src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26 import javax.xml.parsers.ParserConfigurationException;
  27
  28 import org.xml.sax.SAXException;
  29
  30 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  31 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  32 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  33 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  34
  35 import jalview.analysis.*;
  36 import jalview.commands.*;
  37 import jalview.datamodel.*;
  38 import jalview.io.*;
  39 import jalview.schemes.*;
  40 import jalview.util.GroupUrlLink;
  41 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  42 import jalview.util.UrlLink;
  43
  44 /**
  45  * DOCUMENT ME!
  46  *
  47  * @author $author$
  48  * @version $Revision: 1.118 $
  49  */
  50 public class PopupMenu extends JPopupMenu
  51 {
  52   JMenu groupMenu = new JMenu();
  53
  54   JMenuItem groupName = new JMenuItem();
  55
  56   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  65
  66   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  71
  72   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  73
  74   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  75
  76   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  77
  78   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  79
  80   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  81   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  82
  83   // protected JRadioButtonMenuItem covariationColour = new
  84   // JRadioButtonMenuItem();
  85
  86   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  87
  88   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  89
  90   AlignmentPanel ap;
  91
  92   JMenu sequenceMenu = new JMenu();
  93
  94   JMenuItem sequenceName = new JMenuItem();
  95
  96   JMenuItem sequenceDetails = new JMenuItem();
  97
  98   JMenuItem sequenceSelDetails = new JMenuItem();
  99
 100   SequenceI sequence;
 101
 102   JMenuItem unGroupMenuItem = new JMenuItem();
 103
 104   JMenuItem outline = new JMenuItem();
 105
 106   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 107
 108   JMenu colourMenu = new JMenu();
 109
 110   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 111
 112   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 113
 114   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 115
 116   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 117
 118   JMenu editMenu = new JMenu();
 119
 120   JMenuItem cut = new JMenuItem();
 121
 122   JMenuItem copy = new JMenuItem();
 123
 124   JMenuItem upperCase = new JMenuItem();
 125
 126   JMenuItem lowerCase = new JMenuItem();
 127
 128   JMenuItem toggle = new JMenuItem();
 129
 130   JMenu pdbMenu = new JMenu();
 131
 132   JMenuItem pdbFromFile = new JMenuItem();
 133
 134   JMenuItem enterPDB = new JMenuItem();
 135
 136   JMenuItem discoverPDB = new JMenuItem();
 137
 138   JMenu outputMenu = new JMenu();
 139
 140   JMenuItem sequenceFeature = new JMenuItem();
 141
 142   JMenuItem textColour = new JMenuItem();
 143
 144   JMenu jMenu1 = new JMenu();
 145
 146   JMenu structureMenu = new JMenu();
 147
 148   JMenu viewStructureMenu = new JMenu();
 149
 150   // JMenu colStructureMenu = new JMenu();
 151   JMenuItem editSequence = new JMenuItem();
 152
 153   // JMenuItem annotationMenuItem = new JMenuItem();
 154
 155   JMenu groupLinksMenu;
 156
 157   /**
 158    * Creates a new PopupMenu object.
 159    *
 160    * @param ap
 161    *          DOCUMENT ME!
 162    * @param seq
 163    *          DOCUMENT ME!
 164    */
 165   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 166   {
 167     this(ap, seq, links, null);
 168   }
 169
 170   /**
 171    *
 172    * @param ap
 173    * @param seq
 174    * @param links
 175    * @param groupLinks
 176    */
 177   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 178           Vector links, Vector groupLinks)
 179   {
 180     // /////////////////////////////////////////////////////////
 181     // If this is activated from the sequence panel, the user may want to
 182     // edit or annotate a particular residue. Therefore display the residue menu
 183     //
 184     // If from the IDPanel, we must display the sequence menu
 185     // ////////////////////////////////////////////////////////
 186     this.ap = ap;
 187     sequence = seq;
 188
 189     ButtonGroup colours = new ButtonGroup();
 190     colours.add(noColourmenuItem);
 191     colours.add(clustalColour);
 192     colours.add(zappoColour);
 193     colours.add(taylorColour);
 194     colours.add(hydrophobicityColour);
 195     colours.add(helixColour);
 196     colours.add(strandColour);
 197     colours.add(turnColour);
 198     colours.add(buriedColour);
 199     colours.add(abovePIDColour);
 200     colours.add(userDefinedColour);
 201     colours.add(PIDColour);
 202     colours.add(BLOSUM62Colour);
 203     colours.add(purinePyrimidineColour);
 204     colours.add(RNAInteractionColour);
 205     // colours.add(covariationColour);
 206
 207     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 208     {
 209       JMenuItem item = new JMenuItem(
 210               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 211
 212       item.addActionListener(new java.awt.event.ActionListener()
 213       {
 214         public void actionPerformed(ActionEvent e)
 215         {
 216           outputText_actionPerformed(e);
 217         }
 218       });
 219
 220       outputMenu.add(item);
 221     }
 222
 223     try
 224     {
 225       jbInit();
 226     } catch (Exception e)
 227     {
 228       e.printStackTrace();
 229     }
 230
 231     JMenuItem menuItem;
 232     if (seq != null)
 233     {
 234       sequenceMenu.setText(sequence.getName());
 235
 236       if (seq.getDatasetSequence().getPDBId() != null
 237               && seq.getDatasetSequence().getPDBId().size() > 0)
 238       {
 239         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 240                 .elements();
 241
 242         while (e.hasMoreElements())
 243         {
 244           final PDBEntry pdb = (PDBEntry) e.nextElement();
 245
 246           menuItem = new JMenuItem();
 247           menuItem.setText(pdb.getId());
 248           menuItem.addActionListener(new java.awt.event.ActionListener()
 249           {
 250             public void actionPerformed(ActionEvent e)
 251             {
 252               // TODO re JAL-860: optionally open dialog or provide a menu entry
 253               // allowing user to open just one structure per sequence
 254               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 255               { pdb })[0], null, ap);
 256               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 257             }
 258
 259           });
 260           viewStructureMenu.add(menuItem);
 261
 262           /*
 263            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 264            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 265            * public void actionPerformed(ActionEvent e) {
 266            * colourByStructure(pdb.getId()); } });
 267            * colStructureMenu.add(menuItem);
 268            */
 269         }
 270       }
 271       else
 272       {
 273         if (ap.av.getAlignment().isNucleotide() == false)
 274         {
 275           structureMenu.remove(viewStructureMenu);
 276         }
 277         // structureMenu.remove(colStructureMenu);
 278       }
 279
 280       if (ap.av.getAlignment().isNucleotide() == true)
 281       {
 282         AlignmentAnnotation[] aa = ap.av.getAlignment()
 283                 .getAlignmentAnnotation();
 284         for (int i = 0; i < aa.length; i++)
 285         {
 286           if (aa[i].getRNAStruc() != null)
 287           {
 288             final String rnastruc = aa[i].getRNAStruc();
 289             final String structureLine = aa[i].label;
 290             menuItem = new JMenuItem();
 291             menuItem.setText("2D RNA " + structureLine);
 292             menuItem.addActionListener(new java.awt.event.ActionListener()
 293
 294             {
 295               public void actionPerformed(ActionEvent e)
 296               {
 297                         //System.out.println("1:"+structureLine);
 298                         System.out.println("1:sname"+seq.getName());
 299                         System.out.println("2:seq"+seq);
 300
 301                         //System.out.println("3:"+seq.getSequenceAsString());
 302                         System.out.println("3:strucseq"+rnastruc);
