
 868         outline_actionPerformed();
 869       }
 870     });
 871     nucleotideMenuItem.setText("Nucleotide");
 872     nucleotideMenuItem.addActionListener(new ActionListener()
 873     {
 874       public void actionPerformed(ActionEvent e)
 875       {
 876         nucleotideMenuItem_actionPerformed();
 877       }
 878     });
 879     colourMenu.setText("Group Colour");
 880     showBoxes.setText("Boxes");
 881     showBoxes.setState(true);
 882     showBoxes.addActionListener(new ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         showBoxes_actionPerformed();
 887       }
 888     });
 889     showText.setText("Text");
 890     showText.setState(true);
 891     showText.addActionListener(new ActionListener()
 892     {
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         showText_actionPerformed();
 896       }
 897     });
 898     showColourText.setText("Colour Text");
 899     showColourText.addActionListener(new ActionListener()
 900     {
 901       public void actionPerformed(ActionEvent e)
 902       {
 903         showColourText_actionPerformed();
 904       }
 905     });
 906     displayNonconserved.setText("Show Nonconserved");
 907     displayNonconserved.setState(true);
 908     displayNonconserved.addActionListener(new ActionListener()
 909     {
 910       public void actionPerformed(ActionEvent e)
 911       {
 912         showNonconserved_actionPerformed();
 913       }
 914     });
 915     editMenu.setText("Edit");
 916     cut.setText("Cut");
 917     cut.addActionListener(new ActionListener()
 918     {
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         cut_actionPerformed();
 922       }
 923     });
 924     upperCase.setText("To Upper Case");
 925     upperCase.addActionListener(new ActionListener()
 926     {
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         changeCase(e);
 930       }
 931     });
 932     copy.setText("Copy");
 933     copy.addActionListener(new ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         copy_actionPerformed();
 938       }
 939     });
 940     lowerCase.setText("To Lower Case");
 941     lowerCase.addActionListener(new ActionListener()
 942     {
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         changeCase(e);
 946       }
 947     });
 948     toggle.setText("Toggle Case");
 949     toggle.addActionListener(new ActionListener()
 950     {
 951       public void actionPerformed(ActionEvent e)
 952       {
 953         changeCase(e);
 954       }
 955     });
 956     pdbMenu.setText("Associate Structure with Sequence");
 957     pdbFromFile.setText("From File");
 958     pdbFromFile.addActionListener(new ActionListener()
 959     {
 960       public void actionPerformed(ActionEvent e)
 961       {
 962         pdbFromFile_actionPerformed();
 963       }
 964     });
 965     enterPDB.setText("Enter PDB Id");
 966     enterPDB.addActionListener(new ActionListener()
 967     {
 968       public void actionPerformed(ActionEvent e)
 969       {
 970         enterPDB_actionPerformed();
 971       }
 972     });
 973     discoverPDB.setText("Discover PDB ids");
 974     discoverPDB.addActionListener(new ActionListener()
 975     {
 976       public void actionPerformed(ActionEvent e)
 977       {
 978         discoverPDB_actionPerformed();
 979       }
 980     });
 981     outputMenu.setText("Output to Textbox...");
 982     sequenceFeature.setText("Create Sequence Feature");
 983     sequenceFeature.addActionListener(new ActionListener()
 984     {
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         sequenceFeature_actionPerformed();
 988       }
 989     });
 990     textColour.setText("Text Colour");
 991     textColour.addActionListener(new ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         textColour_actionPerformed();
 996       }
 997     });
 998     jMenu1.setText("Group");
 999     structureMenu.setText("Structure");
1000     viewStructureMenu.setText("View Structure");
1001     // colStructureMenu.setText("Colour By Structure");
1002     editSequence.setText("Edit Sequence...");
1003     editSequence.addActionListener(new ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent actionEvent)
1006       {
1007         editSequence_actionPerformed(actionEvent);
1008       }
1009     });
1010     /*
1011      * annotationMenuItem.setText("By Annotation");
