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
 474       /*
 475        * else if (sg.cs instanceof CovariationColourScheme) {
 476        * covariationColour.setSelected(true); }
 477        */
 478       else
 479       {
 480         noColourmenuItem.setSelected(true);
 481       }
 482
 483       if (sg.cs != null && sg.cs.conservationApplied())
 484       {
 485         conservationMenuItem.setSelected(true);
 486       }
 487       displayNonconserved.setSelected(sg.getShowNonconserved());
 488       showText.setSelected(sg.getDisplayText());
 489       showColourText.setSelected(sg.getColourText());
 490       showBoxes.setSelected(sg.getDisplayBoxes());
 491       // add any groupURLs to the groupURL submenu and make it visible
 492       if (groupLinks != null && groupLinks.size() > 0)
 493       {
 494         buildGroupURLMenu(sg, groupLinks);
 495       }
 496       // Add a 'show all structures' for the current selection
 497       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 498       SequenceI sqass = null;
 499       for (SequenceI sq : ap.av.getSequenceSelection())
 500       {
 501         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 502                 .getPDBId();
 503         if (pes != null)
 504         {
 505           for (PDBEntry pe : pes)
 506           {
 507             pdbe.put(pe.getId(), pe);
 508             if (sqass == null)
 509             {
 510               sqass = sq;
 511             }
 512           }
 513         }
 514       }
 515       if (pdbe.size() > 0)
 516       {
 517         final PDBEntry[] pe = pdbe.values().toArray(
 518                 new PDBEntry[pdbe.size()]);
 519         final JMenuItem gpdbview;
 520         if (pdbe.size() == 1)
 521         {
 522           structureMenu.add(gpdbview = new JMenuItem("View structure for "
 523                   + sqass.getDisplayId(false)));
 524         }
 525         else
 526         {
 527           structureMenu.add(gpdbview = new JMenuItem("View all "
 528                   + pdbe.size() + " structures."));
 529         }
 530         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 531         gpdbview.addActionListener(new ActionListener()
 532         {
 533
 534           @Override
 535           public void actionPerformed(ActionEvent e)
 536           {
 537             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 538           }
 539         });
 540       }
 541     }
 542     else
 543     {
 544       groupMenu.setVisible(false);
 545       editMenu.setVisible(false);
 546     }
 547
 548     if (!ap.av.getAlignment().getGroups().contains(sg))
 549     {
 550       unGroupMenuItem.setVisible(false);
 551     }
 552
 553     if (seq == null)
 554     {
 555       sequenceMenu.setVisible(false);
 556       structureMenu.setVisible(false);
 557     }
 558
 559     if (links != null && links.size() > 0)
 560     {
 561
 562       JMenu linkMenu = new JMenu("Link");
 563       Vector linkset = new Vector();
 564       for (int i = 0; i < links.size(); i++)
 565       {
 566         String link = links.elementAt(i).toString();
 567         UrlLink urlLink = null;
 568         try
 569         {
 570           urlLink = new UrlLink(link);
 571         } catch (Exception foo)
 572         {
 573           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 574                   + "'", foo);
 575           continue;
 576         }
 577         ;
 578         if (!urlLink.isValid())
 579         {
 580           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 581           continue;
 582         }
 583         final String label = urlLink.getLabel();
 584         if (seq != null && urlLink.isDynamic())
 585         {
 586
 587           // collect matching db-refs
 588           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 589                   seq.getDBRef(), new String[]
 590                   { urlLink.getTarget() });
 591           // collect id string too
 592           String id = seq.getName();
 593           String descr = seq.getDescription();
 594           if (descr != null && descr.length() < 1)
 595           {
 596             descr = null;
 597           }
 598
 599           if (dbr != null)
 600           {
 601             for (int r = 0; r < dbr.length; r++)
 602             {
 603               if (id != null && dbr[r].getAccessionId().equals(id))
 604               {
 605                 // suppress duplicate link creation for the bare sequence ID
 606                 // string with this link
 607                 id = null;
 608               }
 609               // create Bare ID link for this RUL
 610               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 611                       true);
 612               if (urls != null)
 613               {
 614                 for (int u = 0; u < urls.length; u += 2)
 615                 {
 616                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 617                   {
 618                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 619                     addshowLink(linkMenu, label + "|" + urls[u],
 620                             urls[u + 1]);
 621                   }
 622                 }
 623               }
 624             }
 625           }
 626           if (id != null)
 627           {
 628             // create Bare ID link for this RUL
 629             String[] urls = urlLink.makeUrls(id, true);
 630             if (urls != null)
 631             {
 632               for (int u = 0; u < urls.length; u += 2)
 633               {
 634                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 635                 {
 636                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 637                   addshowLink(linkMenu, label, urls[u + 1]);
 638                 }
 639               }
 640             }
 641           }
 642           // Create urls from description but only for URL links which are regex
 643           // links
 644           if (descr != null && urlLink.getRegexReplace() != null)
 645           {
 646             // create link for this URL from description where regex matches
 647             String[] urls = urlLink.makeUrls(descr, true);
 648             if (urls != null)
 649             {
 650               for (int u = 0; u < urls.length; u += 2)
 651               {
 652                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 653                 {
 654                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 655                   addshowLink(linkMenu, label, urls[u + 1]);
 656                 }
 657               }
 658             }
 659           }
 660         }
 661         else
 662         {
 663           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 664           {
 665             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 666             // Add a non-dynamic link
 667             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 668           }
 669         }
 670       }
 671       if (sequence != null)
 672       {
 673         sequenceMenu.add(linkMenu);
 674       }
 675       else
 676       {
 677         add(linkMenu);
 678       }
 679     }
 680   }
 681
 682   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 683   {
 684
 685     // TODO: usability: thread off the generation of group url content so root
 686     // menu appears asap
 687     // sequence only URLs
 688     // ID/regex match URLs
 689     groupLinksMenu = new JMenu("Group Link");
 690     JMenu[] linkMenus = new JMenu[]
 691     { null, new JMenu("IDS"), new JMenu("Sequences"),
 692         new JMenu("IDS and Sequences") }; // three types of url that might be
 693                                           // created.