 303                         //System.out.println("4:struc"+seq.getRNA());
 304                         System.out.println("5:name"+seq.getName());
 305                         System.out.println("6:ap"+ap);
 306                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 307                             .getName(), ap);
 308                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 309                         System.out.println("end");
 310               }
 311             });
 312             viewStructureMenu.add(menuItem);
 313           }
 314         }
 315
 316         // SequenceFeatures[] test = seq.getSequenceFeatures();
 317
 318         if (seq.getAnnotation() != null)
 319         {
 320           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 321           for (int i = 0; i < seqAnno.length; i++)
 322           {
 323             if (seqAnno[i].getRNAStruc() != null)
 324             {
 325               final String rnastruc = seqAnno[i].getRNAStruc();
 326
 327               // TODO: make rnastrucF a bit more nice
 328               menuItem = new JMenuItem();
 329               menuItem.setText("2D RNA - " + seq.getName());
 330               menuItem.addActionListener(new java.awt.event.ActionListener()
 331               {
 332                 public void actionPerformed(ActionEvent e)
 333                 {
 334                   // TODO: VARNA does'nt print gaps in the sequence
 335
 336                   new AppVarna(seq.getName() + " structure", seq, seq
 337                           .getSequenceAsString(), rnastruc, seq.getName(),
 338                           ap);
 339                 }
 340               });
 341               viewStructureMenu.add(menuItem);
 342             }
 343           }
 344         }
 345
 346       }
 347
 348       menuItem = new JMenuItem("Hide Sequences");
 349       menuItem.addActionListener(new java.awt.event.ActionListener()
 350       {
 351         public void actionPerformed(ActionEvent e)
 352         {
 353           hideSequences(false);
 354         }
 355       });
 356       add(menuItem);
 357
 358       if (ap.av.getSelectionGroup() != null
 359               && ap.av.getSelectionGroup().getSize() > 1)
 360       {
 361         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 362         menuItem.addActionListener(new java.awt.event.ActionListener()
 363         {
 364           public void actionPerformed(ActionEvent e)
 365           {
 366             hideSequences(true);
 367           }
 368         });
 369         sequenceMenu.add(menuItem);
 370       }
 371
 372       if (ap.av.hasHiddenRows())
 373       {
 374         final int index = ap.av.getAlignment().findIndex(seq);
 375
 376         if (ap.av.adjustForHiddenSeqs(index)
 377                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 378         {
 379           menuItem = new JMenuItem("Reveal Sequences");
 380           menuItem.addActionListener(new ActionListener()
 381           {
 382             public void actionPerformed(ActionEvent e)
 383             {
 384               ap.av.showSequence(index);
 385               if (ap.overviewPanel != null)
 386               {
 387                 ap.overviewPanel.updateOverviewImage();
 388               }
 389             }
 390           });
 391           add(menuItem);
 392         }
 393       }
 394     }
 395     // for the case when no sequences are even visible
 396     if (ap.av.hasHiddenRows())
 397     {
 398       {
 399         menuItem = new JMenuItem("Reveal All");
 400         menuItem.addActionListener(new ActionListener()
 401         {
 402           public void actionPerformed(ActionEvent e)
 403           {
 404             ap.av.showAllHiddenSeqs();
 405             if (ap.overviewPanel != null)
 406             {
 407               ap.overviewPanel.updateOverviewImage();
 408             }
 409           }
 410         });
 411
 412         add(menuItem);
 413       }
 414
 415     }
 416
 417     SequenceGroup sg = ap.av.getSelectionGroup();
 418
 419     if (sg != null && sg.getSize() > 0)
 420     {
 421       groupName.setText("Name: " + sg.getName());
 422       groupName.setText("Edit name and description of current group.");
 423
 424       if (sg.cs instanceof ZappoColourScheme)
 425       {
 426         zappoColour.setSelected(true);
 427       }
 428       else if (sg.cs instanceof TaylorColourScheme)
 429       {
 430         taylorColour.setSelected(true);
 431       }
 432       else if (sg.cs instanceof PIDColourScheme)
 433       {
 434         PIDColour.setSelected(true);
 435       }
 436       else if (sg.cs instanceof Blosum62ColourScheme)
 437       {
 438         BLOSUM62Colour.setSelected(true);
 439       }
 440       else if (sg.cs instanceof UserColourScheme)
 441       {
 442         userDefinedColour.setSelected(true);
 443       }
 444       else if (sg.cs instanceof HydrophobicColourScheme)
 445       {
 446         hydrophobicityColour.setSelected(true);
 447       }
 448       else if (sg.cs instanceof HelixColourScheme)
 449       {
 450         helixColour.setSelected(true);
 451       }
 452       else if (sg.cs instanceof StrandColourScheme)
 453       {
 454         strandColour.setSelected(true);
 455       }
 456       else if (sg.cs instanceof TurnColourScheme)
 457       {
 458         turnColour.setSelected(true);
 459       }
 460       else if (sg.cs instanceof BuriedColourScheme)
 461       {
 462         buriedColour.setSelected(true);
 463       }
 464       else if (sg.cs instanceof ClustalxColourScheme)
 465       {
 466         clustalColour.setSelected(true);
 467       }
 468       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 469       {
 470         purinePyrimidineColour.setSelected(true);
 471       }
 472
 473       else if (sg.cs instanceof RNAInteractionColourScheme)
 474       {
 475         RNAInteractionColour.setSelected(true);
 476       }
 477       /*
 478        * else if (sg.cs instanceof CovariationColourScheme) {
 479        * covariationColour.setSelected(true); }
 480        */
 481       else
 482       {
 483         noColourmenuItem.setSelected(true);
 484       }
 485
 486       if (sg.cs != null && sg.cs.conservationApplied())
 487       {
 488         conservationMenuItem.setSelected(true);
 489       }
 490       displayNonconserved.setSelected(sg.getShowNonconserved());
 491       showText.setSelected(sg.getDisplayText());
 492       showColourText.setSelected(sg.getColourText());
 493       showBoxes.setSelected(sg.getDisplayBoxes());
 494       // add any groupURLs to the groupURL submenu and make it visible
 495       if (groupLinks != null && groupLinks.size() > 0)
 496       {
 497         buildGroupURLMenu(sg, groupLinks);
 498       }
 499       // Add a 'show all structures' for the current selection
 500       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 501       SequenceI sqass = null;
 502       for (SequenceI sq : ap.av.getSequenceSelection())
 503       {
 504         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 505                 .getPDBId();
 506         if (pes != null)
 507         {
 508           for (PDBEntry pe : pes)
 509           {
 510             pdbe.put(pe.getId(), pe);
 511             if (sqass == null)
 512             {
 513               sqass = sq;
 514             }
 515           }
 516         }
 517       }
 518       if (pdbe.size() > 0)
 519       {
 520         final PDBEntry[] pe = pdbe.values().toArray(
 521                 new PDBEntry[pdbe.size()]);
 522         final JMenuItem gpdbview;
 523         if (pdbe.size() == 1)
 524         {
 525           structureMenu.add(gpdbview = new JMenuItem("View structure for "
 526                   + sqass.getDisplayId(false)));
 527         }
 528         else
 529         {
 530           structureMenu.add(gpdbview = new JMenuItem("View all "
 531                   + pdbe.size() + " structures."));
 532         }
 533         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 534         gpdbview.addActionListener(new ActionListener()
 535         {
 536
 537           @Override
 538           public void actionPerformed(ActionEvent e)
 539           {
 540             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 541           }
 542         });
 543       }
 544     }
 545     else
 546     {
 547       groupMenu.setVisible(false);
 548       editMenu.setVisible(false);
 549     }
 550
 551     if (!ap.av.getAlignment().getGroups().contains(sg))
 552     {
 553       unGroupMenuItem.setVisible(false);
 554     }
 555