1012      * annotationMenuItem.addActionListener(new ActionListener() { public void
1013      * actionPerformed(ActionEvent actionEvent) {
1014      * annotationMenuItem_actionPerformed(actionEvent); } });
1015      */
1016
1017     add(groupMenu);
1018
1019     add(sequenceMenu);
1020     this.add(structureMenu);
1021     groupMenu.add(editMenu);
1022     groupMenu.add(outputMenu);
1023     groupMenu.add(sequenceFeature);
1024     groupMenu.add(jMenu1);
1025     sequenceMenu.add(sequenceName);
1026     colourMenu.add(textColour);
1027     colourMenu.add(noColourmenuItem);
1028     colourMenu.add(clustalColour);
1029     colourMenu.add(BLOSUM62Colour);
1030     colourMenu.add(PIDColour);
1031     colourMenu.add(zappoColour);
1032     colourMenu.add(taylorColour);
1033     colourMenu.add(hydrophobicityColour);
1034     colourMenu.add(helixColour);
1035     colourMenu.add(strandColour);
1036     colourMenu.add(turnColour);
1037     colourMenu.add(buriedColour);
1038     colourMenu.add(nucleotideMenuItem);
1039     colourMenu.add(purinePyrimidineColour);
1040     //colourMenu.add(covariationColour);
1041     colourMenu.add(userDefinedColour);
1042
1043     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1044     {
1045       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1046               .getUserColourSchemes().keys();
1047
1048       while (userColours.hasMoreElements())
1049       {
1050         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1051         item.addActionListener(new ActionListener()
1052         {
1053           public void actionPerformed(ActionEvent evt)
1054           {
1055             userDefinedColour_actionPerformed(evt);
1056           }
1057         });
1058         colourMenu.add(item);
1059       }
1060     }
1061
1062     colourMenu.addSeparator();
1063     colourMenu.add(abovePIDColour);
1064     colourMenu.add(conservationMenuItem);
1065     // colourMenu.add(annotationMenuItem);
1066     editMenu.add(copy);
1067     editMenu.add(cut);
1068     editMenu.add(editSequence);
1069     editMenu.add(upperCase);
1070     editMenu.add(lowerCase);
1071     editMenu.add(toggle);
1072     pdbMenu.add(pdbFromFile);
1073     pdbMenu.add(enterPDB);
1074     pdbMenu.add(discoverPDB);
1075     jMenu1.add(groupName);
1076     jMenu1.add(unGroupMenuItem);
1077     jMenu1.add(colourMenu);
1078     jMenu1.add(showBoxes);
1079     jMenu1.add(showText);
1080     jMenu1.add(showColourText);
1081     jMenu1.add(outline);
1082     jMenu1.add(displayNonconserved);
1083     structureMenu.add(pdbMenu);
1084     structureMenu.add(viewStructureMenu);
1085     // structureMenu.add(colStructureMenu);
1086     noColourmenuItem.setText("None");
1087     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1088     {
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         noColourmenuItem_actionPerformed();
1092       }
1093     });
1094
1095     clustalColour.setText("Clustalx colours");
1096     clustalColour.addActionListener(new java.awt.event.ActionListener()
1097     {
1098       public void actionPerformed(ActionEvent e)
1099       {
1100         clustalColour_actionPerformed();
1101       }
1102     });
1103     zappoColour.setText("Zappo");
1104     zappoColour.addActionListener(new java.awt.event.ActionListener()
1105     {
1106       public void actionPerformed(ActionEvent e)
1107       {
1108         zappoColour_actionPerformed();
1109       }
1110     });
1111     taylorColour.setText("Taylor");
1112     taylorColour.addActionListener(new java.awt.event.ActionListener()
1113     {
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         taylorColour_actionPerformed();
1117       }
1118     });
1119     hydrophobicityColour.setText("Hydrophobicity");
1120     hydrophobicityColour
1121             .addActionListener(new java.awt.event.ActionListener()
1122             {
1123               public void actionPerformed(ActionEvent e)
1124               {
1125                 hydrophobicityColour_actionPerformed();
1126               }
1127             });
1128     helixColour.setText("Helix propensity");
1129     helixColour.addActionListener(new java.awt.event.ActionListener()
1130     {
1131       public void actionPerformed(ActionEvent e)
1132       {
1133         helixColour_actionPerformed();
1134       }
1135     });
1136     strandColour.setText("Strand propensity");