 694     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 695     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 696     Hashtable commonDbrefs = new Hashtable();
 697     for (int sq = 0; sq < seqs.length; sq++)
 698     {
 699
 700       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 701               .findPosition(sg.getEndRes());
 702       // just collect ids from dataset sequence
 703       // TODO: check if IDs collected from selecton group intersects with the
 704       // current selection, too
 705       SequenceI sqi = seqs[sq];
 706       while (sqi.getDatasetSequence() != null)
 707       {
 708         sqi = sqi.getDatasetSequence();
 709       }
 710       DBRefEntry[] dbr = sqi.getDBRef();
 711       if (dbr != null && dbr.length > 0)
 712       {
 713         for (int d = 0; d < dbr.length; d++)
 714         {
 715           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 716           Object[] sarray = (Object[]) commonDbrefs.get(src);
 717           if (sarray == null)
 718           {
 719             sarray = new Object[2];
 720             sarray[0] = new int[]
 721             { 0 };
 722             sarray[1] = new String[seqs.length];
 723
 724             commonDbrefs.put(src, sarray);
 725           }
 726
 727           if (((String[]) sarray[1])[sq] == null)
 728           {
 729             if (!dbr[d].hasMap()
 730                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 731             {
 732               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 733               ((int[]) sarray[0])[0]++;
 734             }
 735           }
 736         }
 737       }
 738     }
 739     // now create group links for all distinct ID/sequence sets.
 740     boolean addMenu = false; // indicates if there are any group links to give
 741                              // to user
 742     for (int i = 0; i < groupLinks.size(); i++)
 743     {
 744       String link = groupLinks.elementAt(i).toString();
 745       GroupUrlLink urlLink = null;
 746       try
 747       {
 748         urlLink = new GroupUrlLink(link);
 749       } catch (Exception foo)
 750       {
 751         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 752                 + "'", foo);
 753         continue;
 754       }
 755       ;
 756       if (!urlLink.isValid())
 757       {
 758         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 759         continue;
 760       }
 761       final String label = urlLink.getLabel();
 762       boolean usingNames = false;
 763       // Now see which parts of the group apply for this URL
 764       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 765       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 766       String[] seqstr, ids; // input to makeUrl
 767       if (idset != null)
 768       {
 769         int numinput = ((int[]) idset[0])[0];
 770         String[] allids = ((String[]) idset[1]);
 771         seqstr = new String[numinput];
 772         ids = new String[numinput];
 773         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 774         {
 775           if (allids[sq] != null)
 776           {
 777             ids[idcount] = allids[sq];
 778             seqstr[idcount++] = idandseqs[1][sq];
 779           }
 780         }
 781       }
 782       else
 783       {
 784         // just use the id/seq set
 785         seqstr = idandseqs[1];
 786         ids = idandseqs[0];
 787         usingNames = true;
 788       }
 789       // and try and make the groupURL!
 790
 791       Object[] urlset = null;
 792       try
 793       {
 794         urlset = urlLink.makeUrlStubs(ids, seqstr,
 795                 "FromJalview" + System.currentTimeMillis(), false);
 796       } catch (UrlStringTooLongException e)
 797       {
 798       }
 799       if (urlset != null)
 800       {
 801         int type = urlLink.getGroupURLType() & 3;
 802         // System.out.println(urlLink.getGroupURLType()
 803         // +" "+((String[])urlset[3])[0]);
 804         // first two bits ofurlLink type bitfield are sequenceids and sequences
 805         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 806         addshowLink(linkMenus[type], label
 807                 + (((type & 1) == 1) ? ("("
 808                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 809                 urlLink, urlset);
 810         addMenu = true;
 811       }
 812     }
 813     if (addMenu)
 814     {
 815       groupLinksMenu = new JMenu("Group Links");
 816       for (int m = 0; m < linkMenus.length; m++)
 817       {
 818         if (linkMenus[m] != null
 819                 && linkMenus[m].getMenuComponentCount() > 0)
 820         {
 821           groupLinksMenu.add(linkMenus[m]);
 822         }
 823       }
 824
 825       groupMenu.add(groupLinksMenu);
 826     }
 827   }
 828
 829   /**
 830    * add a show URL menu item to the given linkMenu
 831    *
 832    * @param linkMenu
 833    * @param label
 834    *          - menu label string
 835    * @param url
 836    *          - url to open
 837    */
 838   private void addshowLink(JMenu linkMenu, String label, final String url)
 839   {
 840     JMenuItem item = new JMenuItem(label);
 841     item.setToolTipText("open URL: " + url);
 842     item.addActionListener(new java.awt.event.ActionListener()
 843     {
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         new Thread(new Runnable()
 847         {
 848
 849           public void run()
 850           {
 851             showLink(url);
 852           }
 853
 854         }).start();
 855       }
 856     });
 857
 858     linkMenu.add(item);
 859   }
 860
 861   /**
 862    * add a late bound groupURL item to the given linkMenu
 863    *
 864    * @param linkMenu
 865    * @param label
 866    *          - menu label string
 867    * @param urlgenerator
 868    *          GroupURLLink used to generate URL
 869    * @param urlstub
 870    *          Object array returned from the makeUrlStubs function.
 871    */
 872   private void addshowLink(JMenu linkMenu, String label,
 873           final GroupUrlLink urlgenerator, final Object[] urlstub)
 874   {
 875     JMenuItem item = new JMenuItem(label);
 876     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 877             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 878                                                                              // put
 879                                                                              // in
 880                                                                              // info
 881                                                                              // about
 882                                                                              // what
 883                                                                              // is
 884                                                                              // being
 885                                                                              // sent.