 556     if (seq == null)
 557     {
 558       sequenceMenu.setVisible(false);
 559       structureMenu.setVisible(false);
 560     }
 561
 562     if (links != null && links.size() > 0)
 563     {
 564
 565       JMenu linkMenu = new JMenu("Link");
 566       Vector linkset = new Vector();
 567       for (int i = 0; i < links.size(); i++)
 568       {
 569         String link = links.elementAt(i).toString();
 570         UrlLink urlLink = null;
 571         try
 572         {
 573           urlLink = new UrlLink(link);
 574         } catch (Exception foo)
 575         {
 576           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 577                   + "'", foo);
 578           continue;
 579         }
 580         ;
 581         if (!urlLink.isValid())
 582         {
 583           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 584           continue;
 585         }
 586         final String label = urlLink.getLabel();
 587         if (seq != null && urlLink.isDynamic())
 588         {
 589
 590           // collect matching db-refs
 591           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 592                   seq.getDBRef(), new String[]
 593                   { urlLink.getTarget() });
 594           // collect id string too
 595           String id = seq.getName();
 596           String descr = seq.getDescription();
 597           if (descr != null && descr.length() < 1)
 598           {
 599             descr = null;
 600           }
 601
 602           if (dbr != null)
 603           {
 604             for (int r = 0; r < dbr.length; r++)
 605             {
 606               if (id != null && dbr[r].getAccessionId().equals(id))
 607               {
 608                 // suppress duplicate link creation for the bare sequence ID
 609                 // string with this link
 610                 id = null;
 611               }
 612               // create Bare ID link for this RUL
 613               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 614                       true);
 615               if (urls != null)
 616               {
 617                 for (int u = 0; u < urls.length; u += 2)
 618                 {
 619                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 620                   {
 621                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 622                     addshowLink(linkMenu, label + "|" + urls[u],
 623                             urls[u + 1]);
 624                   }
 625                 }
 626               }
 627             }
 628           }
 629           if (id != null)
 630           {
 631             // create Bare ID link for this RUL
 632             String[] urls = urlLink.makeUrls(id, true);
 633             if (urls != null)
 634             {
 635               for (int u = 0; u < urls.length; u += 2)
 636               {
 637                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 638                 {
 639                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 640                   addshowLink(linkMenu, label, urls[u + 1]);
 641                 }
 642               }
 643             }
 644           }
 645           // Create urls from description but only for URL links which are regex
 646           // links
 647           if (descr != null && urlLink.getRegexReplace() != null)
 648           {
 649             // create link for this URL from description where regex matches
 650             String[] urls = urlLink.makeUrls(descr, true);
 651             if (urls != null)
 652             {
 653               for (int u = 0; u < urls.length; u += 2)
 654               {
 655                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 656                 {
 657                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 658                   addshowLink(linkMenu, label, urls[u + 1]);
 659                 }
 660               }
 661             }
 662           }
 663         }
 664         else
 665         {
 666           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 667           {
 668             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 669             // Add a non-dynamic link
 670             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 671           }
 672         }
 673       }
 674       if (sequence != null)
 675       {
 676         sequenceMenu.add(linkMenu);
 677       }
 678       else
 679       {
 680         add(linkMenu);
 681       }
 682     }
 683   }
 684
 685   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 686   {
 687
 688     // TODO: usability: thread off the generation of group url content so root
 689     // menu appears asap
 690     // sequence only URLs
 691     // ID/regex match URLs
 692     groupLinksMenu = new JMenu("Group Link");
 693     JMenu[] linkMenus = new JMenu[]
 694     { null, new JMenu("IDS"), new JMenu("Sequences"),
 695         new JMenu("IDS and Sequences") }; // three types of url that might be
 696                                           // created.
 697     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 698     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 699     Hashtable commonDbrefs = new Hashtable();
 700     for (int sq = 0; sq < seqs.length; sq++)
 701     {
 702
 703       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 704               .findPosition(sg.getEndRes());
 705       // just collect ids from dataset sequence
 706       // TODO: check if IDs collected from selecton group intersects with the
 707       // current selection, too
 708       SequenceI sqi = seqs[sq];
 709       while (sqi.getDatasetSequence() != null)
 710       {
 711         sqi = sqi.getDatasetSequence();
 712       }
 713       DBRefEntry[] dbr = sqi.getDBRef();
 714       if (dbr != null && dbr.length > 0)
 715       {
 716         for (int d = 0; d < dbr.length; d++)
 717         {
 718           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 719           Object[] sarray = (Object[]) commonDbrefs.get(src);
 720           if (sarray == null)
 721           {
 722             sarray = new Object[2];
 723             sarray[0] = new int[]
 724             { 0 };
 725             sarray[1] = new String[seqs.length];
 726
 727             commonDbrefs.put(src, sarray);
 728           }
 729
 730           if (((String[]) sarray[1])[sq] == null)
 731           {
 732             if (!dbr[d].hasMap()
 733                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 734             {
 735               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 736               ((int[]) sarray[0])[0]++;
 737             }
 738           }
 739         }
 740       }
 741     }
 742     // now create group links for all distinct ID/sequence sets.
 743     boolean addMenu = false; // indicates if there are any group links to give
 744                              // to user
 745     for (int i = 0; i < groupLinks.size(); i++)
 746     {
 747       String link = groupLinks.elementAt(i).toString();
 748       GroupUrlLink urlLink = null;
 749       try
 750       {
 751         urlLink = new GroupUrlLink(link);
 752       } catch (Exception foo)
 753       {
 754         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 755                 + "'", foo);
 756         continue;
 757       }
 758       ;
 759       if (!urlLink.isValid())
 760       {
 761         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 762         continue;
 763       }
 764       final String label = urlLink.getLabel();
 765       boolean usingNames = false;
 766       // Now see which parts of the group apply for this URL
 767       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 768       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 769       String[] seqstr, ids; // input to makeUrl
 770       if (idset != null)
 771       {
 772         int numinput = ((int[]) idset[0])[0];
 773         String[] allids = ((String[]) idset[1]);
 774         seqstr = new String[numinput];
 775         ids = new String[numinput];
 776         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 777         {
 778           if (allids[sq] != null)
 779           {
 780             ids[idcount] = allids[sq];
 781             seqstr[idcount++] = idandseqs[1][sq];
 782           }
 783         }
 784       }
 785       else
 786       {
 787         // just use the id/seq set
 788         seqstr = idandseqs[1];
 789         ids = idandseqs[0];
 790         usingNames = true;
 791       }
 792       // and try and make the groupURL!