1137     strandColour.addActionListener(new java.awt.event.ActionListener()
1138     {
1139       public void actionPerformed(ActionEvent e)
1140       {
1141         strandColour_actionPerformed();
1142       }
1143     });
1144     turnColour.setText("Turn propensity");
1145     turnColour.addActionListener(new java.awt.event.ActionListener()
1146     {
1147       public void actionPerformed(ActionEvent e)
1148       {
1149         turnColour_actionPerformed();
1150       }
1151     });
1152     buriedColour.setText("Buried Index");
1153     buriedColour.addActionListener(new java.awt.event.ActionListener()
1154     {
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         buriedColour_actionPerformed();
1158       }
1159     });
1160     abovePIDColour.setText("Above % Identity");
1161     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1162     {
1163       public void actionPerformed(ActionEvent e)
1164       {
1165         abovePIDColour_actionPerformed();
1166       }
1167     });
1168     userDefinedColour.setText("User Defined...");
1169     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1170     {
1171       public void actionPerformed(ActionEvent e)
1172       {
1173         userDefinedColour_actionPerformed(e);
1174       }
1175     });
1176     PIDColour.setText("Percentage Identity");
1177     PIDColour.addActionListener(new java.awt.event.ActionListener()
1178     {
1179       public void actionPerformed(ActionEvent e)
1180       {
1181         PIDColour_actionPerformed();
1182       }
1183     });
1184     BLOSUM62Colour.setText("BLOSUM62");
1185     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1186     {
1187       public void actionPerformed(ActionEvent e)
1188       {
1189         BLOSUM62Colour_actionPerformed();
1190       }
1191     });
1192     purinePyrimidineColour.setText("Purine/Pyrimidine");
1193     purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
1194     {
1195       public void actionPerformed(ActionEvent e)
1196       {
1197           purinePyrimidineColour_actionPerformed();
1198       }
1199     });
1200    /*
1201     covariationColour.addActionListener(new java.awt.event.ActionListener()
1202     {
1203       public void actionPerformed(ActionEvent e)
1204       {
1205           covariationColour_actionPerformed();
1206       }
1207     });*/
1208
1209     conservationMenuItem.setText("Conservation");
1210     conservationMenuItem
1211             .addActionListener(new java.awt.event.ActionListener()
1212             {
1213               public void actionPerformed(ActionEvent e)
1214               {
1215                 conservationMenuItem_actionPerformed();
1216               }
1217             });
1218   }
1219
1220   protected void showNonconserved_actionPerformed()
1221   {
1222     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1223     refresh();
1224   }
1225
1226   /**
1227    * call to refresh view after settings change
1228    */
1229   void refresh()
1230   {
1231     ap.updateAnnotation();
1232     ap.paintAlignment(true);
1233
1234     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1235   }
1236
1237   /**
1238    * DOCUMENT ME!
1239    *
1240    * @param e
1241    *          DOCUMENT ME!
1242    */
1243   protected void clustalColour_actionPerformed()
1244   {
1245     SequenceGroup sg = getGroup();
1246     sg.cs = new ClustalxColourScheme(
1247             sg.getSequences(ap.av.hiddenRepSequences),
1248             ap.av.alignment.getWidth());
1249     refresh();
1250   }
1251
1252   /**
1253    * DOCUMENT ME!
1254    *
1255    * @param e
1256    *          DOCUMENT ME!
1257    */
1258   protected void zappoColour_actionPerformed()
1259   {
1260     getGroup().cs = new ZappoColourScheme();
1261     refresh();
1262   }
1263
1264   /**
1265    * DOCUMENT ME!
1266    *
1267    * @param e
1268    *          DOCUMENT ME!
1269    */
1270   protected void taylorColour_actionPerformed()
1271   {
1272     getGroup().cs = new TaylorColourScheme();
1273     refresh();
1274   }
1275
1276   /**
1277    * DOCUMENT ME!
1278    *
1279    * @param e
1280    *          DOCUMENT ME!
1281    */
1282   protected void hydrophobicityColour_actionPerformed()
1283   {
1284     getGroup().cs = new HydrophobicColourScheme();
1285     refresh();
1286   }
1287
1288   /**
1289    * DOCUMENT ME!
1290    *
1291    * @param e
1292    *          DOCUMENT ME!