 886     item.addActionListener(new java.awt.event.ActionListener()
 887     {
 888       public void actionPerformed(ActionEvent e)
 889       {
 890         new Thread(new Runnable()
 891         {
 892
 893           public void run()
 894           {
 895             try
 896             {
 897               showLink(urlgenerator.constructFrom(urlstub));
 898             } catch (UrlStringTooLongException e)
 899             {
 900             }
 901           }
 902
 903         }).start();
 904       }
 905     });
 906
 907     linkMenu.add(item);
 908   }
 909
 910   /**
 911    * DOCUMENT ME!
 912    *
 913    * @throws Exception
 914    *           DOCUMENT ME!
 915    */
 916   private void jbInit() throws Exception
 917   {
 918     groupMenu.setText("Group");
 919     groupMenu.setText("Selection");
 920     groupName.setText("Name");
 921     groupName.addActionListener(new java.awt.event.ActionListener()
 922     {
 923       public void actionPerformed(ActionEvent e)
 924       {
 925         groupName_actionPerformed();
 926       }
 927     });
 928     sequenceMenu.setText("Sequence");
 929     sequenceName.setText("Edit Name/Description");
 930     sequenceName.addActionListener(new java.awt.event.ActionListener()
 931     {
 932       public void actionPerformed(ActionEvent e)
 933       {
 934         sequenceName_actionPerformed();
 935       }
 936     });
 937     sequenceDetails.setText("Sequence Details ...");
 938     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 939     {
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         sequenceDetails_actionPerformed();
 943       }
 944     });
 945     sequenceSelDetails.setText("Sequence Details ...");
 946     sequenceSelDetails
 947             .addActionListener(new java.awt.event.ActionListener()
 948             {
 949               public void actionPerformed(ActionEvent e)
 950               {
 951                 sequenceSelectionDetails_actionPerformed();
 952               }
 953             });
 954     PIDColour.setFocusPainted(false);
 955     unGroupMenuItem.setText("Remove Group");
 956     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 957     {
 958       public void actionPerformed(ActionEvent e)
 959       {
 960         unGroupMenuItem_actionPerformed();
 961       }
 962     });
 963
 964     outline.setText("Border colour");
 965     outline.addActionListener(new java.awt.event.ActionListener()
 966     {
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         outline_actionPerformed();
 970       }
 971     });
 972     nucleotideMenuItem.setText("Nucleotide");
 973     nucleotideMenuItem.addActionListener(new ActionListener()
 974     {
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         nucleotideMenuItem_actionPerformed();
 978       }
 979     });
 980     colourMenu.setText("Group Colour");
 981     showBoxes.setText("Boxes");
 982     showBoxes.setState(true);
 983     showBoxes.addActionListener(new ActionListener()
 984     {
 985       public void actionPerformed(ActionEvent e)
 986       {
 987         showBoxes_actionPerformed();
 988       }
 989     });
 990     showText.setText("Text");
 991     showText.setState(true);
 992     showText.addActionListener(new ActionListener()
 993     {
 994       public void actionPerformed(ActionEvent e)
 995       {
 996         showText_actionPerformed();
 997       }
 998     });
 999     showColourText.setText("Colour Text");
1000     showColourText.addActionListener(new ActionListener()
1001     {
1002       public void actionPerformed(ActionEvent e)
1003       {
1004         showColourText_actionPerformed();
1005       }
1006     });
1007     displayNonconserved.setText("Show Nonconserved");
1008     displayNonconserved.setState(true);
1009     displayNonconserved.addActionListener(new ActionListener()
1010     {
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         showNonconserved_actionPerformed();
1014       }
1015     });
1016     editMenu.setText("Edit");
1017     cut.setText("Cut");
1018     cut.addActionListener(new ActionListener()
1019     {
1020       public void actionPerformed(ActionEvent e)
1021       {
1022         cut_actionPerformed();
1023       }
1024     });
1025     upperCase.setText("To Upper Case");
1026     upperCase.addActionListener(new ActionListener()
1027     {
1028       public void actionPerformed(ActionEvent e)
1029       {
1030         changeCase(e);
1031       }
1032     });
1033     copy.setText("Copy");
1034     copy.addActionListener(new ActionListener()
1035     {
1036       public void actionPerformed(ActionEvent e)
1037       {
1038         copy_actionPerformed();
1039       }
1040     });
1041     lowerCase.setText("To Lower Case");
1042     lowerCase.addActionListener(new ActionListener()
1043     {
1044       public void actionPerformed(ActionEvent e)
1045       {
1046         changeCase(e);
1047       }
1048     });
1049     toggle.setText("Toggle Case");
1050     toggle.addActionListener(new ActionListener()
1051     {
1052       public void actionPerformed(ActionEvent e)
1053       {
1054         changeCase(e);
1055       }
1056     });
1057     pdbMenu.setText("Associate Structure with Sequence");
1058     pdbFromFile.setText("From File");
1059     pdbFromFile.addActionListener(new ActionListener()
1060     {
1061       public void actionPerformed(ActionEvent e)
1062       {
1063         try {
1064                         pdbFromFile_actionPerformed();
1065                 } catch (Exception e1) {
1066                         // TODO Auto-generated catch block
1067                         e1.printStackTrace();
1068                 }
1069       }
1070     });
1071 //    RNAFold.setText("From RNA Fold with predict2D");
1072 //    RNAFold.addActionListener(new ActionListener()
1073 //    {
1074 //      public void actionPerformed(ActionEvent e)
1075 //      {
1076 //        try {
1077 //                      RNAFold_actionPerformed();
1078 //              } catch (Exception e1) {
1079 //                      // TODO Auto-generated catch block
1080 //                      e1.printStackTrace();
1081 //              }
1082 //      }
1083 //    });
1084 //    ContraFold.setText("From Contra Fold with predict2D");