 793
 794       Object[] urlset = null;
 795       try
 796       {
 797         urlset = urlLink.makeUrlStubs(ids, seqstr,
 798                 "FromJalview" + System.currentTimeMillis(), false);
 799       } catch (UrlStringTooLongException e)
 800       {
 801       }
 802       if (urlset != null)
 803       {
 804         int type = urlLink.getGroupURLType() & 3;
 805         // System.out.println(urlLink.getGroupURLType()
 806         // +" "+((String[])urlset[3])[0]);
 807         // first two bits ofurlLink type bitfield are sequenceids and sequences
 808         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 809         addshowLink(linkMenus[type], label
 810                 + (((type & 1) == 1) ? ("("
 811                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 812                 urlLink, urlset);
 813         addMenu = true;
 814       }
 815     }
 816     if (addMenu)
 817     {
 818       groupLinksMenu = new JMenu("Group Links");
 819       for (int m = 0; m < linkMenus.length; m++)
 820       {
 821         if (linkMenus[m] != null
 822                 && linkMenus[m].getMenuComponentCount() > 0)
 823         {
 824           groupLinksMenu.add(linkMenus[m]);
 825         }
 826       }
 827
 828       groupMenu.add(groupLinksMenu);
 829     }
 830   }
 831
 832   /**
 833    * add a show URL menu item to the given linkMenu
 834    *
 835    * @param linkMenu
 836    * @param label
 837    *          - menu label string
 838    * @param url
 839    *          - url to open
 840    */
 841   private void addshowLink(JMenu linkMenu, String label, final String url)
 842   {
 843     JMenuItem item = new JMenuItem(label);
 844     item.setToolTipText("open URL: " + url);
 845     item.addActionListener(new java.awt.event.ActionListener()
 846     {
 847       public void actionPerformed(ActionEvent e)
 848       {
 849         new Thread(new Runnable()
 850         {
 851
 852           public void run()
 853           {
 854             showLink(url);
 855           }
 856
 857         }).start();
 858       }
 859     });
 860
 861     linkMenu.add(item);
 862   }
 863
 864   /**
 865    * add a late bound groupURL item to the given linkMenu
 866    *
 867    * @param linkMenu
 868    * @param label
 869    *          - menu label string
 870    * @param urlgenerator
 871    *          GroupURLLink used to generate URL
 872    * @param urlstub
 873    *          Object array returned from the makeUrlStubs function.
 874    */
 875   private void addshowLink(JMenu linkMenu, String label,
 876           final GroupUrlLink urlgenerator, final Object[] urlstub)
 877   {
 878     JMenuItem item = new JMenuItem(label);
 879     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 880             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 881                                                                              // put
 882                                                                              // in
 883                                                                              // info
 884                                                                              // about
 885                                                                              // what
 886                                                                              // is
 887                                                                              // being
 888                                                                              // sent.
 889     item.addActionListener(new java.awt.event.ActionListener()
 890     {
 891       public void actionPerformed(ActionEvent e)
 892       {
 893         new Thread(new Runnable()
 894         {
 895
 896           public void run()
 897           {
 898             try
 899             {
 900               showLink(urlgenerator.constructFrom(urlstub));
 901             } catch (UrlStringTooLongException e)
 902             {
 903             }
 904           }
 905
 906         }).start();
 907       }
 908     });
 909
 910     linkMenu.add(item);
 911   }
 912
 913   /**
 914    * DOCUMENT ME!
 915    *
 916    * @throws Exception
 917    *           DOCUMENT ME!
 918    */
 919   private void jbInit() throws Exception
 920   {
 921     groupMenu.setText("Group");
 922     groupMenu.setText("Selection");
 923     groupName.setText("Name");
 924     groupName.addActionListener(new java.awt.event.ActionListener()
 925     {
 926       public void actionPerformed(ActionEvent e)
 927       {
 928         groupName_actionPerformed();
 929       }
 930     });
 931     sequenceMenu.setText("Sequence");
 932     sequenceName.setText("Edit Name/Description");
 933     sequenceName.addActionListener(new java.awt.event.ActionListener()
 934     {
 935       public void actionPerformed(ActionEvent e)
 936       {
 937         sequenceName_actionPerformed();
 938       }
 939     });
 940     sequenceDetails.setText("Sequence Details ...");
 941     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 942     {
 943       public void actionPerformed(ActionEvent e)
 944       {
 945         sequenceDetails_actionPerformed();
 946       }
 947     });
 948     sequenceSelDetails.setText("Sequence Details ...");
 949     sequenceSelDetails
 950             .addActionListener(new java.awt.event.ActionListener()
 951             {
 952               public void actionPerformed(ActionEvent e)
 953               {
 954                 sequenceSelectionDetails_actionPerformed();
 955               }
 956             });
 957     PIDColour.setFocusPainted(false);
 958     unGroupMenuItem.setText("Remove Group");
 959     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 960     {
 961       public void actionPerformed(ActionEvent e)
 962       {
 963         unGroupMenuItem_actionPerformed();
 964       }
 965     });
 966
 967     outline.setText("Border colour");
 968     outline.addActionListener(new java.awt.event.ActionListener()
 969     {
 970       public void actionPerformed(ActionEvent e)
 971       {
 972         outline_actionPerformed();
 973       }
 974     });
 975     nucleotideMenuItem.setText("Nucleotide");
 976     nucleotideMenuItem.addActionListener(new ActionListener()
 977     {
 978       public void actionPerformed(ActionEvent e)
 979       {
 980         nucleotideMenuItem_actionPerformed();
 981       }
 982     });
 983     colourMenu.setText("Group Colour");
 984     showBoxes.setText("Boxes");
 985     showBoxes.setState(true);
 986     showBoxes.addActionListener(new ActionListener()
 987     {
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         showBoxes_actionPerformed();
 991       }
 992     });
 993     showText.setText("Text");
 994     showText.setState(true);
 995     showText.addActionListener(new ActionListener()
 996     {
 997       public void actionPerformed(ActionEvent e)
 998       {
 999         showText_actionPerformed();
1000       }
1001     });
1002     showColourText.setText("Colour Text");
1003     showColourText.addActionListener(new ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         showColourText_actionPerformed();
1008       }
1009     });
1010     displayNonconserved.setText("Show Nonconserved");
1011     displayNonconserved.setState(true);
1012     displayNonconserved.addActionListener(new ActionListener()
1013     {
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         showNonconserved_actionPerformed();
1017       }
1018     });
1019     editMenu.setText("Edit");
1020     cut.setText("Cut");
1021     cut.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         cut_actionPerformed();
1026       }
1027     });
1028     upperCase.setText("To Upper Case");
1029     upperCase.addActionListener(new ActionListener()
1030     {
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         changeCase(e);
1034       }
1035     });
1036     copy.setText("Copy");
1037     copy.addActionListener(new ActionListener()
1038     {
1039       public void actionPerformed(ActionEvent e)