1293    */
1294   protected void helixColour_actionPerformed()
1295   {
1296     getGroup().cs = new HelixColourScheme();
1297     refresh();
1298   }
1299
1300   /**
1301    * DOCUMENT ME!
1302    *
1303    * @param e
1304    *          DOCUMENT ME!
1305    */
1306   protected void strandColour_actionPerformed()
1307   {
1308     getGroup().cs = new StrandColourScheme();
1309     refresh();
1310   }
1311
1312   /**
1313    * DOCUMENT ME!
1314    *
1315    * @param e
1316    *          DOCUMENT ME!
1317    */
1318   protected void turnColour_actionPerformed()
1319   {
1320     getGroup().cs = new TurnColourScheme();
1321     refresh();
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   protected void buriedColour_actionPerformed()
1331   {
1332     getGroup().cs = new BuriedColourScheme();
1333     refresh();
1334   }
1335
1336   /**
1337    * DOCUMENT ME!
1338    *
1339    * @param e
1340    *          DOCUMENT ME!
1341    */
1342   public void nucleotideMenuItem_actionPerformed()
1343   {
1344     getGroup().cs = new NucleotideColourScheme();
1345     refresh();
1346   }
1347
1348   protected void purinePyrimidineColour_actionPerformed()
1349   {
1350     getGroup().cs = new PurinePyrimidineColourScheme();
1351     refresh();
1352   }
1353   /*
1354   protected void covariationColour_actionPerformed()
1355   {
1356     getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
1357     refresh();
1358   }
1359 */
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   protected void abovePIDColour_actionPerformed()
1367   {
1368     SequenceGroup sg = getGroup();
1369     if (sg.cs == null)
1370     {
1371       return;
1372     }
1373
1374     if (abovePIDColour.isSelected())
1375     {
1376       sg.cs.setConsensus(AAFrequency.calculate(
1377               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1378               sg.getEndRes() + 1));
1379
1380       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1381               .getName());
1382
1383       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1384
1385       SliderPanel.showPIDSlider();
1386     }
1387     else
1388     // remove PIDColouring
1389     {
1390       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1391     }
1392
1393     refresh();
1394   }
1395
1396   /**
1397    * DOCUMENT ME!
1398    *
1399    * @param e
1400    *          DOCUMENT ME!
1401    */
1402   protected void userDefinedColour_actionPerformed(ActionEvent e)
1403   {
1404     SequenceGroup sg = getGroup();
1405
1406     if (e.getActionCommand().equals("User Defined..."))
1407     {
1408       new UserDefinedColours(ap, sg);
1409     }
1410     else
1411     {
1412       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1413               .getUserColourSchemes().get(e.getActionCommand());
1414
1415       sg.cs = udc;
1416     }
1417     refresh();
1418   }
1419
1420   /**
1421    * DOCUMENT ME!
1422    *
1423    * @param e
1424    *          DOCUMENT ME!
1425    */
1426   protected void PIDColour_actionPerformed()
1427   {
1428     SequenceGroup sg = getGroup();
1429     sg.cs = new PIDColourScheme();
1430     sg.cs.setConsensus(AAFrequency.calculate(
1431             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1432             sg.getEndRes() + 1));
1433     refresh();
1434   }
1435
1436   /**
1437    * DOCUMENT ME!
1438    *
1439    * @param e
1440    *          DOCUMENT ME!
1441    */
1442   protected void BLOSUM62Colour_actionPerformed()
1443   {
1444     SequenceGroup sg = getGroup();
1445
1446     sg.cs = new Blosum62ColourScheme();
1447
1448     sg.cs.setConsensus(AAFrequency.calculate(
1449             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1450             sg.getEndRes() + 1));
1451
1452     refresh();
1453   }
1454
1455   /**
1456    * DOCUMENT ME!
1457    *
1458    * @param e
1459    *          DOCUMENT ME!
1460    */
1461   protected void noColourmenuItem_actionPerformed()
1462   {
1463     getGroup().cs = null;
1464     refresh();
1465   }
1466
1467   /**
1468    * DOCUMENT ME!
1469    *
1470    * @param e
1471    *          DOCUMENT ME!