1085 //    ContraFold.addActionListener(new ActionListener()
1086 //    {
1087 //      public void actionPerformed(ActionEvent e)
1088 //      {
1089 //        try {
1090 //                      ContraFold_actionPerformed();
1091 //              } catch (Exception e1) {
1092 //                      // TODO Auto-generated catch block
1093 //                      e1.printStackTrace();
1094 //              }
1095 //      }
1096 //    });
1097     enterPDB.setText("Enter PDB Id");
1098     enterPDB.addActionListener(new ActionListener()
1099     {
1100       public void actionPerformed(ActionEvent e)
1101       {
1102         enterPDB_actionPerformed();
1103       }
1104     });
1105     discoverPDB.setText("Discover PDB ids");
1106     discoverPDB.addActionListener(new ActionListener()
1107     {
1108       public void actionPerformed(ActionEvent e)
1109       {
1110         discoverPDB_actionPerformed();
1111       }
1112     });
1113     outputMenu.setText("Output to Textbox...");
1114     sequenceFeature.setText("Create Sequence Feature");
1115     sequenceFeature.addActionListener(new ActionListener()
1116     {
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         sequenceFeature_actionPerformed();
1120       }
1121     });
1122     textColour.setText("Text Colour");
1123     textColour.addActionListener(new ActionListener()
1124     {
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         textColour_actionPerformed();
1128       }
1129     });
1130     jMenu1.setText("Group");
1131     structureMenu.setText("Structure");
1132     viewStructureMenu.setText("View Structure");
1133     // colStructureMenu.setText("Colour By Structure");
1134     editSequence.setText("Edit Sequence...");
1135     editSequence.addActionListener(new ActionListener()
1136     {
1137       public void actionPerformed(ActionEvent actionEvent)
1138       {
1139         editSequence_actionPerformed(actionEvent);
1140       }
1141     });
1142
1143     /*
1144      * annotationMenuItem.setText("By Annotation");
1145      * annotationMenuItem.addActionListener(new ActionListener() { public void
1146      * actionPerformed(ActionEvent actionEvent) {
1147      * annotationMenuItem_actionPerformed(actionEvent); } });
1148      */
1149     groupMenu.add(sequenceSelDetails);
1150     add(groupMenu);
1151     add(sequenceMenu);
1152     this.add(structureMenu);
1153     groupMenu.add(editMenu);
1154     groupMenu.add(outputMenu);
1155     groupMenu.add(sequenceFeature);
1156     groupMenu.add(jMenu1);
1157     sequenceMenu.add(sequenceName);
1158     sequenceMenu.add(sequenceDetails);
1159     colourMenu.add(textColour);
1160     colourMenu.add(noColourmenuItem);
1161     colourMenu.add(clustalColour);
1162     colourMenu.add(BLOSUM62Colour);
1163     colourMenu.add(PIDColour);
1164     colourMenu.add(zappoColour);
1165     colourMenu.add(taylorColour);
1166     colourMenu.add(hydrophobicityColour);
1167     colourMenu.add(helixColour);
1168     colourMenu.add(strandColour);
1169     colourMenu.add(turnColour);
1170     colourMenu.add(buriedColour);
1171     colourMenu.add(nucleotideMenuItem);
1172     if (ap.getAlignment().isNucleotide()) {
1173         // JBPNote - commented since the colourscheme isn't functional
1174         //  colourMenu.add(RNAInteractionColour);
1175         colourMenu.add(purinePyrimidineColour);
1176     }
1177     // colourMenu.add(covariationColour);
1178     colourMenu.add(userDefinedColour);
1179
1180     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1181     {
1182       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1183               .getUserColourSchemes().keys();
1184
1185       while (userColours.hasMoreElements())
1186       {
1187         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1188         item.addActionListener(new ActionListener()
1189         {
1190           public void actionPerformed(ActionEvent evt)
1191           {
1192             userDefinedColour_actionPerformed(evt);
1193           }
1194         });
1195         colourMenu.add(item);
1196       }
1197     }
1198
1199     colourMenu.addSeparator();
1200     colourMenu.add(abovePIDColour);
1201     colourMenu.add(conservationMenuItem);
1202     // colourMenu.add(annotationMenuItem);
1203     editMenu.add(copy);
1204     editMenu.add(cut);
1205     editMenu.add(editSequence);
1206     editMenu.add(upperCase);
1207     editMenu.add(lowerCase);
1208     editMenu.add(toggle);
1209     pdbMenu.add(pdbFromFile);
1210     pdbMenu.add(enterPDB);
1211     pdbMenu.add(discoverPDB);
1212     jMenu1.add(groupName);
1213     jMenu1.add(unGroupMenuItem);
1214     jMenu1.add(colourMenu);
1215     jMenu1.add(showBoxes);
1216     jMenu1.add(showText);
1217     jMenu1.add(showColourText);
1218     jMenu1.add(outline);
1219     jMenu1.add(displayNonconserved);
1220     structureMenu.add(pdbMenu);
1221     structureMenu.add(viewStructureMenu);
1222     // structureMenu.add(colStructureMenu);
1223     noColourmenuItem.setText("None");
1224     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1225     {
1226       public void actionPerformed(ActionEvent e)
1227       {
1228         noColourmenuItem_actionPerformed();
1229       }
1230     });
1231
1232     clustalColour.setText("Clustalx colours");
1233     clustalColour.addActionListener(new java.awt.event.ActionListener()
1234     {
1235       public void actionPerformed(ActionEvent e)
1236       {
1237         clustalColour_actionPerformed();
1238       }
1239     });
1240     zappoColour.setText("Zappo");
1241     zappoColour.addActionListener(new java.awt.event.ActionListener()
1242     {
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         zappoColour_actionPerformed();
1246       }
1247     });
1248     taylorColour.setText("Taylor");
1249     taylorColour.addActionListener(new java.awt.event.ActionListener()
1250     {
1251       public void actionPerformed(ActionEvent e)
1252       {
1253         taylorColour_actionPerformed();
1254       }
1255     });
1256     hydrophobicityColour.setText("Hydrophobicity");
1257     hydrophobicityColour
1258             .addActionListener(new java.awt.event.ActionListener()
1259             {