1040       {
1041         copy_actionPerformed();
1042       }
1043     });
1044     lowerCase.setText("To Lower Case");
1045     lowerCase.addActionListener(new ActionListener()
1046     {
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         changeCase(e);
1050       }
1051     });
1052     toggle.setText("Toggle Case");
1053     toggle.addActionListener(new ActionListener()
1054     {
1055       public void actionPerformed(ActionEvent e)
1056       {
1057         changeCase(e);
1058       }
1059     });
1060     pdbMenu.setText("Associate Structure with Sequence");
1061     pdbFromFile.setText("From File");
1062     pdbFromFile.addActionListener(new ActionListener()
1063     {
1064       public void actionPerformed(ActionEvent e)
1065       {
1066         pdbFromFile_actionPerformed();
1067       }
1068     });
1069     enterPDB.setText("Enter PDB Id");
1070     enterPDB.addActionListener(new ActionListener()
1071     {
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         enterPDB_actionPerformed();
1075       }
1076     });
1077     discoverPDB.setText("Discover PDB ids");
1078     discoverPDB.addActionListener(new ActionListener()
1079     {
1080       public void actionPerformed(ActionEvent e)
1081       {
1082         discoverPDB_actionPerformed();
1083       }
1084     });
1085     outputMenu.setText("Output to Textbox...");
1086     sequenceFeature.setText("Create Sequence Feature");
1087     sequenceFeature.addActionListener(new ActionListener()
1088     {
1089       public void actionPerformed(ActionEvent e)
1090       {
1091         sequenceFeature_actionPerformed();
1092       }
1093     });
1094     textColour.setText("Text Colour");
1095     textColour.addActionListener(new ActionListener()
1096     {
1097       public void actionPerformed(ActionEvent e)
1098       {
1099         textColour_actionPerformed();
1100       }
1101     });
1102     jMenu1.setText("Group");
1103     structureMenu.setText("Structure");
1104     viewStructureMenu.setText("View Structure");
1105     // colStructureMenu.setText("Colour By Structure");
1106     editSequence.setText("Edit Sequence...");
1107     editSequence.addActionListener(new ActionListener()
1108     {
1109       public void actionPerformed(ActionEvent actionEvent)
1110       {
1111         editSequence_actionPerformed(actionEvent);
1112       }
1113     });
1114
1115     /*
1116      * annotationMenuItem.setText("By Annotation");
1117      * annotationMenuItem.addActionListener(new ActionListener() { public void
1118      * actionPerformed(ActionEvent actionEvent) {
1119      * annotationMenuItem_actionPerformed(actionEvent); } });
1120      */
1121     groupMenu.add(sequenceSelDetails);
1122     add(groupMenu);
1123     add(sequenceMenu);
1124     this.add(structureMenu);
1125     groupMenu.add(editMenu);
1126     groupMenu.add(outputMenu);
1127     groupMenu.add(sequenceFeature);
1128     groupMenu.add(jMenu1);
1129     sequenceMenu.add(sequenceName);
1130     sequenceMenu.add(sequenceDetails);
1131     colourMenu.add(textColour);
1132     colourMenu.add(noColourmenuItem);
1133     colourMenu.add(clustalColour);
1134     colourMenu.add(BLOSUM62Colour);
1135     colourMenu.add(PIDColour);
1136     colourMenu.add(zappoColour);
1137     colourMenu.add(taylorColour);
1138     colourMenu.add(hydrophobicityColour);
1139     colourMenu.add(helixColour);
1140     colourMenu.add(strandColour);
1141     colourMenu.add(turnColour);
1142     colourMenu.add(buriedColour);
1143     colourMenu.add(nucleotideMenuItem);
1144     if (ap.getAlignment().isNucleotide()) {
1145       colourMenu.add(RNAInteractionColour);
1146         colourMenu.add(purinePyrimidineColour);
1147     }
1148     // colourMenu.add(covariationColour);
1149     colourMenu.add(userDefinedColour);
1150
1151     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1152     {
1153       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1154               .getUserColourSchemes().keys();
1155
1156       while (userColours.hasMoreElements())
1157       {
1158         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1159         item.addActionListener(new ActionListener()
1160         {
1161           public void actionPerformed(ActionEvent evt)
1162           {
1163             userDefinedColour_actionPerformed(evt);
1164           }
1165         });
1166         colourMenu.add(item);
1167       }
1168     }
1169
1170     colourMenu.addSeparator();
1171     colourMenu.add(abovePIDColour);
1172     colourMenu.add(conservationMenuItem);
1173     // colourMenu.add(annotationMenuItem);
1174     editMenu.add(copy);
1175     editMenu.add(cut);
1176     editMenu.add(editSequence);
1177     editMenu.add(upperCase);
1178     editMenu.add(lowerCase);
1179     editMenu.add(toggle);
1180     pdbMenu.add(pdbFromFile);
1181     pdbMenu.add(enterPDB);
1182     pdbMenu.add(discoverPDB);
1183     jMenu1.add(groupName);
1184     jMenu1.add(unGroupMenuItem);
1185     jMenu1.add(colourMenu);
1186     jMenu1.add(showBoxes);
1187     jMenu1.add(showText);
1188     jMenu1.add(showColourText);
1189     jMenu1.add(outline);
1190     jMenu1.add(displayNonconserved);
1191     structureMenu.add(pdbMenu);
1192     structureMenu.add(viewStructureMenu);
1193     // structureMenu.add(colStructureMenu);
1194     noColourmenuItem.setText("None");
1195     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1196     {
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         noColourmenuItem_actionPerformed();
1200       }
1201     });
1202
1203     clustalColour.setText("Clustalx colours");
1204     clustalColour.addActionListener(new java.awt.event.ActionListener()
1205     {
1206       public void actionPerformed(ActionEvent e)
1207       {
1208         clustalColour_actionPerformed();
1209       }
1210     });
1211     zappoColour.setText("Zappo");
1212     zappoColour.addActionListener(new java.awt.event.ActionListener()
1213     {
1214       public void actionPerformed(ActionEvent e)
1215       {
1216         zappoColour_actionPerformed();
1217       }
1218     });
1219     taylorColour.setText("Taylor");
1220     taylorColour.addActionListener(new java.awt.event.ActionListener()
1221     {
1222       public void actionPerformed(ActionEvent e)
1223       {
1224         taylorColour_actionPerformed();
1225       }
1226     });
1227     hydrophobicityColour.setText("Hydrophobicity");
1228     hydrophobicityColour
1229             .addActionListener(new java.awt.event.ActionListener()
1230             {
1231               public void actionPerformed(ActionEvent e)
1232               {
1233                 hydrophobicityColour_actionPerformed();
1234               }
1235             });
1236     helixColour.setText("Helix propensity");
1237     helixColour.addActionListener(new java.awt.event.ActionListener()
1238     {
1239       public void actionPerformed(ActionEvent e)
1240       {
1241         helixColour_actionPerformed();
1242       }
1243     });
1244     strandColour.setText("Strand propensity");
1245     strandColour.addActionListener(new java.awt.event.ActionListener()
1246     {
1247       public void actionPerformed(ActionEvent e)
1248       {
1249         strandColour_actionPerformed();
1250       }
1251     });
1252     turnColour.setText("Turn propensity");
1253     turnColour.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         turnColour_actionPerformed();
1258       }
1259     });
1260     buriedColour.setText("Buried Index");
1261     buriedColour.addActionListener(new java.awt.event.ActionListener()
1262     {
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         buriedColour_actionPerformed();
1266       }
1267     });
1268     abovePIDColour.setText("Above % Identity");
1269     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1270     {
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         abovePIDColour_actionPerformed();
1274       }
1275     });
1276     userDefinedColour.setText("User Defined...");
1277     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1278     {