1472    */
1473   protected void conservationMenuItem_actionPerformed()
1474   {
1475     SequenceGroup sg = getGroup();
1476     if (sg.cs == null)
1477     {
1478       return;
1479     }
1480
1481     if (conservationMenuItem.isSelected())
1482     {
1483       Conservation c = new Conservation("Group",
1484               ResidueProperties.propHash, 3,
1485               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1486               sg.getEndRes() + 1);
1487
1488       c.calculate();
1489       c.verdict(false, ap.av.ConsPercGaps);
1490
1491       sg.cs.setConservation(c);
1492
1493       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1494       SliderPanel.showConservationSlider();
1495     }
1496     else
1497     // remove ConservationColouring
1498     {
1499       sg.cs.setConservation(null);
1500     }
1501
1502     refresh();
1503   }
1504
1505   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1506   {
1507     SequenceGroup sg = getGroup();
1508     if (sg == null)
1509     {
1510       return;
1511     }
1512
1513     AnnotationColourGradient acg = new AnnotationColourGradient(
1514             sequence.getAnnotation()[0], null,
1515             AnnotationColourGradient.NO_THRESHOLD);
1516
1517     acg.predefinedColours = true;
1518     sg.cs = acg;
1519
1520     refresh();
1521   }
1522
1523   /**
1524    * DOCUMENT ME!
1525    *
1526    * @param e
1527    *          DOCUMENT ME!
1528    */
1529   protected void groupName_actionPerformed()
1530   {
1531
1532     SequenceGroup sg = getGroup();
1533     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1534             sg.getDescription(), "       Group Name ",
1535             "Group Description ", "Edit Group Name/Description",
1536             ap.alignFrame);
1537
1538     if (!dialog.accept)
1539     {
1540       return;
1541     }
1542
1543     sg.setName(dialog.getName());
1544     sg.setDescription(dialog.getDescription());
1545     refresh();
1546   }
1547
1548   /**
1549    * Get selection group - adding it to the alignment if necessary.
1550    *
1551    * @return sequence group to operate on
1552    */
1553   SequenceGroup getGroup()
1554   {
1555     SequenceGroup sg = ap.av.getSelectionGroup();
1556     // this method won't add a new group if it already exists
1557     if (sg != null)
1558     {
1559       ap.av.alignment.addGroup(sg);
1560     }
1561
1562     return sg;
1563   }
1564
1565   /**
1566    * DOCUMENT ME!
1567    *
1568    * @param e
1569    *          DOCUMENT ME!
1570    */
1571   void sequenceName_actionPerformed()
1572   {
1573     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1574             sequence.getDescription(), "       Sequence Name ",
1575             "Sequence Description ", "Edit Sequence Name/Description",
1576             ap.alignFrame);
1577
1578     if (!dialog.accept)
1579     {
1580       return;
1581     }
1582
1583     if (dialog.getName() != null)
1584     {
1585       if (dialog.getName().indexOf(" ") > -1)
1586       {
1587         JOptionPane.showMessageDialog(ap,
1588                 "Spaces have been converted to \"_\"",
1589                 "No spaces allowed in Sequence Name",
1590                 JOptionPane.WARNING_MESSAGE);
1591       }
1592
1593       sequence.setName(dialog.getName().replace(' ', '_'));
1594       ap.paintAlignment(false);
1595     }
1596
1597     sequence.setDescription(dialog.getDescription());
1598
1599     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1600             .getSequences());
1601
1602   }
1603
1604   /**
1605    * DOCUMENT ME!
1606    *
1607    * @param e
1608    *          DOCUMENT ME!
1609    */
1610   void unGroupMenuItem_actionPerformed()
1611   {
1612     SequenceGroup sg = ap.av.getSelectionGroup();
1613     ap.av.alignment.deleteGroup(sg);
1614     ap.av.setSelectionGroup(null);
1615     refresh();
1616   }
1617
1618   /**
1619    * DOCUMENT ME!
1620    *
1621    * @param e
1622    *          DOCUMENT ME!
1623    */
1624   protected void outline_actionPerformed()
1625   {
1626     SequenceGroup sg = getGroup();
1627     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1628             Color.BLUE);
1629
1630     if (col != null)
1631     {
1632       sg.setOutlineColour(col);
1633     }
1634
1635     refresh();
1636   }
1637
1638   /**
1639    * DOCUMENT ME!