1260               public void actionPerformed(ActionEvent e)
1261               {
1262                 hydrophobicityColour_actionPerformed();
1263               }
1264             });
1265     helixColour.setText("Helix propensity");
1266     helixColour.addActionListener(new java.awt.event.ActionListener()
1267     {
1268       public void actionPerformed(ActionEvent e)
1269       {
1270         helixColour_actionPerformed();
1271       }
1272     });
1273     strandColour.setText("Strand propensity");
1274     strandColour.addActionListener(new java.awt.event.ActionListener()
1275     {
1276       public void actionPerformed(ActionEvent e)
1277       {
1278         strandColour_actionPerformed();
1279       }
1280     });
1281     turnColour.setText("Turn propensity");
1282     turnColour.addActionListener(new java.awt.event.ActionListener()
1283     {
1284       public void actionPerformed(ActionEvent e)
1285       {
1286         turnColour_actionPerformed();
1287       }
1288     });
1289     buriedColour.setText("Buried Index");
1290     buriedColour.addActionListener(new java.awt.event.ActionListener()
1291     {
1292       public void actionPerformed(ActionEvent e)
1293       {
1294         buriedColour_actionPerformed();
1295       }
1296     });
1297     abovePIDColour.setText("Above % Identity");
1298     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1299     {
1300       public void actionPerformed(ActionEvent e)
1301       {
1302         abovePIDColour_actionPerformed();
1303       }
1304     });
1305     userDefinedColour.setText("User Defined...");
1306     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1307     {
1308       public void actionPerformed(ActionEvent e)
1309       {
1310         userDefinedColour_actionPerformed(e);
1311       }
1312     });
1313     PIDColour.setText("Percentage Identity");
1314     PIDColour.addActionListener(new java.awt.event.ActionListener()
1315     {
1316       public void actionPerformed(ActionEvent e)
1317       {
1318         PIDColour_actionPerformed();
1319       }
1320     });
1321     BLOSUM62Colour.setText("BLOSUM62");
1322     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1323     {
1324       public void actionPerformed(ActionEvent e)
1325       {
1326         BLOSUM62Colour_actionPerformed();
1327       }
1328     });
1329     purinePyrimidineColour.setText("Purine/Pyrimidine");
1330     purinePyrimidineColour
1331             .addActionListener(new java.awt.event.ActionListener()
1332             {
1333               public void actionPerformed(ActionEvent e)
1334               {
1335                 purinePyrimidineColour_actionPerformed();
1336               }
1337             });
1338
1339
1340     /*
1341      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1342      * public void actionPerformed(ActionEvent e) {
1343      * covariationColour_actionPerformed(); } });
1344      */
1345
1346     conservationMenuItem.setText("Conservation");
1347     conservationMenuItem
1348             .addActionListener(new java.awt.event.ActionListener()
1349             {
1350               public void actionPerformed(ActionEvent e)
1351               {
1352                 conservationMenuItem_actionPerformed();
1353               }
1354             });
1355   }
1356
1357   protected void sequenceSelectionDetails_actionPerformed()
1358   {
1359     createSequenceDetailsReport(ap.av.getSequenceSelection());
1360   }
1361
1362   protected void sequenceDetails_actionPerformed()
1363   {
1364     createSequenceDetailsReport(new SequenceI[]
1365     { sequence });
1366   }
1367
1368   public void createSequenceDetailsReport(SequenceI[] sequences)
1369   {
1370     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1371     StringBuffer contents = new StringBuffer();
1372     for (SequenceI seq : sequences)
1373     {
1374       contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1375               + "</h2></p><p>");
1376       new SequenceAnnotationReport(null)
1377               .createSequenceAnnotationReport(
1378                       contents,
1379                       seq,
1380                       true,
1381                       true,
1382                       false,
1383                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1384                               : null);
1385       contents.append("</p>");
1386     }
1387     cap.setText("<html>" + contents.toString() + "</html>");
1388
1389     Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1390             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1391                     : "Selection"), 500, 400);
1392
1393   }
1394
1395   protected void showNonconserved_actionPerformed()
1396   {
1397     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1398     refresh();
1399   }
1400
1401   /**
1402    * call to refresh view after settings change
1403    */
1404   void refresh()
1405   {
1406     ap.updateAnnotation();
1407     ap.paintAlignment(true);
1408
1409     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1410   }
1411
1412   /**
1413    * DOCUMENT ME!
1414    *
1415    * @param e
1416    *          DOCUMENT ME!
1417    */
1418   protected void clustalColour_actionPerformed()
1419   {
1420     SequenceGroup sg = getGroup();
1421     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1422     refresh();
1423   }
1424
1425   /**
1426    * DOCUMENT ME!
1427    *
1428    * @param e
1429    *          DOCUMENT ME!
1430    */
1431   protected void zappoColour_actionPerformed()
1432   {
1433     getGroup().cs = new ZappoColourScheme();
1434     refresh();
1435   }
1436
1437   /**
1438    * DOCUMENT ME!
1439    *
1440    * @param e
1441    *          DOCUMENT ME!
1442    */
1443   protected void taylorColour_actionPerformed()
1444   {
1445     getGroup().cs = new TaylorColourScheme();
1446     refresh();
1447   }
1448
1449   /**
1450    * DOCUMENT ME!
1451    *
1452    * @param e
1453    *          DOCUMENT ME!
1454    */
1455   protected void hydrophobicityColour_actionPerformed()
1456   {
1457     getGroup().cs = new HydrophobicColourScheme();
1458     refresh();
1459   }
1460
1461   /**
1462    * DOCUMENT ME!
1463    *
1464    * @param e
1465    *          DOCUMENT ME!