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         userDefinedColour_actionPerformed(e);
1282       }
1283     });
1284     PIDColour.setText("Percentage Identity");
1285     PIDColour.addActionListener(new java.awt.event.ActionListener()
1286     {
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         PIDColour_actionPerformed();
1290       }
1291     });
1292     BLOSUM62Colour.setText("BLOSUM62");
1293     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1294     {
1295       public void actionPerformed(ActionEvent e)
1296       {
1297         BLOSUM62Colour_actionPerformed();
1298       }
1299     });
1300     purinePyrimidineColour.setText("Purine/Pyrimidine");
1301     purinePyrimidineColour
1302             .addActionListener(new java.awt.event.ActionListener()
1303             {
1304               public void actionPerformed(ActionEvent e)
1305               {
1306                 purinePyrimidineColour_actionPerformed();
1307               }
1308             });
1309
1310     RNAInteractionColour.setText("RNA Interaction type");
1311     RNAInteractionColour
1312             .addActionListener(new java.awt.event.ActionListener()
1313             {
1314               public void actionPerformed(ActionEvent e)
1315               {
1316                 RNAInteractionColour_actionPerformed();
1317               }
1318             });
1319     /*
1320      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1321      * public void actionPerformed(ActionEvent e) {
1322      * covariationColour_actionPerformed(); } });
1323      */
1324
1325     conservationMenuItem.setText("Conservation");
1326     conservationMenuItem
1327             .addActionListener(new java.awt.event.ActionListener()
1328             {
1329               public void actionPerformed(ActionEvent e)
1330               {
1331                 conservationMenuItem_actionPerformed();
1332               }
1333             });
1334   }
1335
1336   protected void sequenceSelectionDetails_actionPerformed()
1337   {
1338     createSequenceDetailsReport(ap.av.getSequenceSelection());
1339   }
1340
1341   protected void sequenceDetails_actionPerformed()
1342   {
1343     createSequenceDetailsReport(new SequenceI[]
1344     { sequence });
1345   }
1346
1347   public void createSequenceDetailsReport(SequenceI[] sequences)
1348   {
1349     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1350     StringBuffer contents = new StringBuffer();
1351     for (SequenceI seq : sequences)
1352     {
1353       contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1354               + "</h2></p><p>");
1355       new SequenceAnnotationReport(null)
1356               .createSequenceAnnotationReport(
1357                       contents,
1358                       seq,
1359                       true,
1360                       true,
1361                       false,
1362                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1363                               : null);
1364       contents.append("</p>");
1365     }
1366     cap.setText("<html>" + contents.toString() + "</html>");
1367
1368     Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1369             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1370                     : "Selection"), 500, 400);
1371
1372   }
1373
1374   protected void showNonconserved_actionPerformed()
1375   {
1376     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1377     refresh();
1378   }
1379
1380   /**
1381    * call to refresh view after settings change
1382    */
1383   void refresh()
1384   {
1385     ap.updateAnnotation();
1386     ap.paintAlignment(true);
1387
1388     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1389   }
1390
1391   /**
1392    * DOCUMENT ME!
1393    *
1394    * @param e
1395    *          DOCUMENT ME!
1396    */
1397   protected void clustalColour_actionPerformed()
1398   {
1399     SequenceGroup sg = getGroup();
1400     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1401     refresh();
1402   }
1403
1404   /**
1405    * DOCUMENT ME!
1406    *
1407    * @param e
1408    *          DOCUMENT ME!
1409    */
1410   protected void zappoColour_actionPerformed()
1411   {
1412     getGroup().cs = new ZappoColourScheme();
1413     refresh();
1414   }
1415
1416   /**
1417    * DOCUMENT ME!
1418    *
1419    * @param e
1420    *          DOCUMENT ME!
1421    */
1422   protected void taylorColour_actionPerformed()
1423   {
1424     getGroup().cs = new TaylorColourScheme();
1425     refresh();
1426   }
1427
1428   /**
1429    * DOCUMENT ME!
1430    *
1431    * @param e
1432    *          DOCUMENT ME!
1433    */
1434   protected void hydrophobicityColour_actionPerformed()
1435   {
1436     getGroup().cs = new HydrophobicColourScheme();
1437     refresh();
1438   }
1439
1440   /**
1441    * DOCUMENT ME!
1442    *
1443    * @param e
1444    *          DOCUMENT ME!
1445    */
1446   protected void helixColour_actionPerformed()
1447   {
1448     getGroup().cs = new HelixColourScheme();
1449     refresh();
1450   }
1451
1452   /**
1453    * DOCUMENT ME!
1454    *
1455    * @param e
1456    *          DOCUMENT ME!
1457    */
1458   protected void strandColour_actionPerformed()
1459   {
1460     getGroup().cs = new StrandColourScheme();
1461     refresh();
1462   }
1463
1464   /**
1465    * DOCUMENT ME!
1466    *
1467    * @param e
1468    *          DOCUMENT ME!
1469    */
1470   protected void turnColour_actionPerformed()
1471   {
1472     getGroup().cs = new TurnColourScheme();
1473     refresh();
1474   }
1475
1476   /**
1477    * DOCUMENT ME!
1478    *
1479    * @param e
1480    *          DOCUMENT ME!
1481    */
1482   protected void buriedColour_actionPerformed()
1483   {
1484     getGroup().cs = new BuriedColourScheme();
1485     refresh();
1486   }
1487
1488   /**
1489    * DOCUMENT ME!
1490    *
1491    * @param e
1492    *          DOCUMENT ME!
1493    */
1494   public void nucleotideMenuItem_actionPerformed()
1495   {
1496     getGroup().cs = new NucleotideColourScheme();
1497     refresh();
1498   }
1499
1500   protected void purinePyrimidineColour_actionPerformed()
1501   {
1502     getGroup().cs = new PurinePyrimidineColourScheme();
1503     refresh();
1504   }
1505
1506   protected void RNAInteractionColour_actionPerformed()
1507   {
1508     getGroup().cs = new RNAInteractionColourScheme();
1509     refresh();
1510   }
1511   /*
1512    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1513    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1514    */
1515   /**
1516    * DOCUMENT ME!
1517    *
1518    * @param e
1519    *          DOCUMENT ME!
1520    */
1521   protected void abovePIDColour_actionPerformed()
1522   {
1523     SequenceGroup sg = getGroup();
1524     if (sg.cs == null)
1525     {
1526       return;
1527     }
1528
1529     if (abovePIDColour.isSelected())
1530     {
1531       sg.cs.setConsensus(AAFrequency.calculate(
1532               sg.getSequences(ap.av.getHiddenRepSequences()),
1533               sg.getStartRes(), sg.getEndRes() + 1));
1534
1535       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1536               .getName());
1537
1538       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1539
1540       SliderPanel.showPIDSlider();
1541     }
1542     else
1543     // remove PIDColouring
1544     {
1545       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1546     }
1547
1548     refresh();
1549   }
1550
1551   /**
1552    * DOCUMENT ME!
1553    *
1554    * @param e
1555    *          DOCUMENT ME!
1556    */
1557   protected void userDefinedColour_actionPerformed(ActionEvent e)
1558   {
1559     SequenceGroup sg = getGroup();
1560
1561     if (e.getActionCommand().equals("User Defined..."))
1562     {
1563       new UserDefinedColours(ap, sg);
1564     }
1565     else
1566     {
1567       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1568               .getUserColourSchemes().get(e.getActionCommand());
1569
1570       sg.cs = udc;
1571     }
1572     refresh();
1573   }
1574
1575   /**
1576    * DOCUMENT ME!
