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