1466    */
1467   protected void helixColour_actionPerformed()
1468   {
1469     getGroup().cs = new HelixColourScheme();
1470     refresh();
1471   }
1472
1473   /**
1474    * DOCUMENT ME!
1475    *
1476    * @param e
1477    *          DOCUMENT ME!
1478    */
1479   protected void strandColour_actionPerformed()
1480   {
1481     getGroup().cs = new StrandColourScheme();
1482     refresh();
1483   }
1484
1485   /**
1486    * DOCUMENT ME!
1487    *
1488    * @param e
1489    *          DOCUMENT ME!
1490    */
1491   protected void turnColour_actionPerformed()
1492   {
1493     getGroup().cs = new TurnColourScheme();
1494     refresh();
1495   }
1496
1497   /**
1498    * DOCUMENT ME!
1499    *
1500    * @param e
1501    *          DOCUMENT ME!
1502    */
1503   protected void buriedColour_actionPerformed()
1504   {
1505     getGroup().cs = new BuriedColourScheme();
1506     refresh();
1507   }
1508
1509   /**
1510    * DOCUMENT ME!
1511    *
1512    * @param e
1513    *          DOCUMENT ME!
1514    */
1515   public void nucleotideMenuItem_actionPerformed()
1516   {
1517     getGroup().cs = new NucleotideColourScheme();
1518     refresh();
1519   }
1520
1521   protected void purinePyrimidineColour_actionPerformed()
1522   {
1523     getGroup().cs = new PurinePyrimidineColourScheme();
1524     refresh();
1525   }
1526
1527
1528   /*
1529    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1530    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1531    */
1532   /**
1533    * DOCUMENT ME!
1534    *
1535    * @param e
1536    *          DOCUMENT ME!
1537    */
1538   protected void abovePIDColour_actionPerformed()
1539   {
1540     SequenceGroup sg = getGroup();
1541     if (sg.cs == null)
1542     {
1543       return;
1544     }
1545
1546     if (abovePIDColour.isSelected())
1547     {
1548       sg.cs.setConsensus(AAFrequency.calculate(
1549               sg.getSequences(ap.av.getHiddenRepSequences()),
1550               sg.getStartRes(), sg.getEndRes() + 1));
1551
1552       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1553               .getName());
1554
1555       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1556
1557       SliderPanel.showPIDSlider();
1558     }
1559     else
1560     // remove PIDColouring
1561     {
1562       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1563     }
1564
1565     refresh();
1566   }
1567
1568   /**
1569    * DOCUMENT ME!
1570    *
1571    * @param e
1572    *          DOCUMENT ME!
1573    */
1574   protected void userDefinedColour_actionPerformed(ActionEvent e)
1575   {
1576     SequenceGroup sg = getGroup();
1577
1578     if (e.getActionCommand().equals("User Defined..."))
1579     {
1580       new UserDefinedColours(ap, sg);
1581     }
1582     else
1583     {
1584       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1585               .getUserColourSchemes().get(e.getActionCommand());
1586
1587       sg.cs = udc;
1588     }
1589     refresh();
1590   }
1591
1592   /**
1593    * DOCUMENT ME!
1594    *
1595    * @param e
1596    *          DOCUMENT ME!
1597    */
1598   protected void PIDColour_actionPerformed()
1599   {
1600     SequenceGroup sg = getGroup();
1601     sg.cs = new PIDColourScheme();
1602     sg.cs.setConsensus(AAFrequency.calculate(
1603             sg.getSequences(ap.av.getHiddenRepSequences()),
1604             sg.getStartRes(), sg.getEndRes() + 1));
1605     refresh();
1606   }
1607
1608   /**
1609    * DOCUMENT ME!
1610    *
1611    * @param e
1612    *          DOCUMENT ME!
1613    */
1614   protected void BLOSUM62Colour_actionPerformed()
1615   {
1616     SequenceGroup sg = getGroup();
1617
1618     sg.cs = new Blosum62ColourScheme();
1619
1620     sg.cs.setConsensus(AAFrequency.calculate(
1621             sg.getSequences(ap.av.getHiddenRepSequences()),
1622             sg.getStartRes(), sg.getEndRes() + 1));
1623
1624     refresh();
1625   }
1626
1627   /**
1628    * DOCUMENT ME!
1629    *
1630    * @param e
1631    *          DOCUMENT ME!
1632    */
1633   protected void noColourmenuItem_actionPerformed()
1634   {
1635     getGroup().cs = null;
1636     refresh();
1637   }
1638
1639   /**
1640    * DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   protected void conservationMenuItem_actionPerformed()
1646   {
1647     SequenceGroup sg = getGroup();
1648     if (sg.cs == null)
1649     {
1650       return;
1651     }
1652
1653     if (conservationMenuItem.isSelected())
1654     {
1655       Conservation c = new Conservation("Group",
1656               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1657                       .getHiddenRepSequences()), sg.getStartRes(),
1658               sg.getEndRes() + 1);
1659
1660       c.calculate();
1661       c.verdict(false, ap.av.getConsPercGaps());
1662
1663       sg.cs.setConservation(c);
1664
1665       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1666       SliderPanel.showConservationSlider();
1667     }
1668     else
1669     // remove ConservationColouring
1670     {
1671       sg.cs.setConservation(null);
1672     }
1673
1674     refresh();
1675   }
1676
1677   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1678   {
1679     SequenceGroup sg = getGroup();
1680     if (sg == null)
1681     {
1682       return;
1683     }
1684
1685     AnnotationColourGradient acg = new AnnotationColourGradient(
1686             sequence.getAnnotation()[0], null,
1687             AnnotationColourGradient.NO_THRESHOLD);
1688
1689     acg.predefinedColours = true;
1690     sg.cs = acg;
1691
1692     refresh();
1693   }
1694
1695   /**
1696    * DOCUMENT ME!
1697    *
1698    * @param e
1699    *          DOCUMENT ME!