1577    *
1578    * @param e
1579    *          DOCUMENT ME!
1580    */
1581   protected void PIDColour_actionPerformed()
1582   {
1583     SequenceGroup sg = getGroup();
1584     sg.cs = new PIDColourScheme();
1585     sg.cs.setConsensus(AAFrequency.calculate(
1586             sg.getSequences(ap.av.getHiddenRepSequences()),
1587             sg.getStartRes(), sg.getEndRes() + 1));
1588     refresh();
1589   }
1590
1591   /**
1592    * DOCUMENT ME!
1593    *
1594    * @param e
1595    *          DOCUMENT ME!
1596    */
1597   protected void BLOSUM62Colour_actionPerformed()
1598   {
1599     SequenceGroup sg = getGroup();
1600
1601     sg.cs = new Blosum62ColourScheme();
1602
1603     sg.cs.setConsensus(AAFrequency.calculate(
1604             sg.getSequences(ap.av.getHiddenRepSequences()),
1605             sg.getStartRes(), sg.getEndRes() + 1));
1606
1607     refresh();
1608   }
1609
1610   /**
1611    * DOCUMENT ME!
1612    *
1613    * @param e
1614    *          DOCUMENT ME!
1615    */
1616   protected void noColourmenuItem_actionPerformed()
1617   {
1618     getGroup().cs = null;
1619     refresh();
1620   }
1621
1622   /**
1623    * DOCUMENT ME!
1624    *
1625    * @param e
1626    *          DOCUMENT ME!
1627    */
1628   protected void conservationMenuItem_actionPerformed()
1629   {
1630     SequenceGroup sg = getGroup();
1631     if (sg.cs == null)
1632     {
1633       return;
1634     }
1635
1636     if (conservationMenuItem.isSelected())
1637     {
1638       Conservation c = new Conservation("Group",
1639               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1640                       .getHiddenRepSequences()), sg.getStartRes(),
1641               sg.getEndRes() + 1);
1642
1643       c.calculate();
1644       c.verdict(false, ap.av.getConsPercGaps());
1645
1646       sg.cs.setConservation(c);
1647
1648       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1649       SliderPanel.showConservationSlider();
1650     }
1651     else
1652     // remove ConservationColouring
1653     {
1654       sg.cs.setConservation(null);
1655     }
1656
1657     refresh();
1658   }
1659
1660   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1661   {
1662     SequenceGroup sg = getGroup();
1663     if (sg == null)
1664     {
1665       return;
1666     }
1667
1668     AnnotationColourGradient acg = new AnnotationColourGradient(
1669             sequence.getAnnotation()[0], null,
1670             AnnotationColourGradient.NO_THRESHOLD);
1671
1672     acg.predefinedColours = true;
1673     sg.cs = acg;
1674
1675     refresh();
1676   }
1677
1678   /**
1679    * DOCUMENT ME!
1680    *
1681    * @param e
1682    *          DOCUMENT ME!
1683    */
1684   protected void groupName_actionPerformed()
1685   {
1686
1687     SequenceGroup sg = getGroup();
1688     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1689             sg.getDescription(), "       Group Name ",
1690             "Group Description ", "Edit Group Name/Description",
1691             ap.alignFrame);
1692
1693     if (!dialog.accept)
1694     {
1695       return;
1696     }
1697
1698     sg.setName(dialog.getName());
1699     sg.setDescription(dialog.getDescription());
1700     refresh();
1701   }
1702
1703   /**
1704    * Get selection group - adding it to the alignment if necessary.
1705    *
1706    * @return sequence group to operate on
1707    */
1708   SequenceGroup getGroup()
1709   {
1710     SequenceGroup sg = ap.av.getSelectionGroup();
1711     // this method won't add a new group if it already exists
1712     if (sg != null)
1713     {
1714       ap.av.getAlignment().addGroup(sg);
1715     }
1716
1717     return sg;
1718   }
1719
1720   /**
1721    * DOCUMENT ME!
1722    *
1723    * @param e
1724    *          DOCUMENT ME!
1725    */
1726   void sequenceName_actionPerformed()
1727   {
1728     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1729             sequence.getDescription(), "       Sequence Name ",
1730             "Sequence Description ", "Edit Sequence Name/Description",
1731             ap.alignFrame);
1732
1733     if (!dialog.accept)
1734     {
1735       return;
1736     }
1737
1738     if (dialog.getName() != null)
1739     {
1740       if (dialog.getName().indexOf(" ") > -1)
1741       {
1742         JOptionPane.showMessageDialog(ap,
1743                 "Spaces have been converted to \"_\"",
1744                 "No spaces allowed in Sequence Name",
1745                 JOptionPane.WARNING_MESSAGE);
1746       }
1747
1748       sequence.setName(dialog.getName().replace(' ', '_'));
1749       ap.paintAlignment(false);
1750     }
1751
1752     sequence.setDescription(dialog.getDescription());
1753
1754     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1755             .getSequences());
1756
1757   }
1758
1759   /**
1760    * DOCUMENT ME!
1761    *
1762    * @param e
1763    *          DOCUMENT ME!
1764    */
1765   void unGroupMenuItem_actionPerformed()
1766   {
1767     SequenceGroup sg = ap.av.getSelectionGroup();
1768     ap.av.getAlignment().deleteGroup(sg);
1769     ap.av.setSelectionGroup(null);
1770     refresh();
1771   }
1772
1773   /**
1774    * DOCUMENT ME!
1775    *
1776    * @param e
1777    *          DOCUMENT ME!
1778    */
1779   protected void outline_actionPerformed()
1780   {
1781     SequenceGroup sg = getGroup();
1782     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1783             Color.BLUE);
1784
1785     if (col != null)
1786     {
1787       sg.setOutlineColour(col);
1788     }
1789
1790     refresh();
1791   }
1792
1793   /**
1794    * DOCUMENT ME!
1795    *
1796    * @param e
1797    *          DOCUMENT ME!
1798    */
1799   public void showBoxes_actionPerformed()
1800   {
1801     getGroup().setDisplayBoxes(showBoxes.isSelected());
1802     refresh();
1803   }
1804
1805   /**
1806    * DOCUMENT ME!
1807    *
1808    * @param e
1809    *          DOCUMENT ME!
1810    */
1811   public void showText_actionPerformed()
1812   {
1813     getGroup().setDisplayText(showText.isSelected());
1814     refresh();
1815   }
1816
1817   /**
1818    * DOCUMENT ME!
1819    *
1820    * @param e
1821    *          DOCUMENT ME!
1822    */
1823   public void showColourText_actionPerformed()
1824   {
1825     getGroup().setColourText(showColourText.isSelected());
1826     refresh();
1827   }
1828
1829   public void showLink(String url)
1830   {
1831     try
1832     {
1833       jalview.util.BrowserLauncher.openURL(url);
1834     } catch (Exception ex)
1835     {
1836       JOptionPane
1837               .showInternalMessageDialog(
1838                       Desktop.desktop,
1839                       "Unixers: Couldn't find default web browser."