1640    *
1641    * @param e
1642    *          DOCUMENT ME!
1643    */
1644   public void showBoxes_actionPerformed()
1645   {
1646     getGroup().setDisplayBoxes(showBoxes.isSelected());
1647     refresh();
1648   }
1649
1650   /**
1651    * DOCUMENT ME!
1652    *
1653    * @param e
1654    *          DOCUMENT ME!
1655    */
1656   public void showText_actionPerformed()
1657   {
1658     getGroup().setDisplayText(showText.isSelected());
1659     refresh();
1660   }
1661
1662   /**
1663    * DOCUMENT ME!
1664    *
1665    * @param e
1666    *          DOCUMENT ME!
1667    */
1668   public void showColourText_actionPerformed()
1669   {
1670     getGroup().setColourText(showColourText.isSelected());
1671     refresh();
1672   }
1673
1674   public void showLink(String url)
1675   {
1676     try
1677     {
1678       jalview.util.BrowserLauncher.openURL(url);
1679     } catch (Exception ex)
1680     {
1681       JOptionPane
1682               .showInternalMessageDialog(
1683                       Desktop.desktop,
1684                       "Unixers: Couldn't find default web browser."
1685                               + "\nAdd the full path to your browser in Preferences.",
1686                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1687
1688       ex.printStackTrace();
1689     }
1690   }
1691
1692   void hideSequences(boolean representGroup)
1693   {
1694     SequenceGroup sg = ap.av.getSelectionGroup();
1695     if (sg == null || sg.getSize() < 1)
1696     {
1697       ap.av.hideSequence(new SequenceI[]
1698       { sequence });
1699       return;
1700     }
1701
1702     ap.av.setSelectionGroup(null);
1703
1704     if (representGroup)
1705     {
1706       ap.av.hideRepSequences(sequence, sg);
1707
1708       return;
1709     }
1710
1711     int gsize = sg.getSize();
1712     SequenceI[] hseqs;
1713
1714     hseqs = new SequenceI[gsize];
1715
1716     int index = 0;
1717     for (int i = 0; i < gsize; i++)
1718     {
1719       hseqs[index++] = sg.getSequenceAt(i);
1720     }
1721
1722     ap.av.hideSequence(hseqs);
1723     // refresh(); TODO: ? needed ?
1724     ap.av.sendSelection();
1725   }
1726
1727   public void copy_actionPerformed()
1728   {
1729     ap.alignFrame.copy_actionPerformed(null);
1730   }
1731
1732   public void cut_actionPerformed()
1733   {
1734     ap.alignFrame.cut_actionPerformed(null);
1735   }
1736
1737   void changeCase(ActionEvent e)
1738   {
1739     Object source = e.getSource();
1740     SequenceGroup sg = ap.av.getSelectionGroup();
1741
1742     if (sg != null)
1743     {
1744       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1745               sg.getEndRes() + 1);
1746
1747       String description;
1748       int caseChange;
1749
1750       if (source == toggle)
1751       {
1752         description = "Toggle Case";
1753         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1754       }
1755       else if (source == upperCase)
1756       {
1757         description = "To Upper Case";
1758         caseChange = ChangeCaseCommand.TO_UPPER;
1759       }
1760       else
1761       {
1762         description = "To Lower Case";
1763         caseChange = ChangeCaseCommand.TO_LOWER;
1764       }
1765
1766       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1767               sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1768               caseChange);
1769
1770       ap.alignFrame.addHistoryItem(caseCommand);
1771
1772       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1773               .getSequences());
1774
1775     }
1776   }
1777
1778   public void outputText_actionPerformed(ActionEvent e)
1779   {
1780     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1781     cap.setForInput(null);
1782     Desktop.addInternalFrame(cap,
1783             "Alignment output - " + e.getActionCommand(), 600, 500);
1784
1785     String[] omitHidden = null;
1786
1787     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1788     // or we simply trust the user wants
1789     // wysiwig behaviour
1790     SequenceGroup sg = ap.av.getSelectionGroup();
1791     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1792     omitHidden = ap.av.getViewAsString(true);
1793     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1794     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1795     if (nala != null)
1796     {
1797       for (int i = 0; i < nala.length; i++)
1798       {
1799         AlignmentAnnotation na = nala[i];
1800         oal.addAnnotation(na);
1801       }
1802     }
1803     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1804             oal, omitHidden, csel, sg));
1805     oal = null;
1806   }
1807
1808   public void pdbFromFile_actionPerformed()
1809   {