1700    */
1701   protected void groupName_actionPerformed()
1702   {
1703
1704     SequenceGroup sg = getGroup();
1705     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1706             sg.getDescription(), "       Group Name ",
1707             "Group Description ", "Edit Group Name/Description",
1708             ap.alignFrame);
1709
1710     if (!dialog.accept)
1711     {
1712       return;
1713     }
1714
1715     sg.setName(dialog.getName());
1716     sg.setDescription(dialog.getDescription());
1717     refresh();
1718   }
1719
1720   /**
1721    * Get selection group - adding it to the alignment if necessary.
1722    *
1723    * @return sequence group to operate on
1724    */
1725   SequenceGroup getGroup()
1726   {
1727     SequenceGroup sg = ap.av.getSelectionGroup();
1728     // this method won't add a new group if it already exists
1729     if (sg != null)
1730     {
1731       ap.av.getAlignment().addGroup(sg);
1732     }
1733
1734     return sg;
1735   }
1736
1737   /**
1738    * DOCUMENT ME!
1739    *
1740    * @param e
1741    *          DOCUMENT ME!
1742    */
1743   void sequenceName_actionPerformed()
1744   {
1745     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1746             sequence.getDescription(), "       Sequence Name ",
1747             "Sequence Description ", "Edit Sequence Name/Description",
1748             ap.alignFrame);
1749
1750     if (!dialog.accept)
1751     {
1752       return;
1753     }
1754
1755     if (dialog.getName() != null)
1756     {
1757       if (dialog.getName().indexOf(" ") > -1)
1758       {
1759         JOptionPane.showMessageDialog(ap,
1760                 "Spaces have been converted to \"_\"",
1761                 "No spaces allowed in Sequence Name",
1762                 JOptionPane.WARNING_MESSAGE);
1763       }
1764
1765       sequence.setName(dialog.getName().replace(' ', '_'));
1766       ap.paintAlignment(false);
1767     }
1768
1769     sequence.setDescription(dialog.getDescription());
1770
1771     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1772             .getSequences());
1773
1774   }
1775
1776   /**
1777    * DOCUMENT ME!
1778    *
1779    * @param e
1780    *          DOCUMENT ME!
1781    */
1782   void unGroupMenuItem_actionPerformed()
1783   {
1784     SequenceGroup sg = ap.av.getSelectionGroup();
1785     ap.av.getAlignment().deleteGroup(sg);
1786     ap.av.setSelectionGroup(null);
1787     refresh();
1788   }
1789
1790   /**
1791    * DOCUMENT ME!
1792    *
1793    * @param e
1794    *          DOCUMENT ME!
1795    */
1796   protected void outline_actionPerformed()
1797   {
1798     SequenceGroup sg = getGroup();
1799     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1800             Color.BLUE);
1801
1802     if (col != null)
1803     {
1804       sg.setOutlineColour(col);
1805     }
1806
1807     refresh();
1808   }
1809
1810   /**
1811    * DOCUMENT ME!
1812    *
1813    * @param e
1814    *          DOCUMENT ME!
1815    */
1816   public void showBoxes_actionPerformed()
1817   {
1818     getGroup().setDisplayBoxes(showBoxes.isSelected());
1819     refresh();
1820   }
1821
1822   /**
1823    * DOCUMENT ME!
1824    *
1825    * @param e
1826    *          DOCUMENT ME!
1827    */
1828   public void showText_actionPerformed()
1829   {
1830     getGroup().setDisplayText(showText.isSelected());
1831     refresh();
1832   }
1833
1834   /**
1835    * DOCUMENT ME!
1836    *
1837    * @param e
1838    *          DOCUMENT ME!
1839    */
1840   public void showColourText_actionPerformed()
1841   {
1842     getGroup().setColourText(showColourText.isSelected());
1843     refresh();
1844   }
1845
1846   public void showLink(String url)
1847   {
1848     try
1849     {
1850       jalview.util.BrowserLauncher.openURL(url);
1851     } catch (Exception ex)
1852     {
1853       JOptionPane
1854               .showInternalMessageDialog(
1855                       Desktop.desktop,
1856                       "Unixers: Couldn't find default web browser."
1857                               + "\nAdd the full path to your browser in Preferences.",
1858                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1859
1860       ex.printStackTrace();
1861     }
1862   }
1863
1864   void hideSequences(boolean representGroup)
1865   {
1866     SequenceGroup sg = ap.av.getSelectionGroup();
1867     if (sg == null || sg.getSize() < 1)
1868     {
1869       ap.av.hideSequence(new SequenceI[]
1870       { sequence });
1871       return;
1872     }
1873
1874     ap.av.setSelectionGroup(null);
1875
1876     if (representGroup)
1877     {
1878       ap.av.hideRepSequences(sequence, sg);
1879
1880       return;
1881     }
1882
1883     int gsize = sg.getSize();
1884     SequenceI[] hseqs;
1885
1886     hseqs = new SequenceI[gsize];
1887
1888     int index = 0;
1889     for (int i = 0; i < gsize; i++)
1890     {
1891       hseqs[index++] = sg.getSequenceAt(i);
1892     }
1893
1894     ap.av.hideSequence(hseqs);
1895     // refresh(); TODO: ? needed ?