1840                               + "\nAdd the full path to your browser in Preferences.",
1841                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1842
1843       ex.printStackTrace();
1844     }
1845   }
1846
1847   void hideSequences(boolean representGroup)
1848   {
1849     SequenceGroup sg = ap.av.getSelectionGroup();
1850     if (sg == null || sg.getSize() < 1)
1851     {
1852       ap.av.hideSequence(new SequenceI[]
1853       { sequence });
1854       return;
1855     }
1856
1857     ap.av.setSelectionGroup(null);
1858
1859     if (representGroup)
1860     {
1861       ap.av.hideRepSequences(sequence, sg);
1862
1863       return;
1864     }
1865
1866     int gsize = sg.getSize();
1867     SequenceI[] hseqs;
1868
1869     hseqs = new SequenceI[gsize];
1870
1871     int index = 0;
1872     for (int i = 0; i < gsize; i++)
1873     {
1874       hseqs[index++] = sg.getSequenceAt(i);
1875     }
1876
1877     ap.av.hideSequence(hseqs);
1878     // refresh(); TODO: ? needed ?
1879     ap.av.sendSelection();
1880   }
1881
1882   public void copy_actionPerformed()
1883   {
1884     ap.alignFrame.copy_actionPerformed(null);
1885   }
1886
1887   public void cut_actionPerformed()
1888   {
1889     ap.alignFrame.cut_actionPerformed(null);
1890   }
1891
1892   void changeCase(ActionEvent e)
1893   {
1894     Object source = e.getSource();
1895     SequenceGroup sg = ap.av.getSelectionGroup();
1896
1897     if (sg != null)
1898     {
1899       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1900               sg.getEndRes() + 1);
1901
1902       String description;
1903       int caseChange;
1904
1905       if (source == toggle)
1906       {
1907         description = "Toggle Case";
1908         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1909       }
1910       else if (source == upperCase)
1911       {
1912         description = "To Upper Case";
1913         caseChange = ChangeCaseCommand.TO_UPPER;
1914       }
1915       else
1916       {
1917         description = "To Lower Case";
1918         caseChange = ChangeCaseCommand.TO_LOWER;
1919       }
1920
1921       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1922               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1923               startEnd, caseChange);
1924
1925       ap.alignFrame.addHistoryItem(caseCommand);
1926
1927       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1928               .getSequences());
1929
1930     }
1931   }
1932
1933   public void outputText_actionPerformed(ActionEvent e)
1934   {
1935     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1936     cap.setForInput(null);
1937     Desktop.addInternalFrame(cap,
1938             "Alignment output - " + e.getActionCommand(), 600, 500);
1939
1940     String[] omitHidden = null;
1941
1942     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1943     // or we simply trust the user wants
1944     // wysiwig behaviour
1945     SequenceGroup sg = ap.av.getSelectionGroup();
1946     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1947     omitHidden = ap.av.getViewAsString(true);
1948     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1949     AlignmentAnnotation[] nala = ap.av.getAlignment()
1950             .getAlignmentAnnotation();
1951     if (nala != null)
1952     {
1953       for (int i = 0; i < nala.length; i++)
1954       {
1955         AlignmentAnnotation na = nala[i];
1956         oal.addAnnotation(na);
1957       }
1958     }
1959     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1960             oal, omitHidden, csel, sg));
1961     oal = null;
1962   }
1963
1964   public void pdbFromFile_actionPerformed()
1965   {
1966     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1967             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1968     chooser.setFileView(new jalview.io.JalviewFileView());
1969     chooser.setDialogTitle("Select a PDB file for "
1970             + sequence.getDisplayId(false));
1971     chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1972             + sequence.getDisplayId(false) + "'");
1973
1974     int value = chooser.showOpenDialog(null);
1975
1976     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1977     {
1978       String choice = chooser.getSelectedFile().getPath();
1979       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1980       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1981               jalview.io.AppletFormatAdapter.FILE, sequence, true);
1982     }
1983
1984   }
1985
1986   public void enterPDB_actionPerformed()
1987   {
1988     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1989             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1990
1991     if (id != null && id.length() > 0)
1992     {
1993       PDBEntry entry = new PDBEntry();
1994       entry.setId(id.toUpperCase());
1995       sequence.getDatasetSequence().addPDBId(entry);
1996     }
1997   }
1998
1999   public void discoverPDB_actionPerformed()
2000   {
2001
2002     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2003     { sequence }
2004             : ap.av.getSequenceSelection());
2005     Thread discpdb = new Thread(new Runnable()
2006     {
2007       public void run()
2008       {
2009
2010         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2011                 .fetchDBRefs(false);
2012       }
2013
2014     });
2015     discpdb.start();
2016   }
2017
2018   public void sequenceFeature_actionPerformed()
2019   {
2020     SequenceGroup sg = ap.av.getSelectionGroup();
2021     if (sg == null)
2022     {
2023       return;
2024     }
2025
2026     int rsize = 0, gSize = sg.getSize();
2027     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2028     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2029
2030     for (int i = 0; i < gSize; i++)
2031     {
2032       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2033       int end = sg.findEndRes(sg.getSequenceAt(i));
2034       if (start <= end)
2035       {
2036         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2037         features[rsize] = new SequenceFeature(null, null, null, start, end,
2038                 "Jalview");
2039         rsize++;
2040       }
2041     }
2042     rseqs = new SequenceI[rsize];
2043     tfeatures = new SequenceFeature[rsize];
2044     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2045     System.arraycopy(features, 0, tfeatures, 0, rsize);
2046     features = tfeatures;
2047     seqs = rseqs;
2048     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2049             features, true, ap))
2050     {
2051       ap.alignFrame.setShowSeqFeatures(true);
2052       ap.highlightSearchResults(null);
2053     }
2054   }
2055
2056   public void textColour_actionPerformed()
2057   {
2058     SequenceGroup sg = getGroup();
2059     if (sg != null)
2060     {
2061       new TextColourChooser().chooseColour(ap, sg);
2062     }
2063   }
2064
2065   public void colourByStructure(String pdbid)
2066   {
2067     Annotation[] anots = ap.av.getStructureSelectionManager()
2068             .colourSequenceFromStructure(sequence, pdbid);
2069
2070     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2071             "Coloured by " + pdbid, anots);
2072
2073     ap.av.getAlignment().addAnnotation(an);
2074     an.createSequenceMapping(sequence, 0, true);
2075     // an.adjustForAlignment();
2076     ap.av.getAlignment().setAnnotationIndex(an, 0);
2077
2078     ap.adjustAnnotationHeight();
2079
2080     sequence.addAlignmentAnnotation(an);
2081
2082   }
2083
2084   public void editSequence_actionPerformed(ActionEvent actionEvent)
2085   {
2086     SequenceGroup sg = ap.av.getSelectionGroup();
2087
2088     if (sg != null)
2089     {
2090       if (sequence == null)
2091         sequence = (Sequence) sg.getSequenceAt(0);
2092
2093       EditNameDialog dialog = new EditNameDialog(
2094               sequence.getSequenceAsString(sg.getStartRes(),
2095                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2096               "Edit Sequence", ap.alignFrame);
2097
2098       if (dialog.accept)
2099       {
2100         EditCommand editCommand = new EditCommand("Edit Sequences",
2101                 EditCommand.REPLACE, dialog.getName().replace(' ',
2102                         ap.av.getGapCharacter()),
2103                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2104                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2105
2106         ap.alignFrame.addHistoryItem(editCommand);
2107
2108         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2109                 .getSequences());
2110       }
2111     }
2112   }
2113
2114 }