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