1896     ap.av.sendSelection();
1897   }
1898
1899   public void copy_actionPerformed()
1900   {
1901     ap.alignFrame.copy_actionPerformed(null);
1902   }
1903
1904   public void cut_actionPerformed()
1905   {
1906     ap.alignFrame.cut_actionPerformed(null);
1907   }
1908
1909   void changeCase(ActionEvent e)
1910   {
1911     Object source = e.getSource();
1912     SequenceGroup sg = ap.av.getSelectionGroup();
1913
1914     if (sg != null)
1915     {
1916       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1917               sg.getEndRes() + 1);
1918
1919       String description;
1920       int caseChange;
1921
1922       if (source == toggle)
1923       {
1924         description = "Toggle Case";
1925         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1926       }
1927       else if (source == upperCase)
1928       {
1929         description = "To Upper Case";
1930         caseChange = ChangeCaseCommand.TO_UPPER;
1931       }
1932       else
1933       {
1934         description = "To Lower Case";
1935         caseChange = ChangeCaseCommand.TO_LOWER;
1936       }
1937
1938       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1939               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1940               startEnd, caseChange);
1941
1942       ap.alignFrame.addHistoryItem(caseCommand);
1943
1944       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1945               .getSequences());
1946
1947     }
1948   }
1949
1950   public void outputText_actionPerformed(ActionEvent e)
1951   {
1952     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1953     cap.setForInput(null);
1954     Desktop.addInternalFrame(cap,
1955             "Alignment output - " + e.getActionCommand(), 600, 500);
1956
1957     String[] omitHidden = null;
1958
1959     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1960     // or we simply trust the user wants
1961     // wysiwig behaviour
1962     SequenceGroup sg = ap.av.getSelectionGroup();
1963     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1964     omitHidden = ap.av.getViewAsString(true);
1965     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1966     AlignmentAnnotation[] nala = ap.av.getAlignment()
1967             .getAlignmentAnnotation();
1968     if (nala != null)
1969     {
1970       for (int i = 0; i < nala.length; i++)
1971       {
1972         AlignmentAnnotation na = nala[i];
1973         oal.addAnnotation(na);
1974       }
1975     }
1976     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1977             oal, omitHidden, csel, sg));
1978     oal = null;
1979   }
1980
1981   public void pdbFromFile_actionPerformed() throws Exception
1982   {
1983     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1984             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1985     chooser.setFileView(new jalview.io.JalviewFileView());
1986     chooser.setDialogTitle("Select a PDB file for "
1987             + sequence.getDisplayId(false));
1988     chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1989             + sequence.getDisplayId(false) + "'");
1990
1991     int value = chooser.showOpenDialog(null);
1992
1993     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1994     {
1995       String choice = chooser.getSelectedFile().getPath();
1996       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1997       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1998               jalview.io.AppletFormatAdapter.FILE, sequence, true);
1999     }
2000
2001   }
2002
2003   public void enterPDB_actionPerformed()
2004   {
2005     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2006             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
2007
2008     if (id != null && id.length() > 0)
2009     {
2010       PDBEntry entry = new PDBEntry();
2011       entry.setId(id.toUpperCase());
2012       sequence.getDatasetSequence().addPDBId(entry);
2013     }
2014   }
2015
2016   public void discoverPDB_actionPerformed()
2017   {
2018
2019     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2020     { sequence }
2021             : ap.av.getSequenceSelection());
2022     Thread discpdb = new Thread(new Runnable()
2023     {
2024       public void run()
2025       {
2026
2027         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2028                 .fetchDBRefs(false);
2029       }
2030
2031     });
2032     discpdb.start();
2033   }
2034
2035   public void sequenceFeature_actionPerformed()
2036   {
2037     SequenceGroup sg = ap.av.getSelectionGroup();
2038     if (sg == null)
2039     {
2040       return;
2041     }
2042
2043     int rsize = 0, gSize = sg.getSize();
2044     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2045     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2046
2047     for (int i = 0; i < gSize; i++)
2048     {
2049       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2050       int end = sg.findEndRes(sg.getSequenceAt(i));
2051       if (start <= end)
2052       {
2053         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2054         features[rsize] = new SequenceFeature(null, null, null, start, end,
2055                 "Jalview");
2056         rsize++;
2057       }
2058     }
2059     rseqs = new SequenceI[rsize];
2060     tfeatures = new SequenceFeature[rsize];
2061     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2062     System.arraycopy(features, 0, tfeatures, 0, rsize);
2063     features = tfeatures;
2064     seqs = rseqs;
2065     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2066             features, true, ap))
2067     {
2068       ap.alignFrame.setShowSeqFeatures(true);
2069       ap.highlightSearchResults(null);
2070     }
2071   }
2072
2073   public void textColour_actionPerformed()
2074   {
2075     SequenceGroup sg = getGroup();
2076     if (sg != null)
2077     {
2078       new TextColourChooser().chooseColour(ap, sg);
2079     }
2080   }
2081
2082   public void colourByStructure(String pdbid)
2083   {
2084     Annotation[] anots = ap.av.getStructureSelectionManager()
2085             .colourSequenceFromStructure(sequence, pdbid);
2086
2087     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2088             "Coloured by " + pdbid, anots);
2089
2090     ap.av.getAlignment().addAnnotation(an);
2091     an.createSequenceMapping(sequence, 0, true);
2092     // an.adjustForAlignment();
2093     ap.av.getAlignment().setAnnotationIndex(an, 0);
2094
2095     ap.adjustAnnotationHeight();
2096
2097     sequence.addAlignmentAnnotation(an);
2098
2099   }
2100
2101   public void editSequence_actionPerformed(ActionEvent actionEvent)
2102   {
2103     SequenceGroup sg = ap.av.getSelectionGroup();
2104
2105     if (sg != null)
2106     {
2107       if (sequence == null)
2108         sequence = (Sequence) sg.getSequenceAt(0);
2109
2110       EditNameDialog dialog = new EditNameDialog(
2111               sequence.getSequenceAsString(sg.getStartRes(),
2112                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2113               "Edit Sequence", ap.alignFrame);
2114
2115       if (dialog.accept)
2116       {
2117         EditCommand editCommand = new EditCommand("Edit Sequences",
2118                 EditCommand.REPLACE, dialog.getName().replace(' ',
2119                         ap.av.getGapCharacter()),
2120                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2121                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2122
2123         ap.alignFrame.addHistoryItem(editCommand);
2124
2125         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2126                 .getSequences());
2127       }
2128     }
2129   }
2130
2131 }