1810     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1811             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1812     chooser.setFileView(new jalview.io.JalviewFileView());
1813     chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1814     chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1815
1816     int value = chooser.showOpenDialog(null);
1817
1818     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1819     {
1820       String choice = chooser.getSelectedFile().getPath();
1821       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1822       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1823     }
1824
1825   }
1826
1827   public void enterPDB_actionPerformed()
1828   {
1829     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1830             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1831
1832     if (id != null && id.length() > 0)
1833     {
1834       PDBEntry entry = new PDBEntry();
1835       entry.setId(id.toUpperCase());
1836       sequence.getDatasetSequence().addPDBId(entry);
1837     }
1838   }
1839
1840   public void discoverPDB_actionPerformed()
1841   {
1842
1843     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1844     { sequence }
1845             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1846     Thread discpdb = new Thread(new Runnable()
1847     {
1848       public void run()
1849       {
1850
1851         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1852                 .fetchDBRefs(false);
1853       }
1854
1855     });
1856     discpdb.start();
1857   }
1858
1859   public void sequenceFeature_actionPerformed()
1860   {
1861     SequenceGroup sg = ap.av.getSelectionGroup();
1862     if (sg == null)
1863     {
1864       return;
1865     }
1866
1867     int rsize = 0, gSize = sg.getSize();
1868     SequenceI[] rseqs, seqs = new SequenceI[gSize];
1869     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1870
1871     for (int i = 0; i < gSize; i++)
1872     {
1873       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1874       int end = sg.findEndRes(sg.getSequenceAt(i));
1875       if (start <= end)
1876       {
1877         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1878         features[rsize] = new SequenceFeature(null, null, null, start, end,
1879                 "Jalview");
1880         rsize++;
1881       }
1882     }
1883     rseqs = new SequenceI[rsize];
1884     tfeatures = new SequenceFeature[rsize];
1885     System.arraycopy(seqs, 0, rseqs, 0, rsize);
1886     System.arraycopy(features, 0, tfeatures, 0, rsize);
1887     features = tfeatures;
1888     seqs = rseqs;
1889     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1890             features, true, ap))
1891     {
1892       ap.alignFrame.setShowSeqFeatures(true);
1893       ap.highlightSearchResults(null);
1894     }
1895   }
1896
1897   public void textColour_actionPerformed()
1898   {
1899     SequenceGroup sg = getGroup();
1900     if (sg != null)
1901     {
1902       new TextColourChooser().chooseColour(ap, sg);
1903     }
1904   }
1905
1906   public void colourByStructure(String pdbid)
1907   {
1908     Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
1909                     sequence, pdbid);
1910
1911     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1912             "Coloured by " + pdbid, anots);
1913
1914     ap.av.alignment.addAnnotation(an);
1915     an.createSequenceMapping(sequence, 0, true);
1916     // an.adjustForAlignment();
1917     ap.av.alignment.setAnnotationIndex(an, 0);
1918
1919     ap.adjustAnnotationHeight();
1920
1921     sequence.addAlignmentAnnotation(an);
1922
1923   }
1924
1925   public void editSequence_actionPerformed(ActionEvent actionEvent)
1926   {
1927     SequenceGroup sg = ap.av.getSelectionGroup();
1928
1929     if (sg != null)
1930     {
1931       if (sequence == null)
1932         sequence = (Sequence) sg.getSequenceAt(0);
1933
1934       EditNameDialog dialog = new EditNameDialog(
1935               sequence.getSequenceAsString(sg.getStartRes(),
1936                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
1937               "Edit Sequence", ap.alignFrame);
1938
1939       if (dialog.accept)
1940       {
1941         EditCommand editCommand = new EditCommand("Edit Sequences",
1942                 EditCommand.REPLACE, dialog.getName().replace(' ',
1943                         ap.av.getGapCharacter()),
1944                 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1945                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1946
1947         ap.alignFrame.addHistoryItem(editCommand);
1948
1949         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1950                 .getSequences());
1951       }
1952     }
1953   }
1954
1955 }