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