src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.GroupUrlLink;
  34 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  35 import jalview.util.UrlLink;
  36
  37 /**
  38  * DOCUMENT ME!
  39  *
  40  * @author $author$
  41  * @version $Revision: 1.118 $
  42  */
  43 public class PopupMenu extends JPopupMenu
  44 {
  45   JMenu groupMenu = new JMenu();
  46
  47   JMenuItem groupName = new JMenuItem();
  48
  49   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  62
  63   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  64
  65   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  66
  67   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  70
  71   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  72
  73   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  74
  75   // protected JRadioButtonMenuItem covariationColour = new
  76   // JRadioButtonMenuItem();
  77
  78   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  79
  80   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  81
  82   AlignmentPanel ap;
  83
  84   JMenu sequenceMenu = new JMenu();
  85
  86   JMenuItem sequenceName = new JMenuItem();
  87
  88   Sequence sequence;
  89
  90   JMenuItem unGroupMenuItem = new JMenuItem();
  91
  92   JMenuItem outline = new JMenuItem();
  93
  94   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  95
  96   JMenu colourMenu = new JMenu();
  97
  98   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  99
 100   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 101
 102   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 103
 104   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 105
 106   JMenu editMenu = new JMenu();
 107
 108   JMenuItem cut = new JMenuItem();
 109
 110   JMenuItem copy = new JMenuItem();
 111
 112   JMenuItem upperCase = new JMenuItem();
 113
 114   JMenuItem lowerCase = new JMenuItem();
 115
 116   JMenuItem toggle = new JMenuItem();
 117
 118   JMenu pdbMenu = new JMenu();
 119
 120   JMenuItem pdbFromFile = new JMenuItem();
 121
 122   JMenuItem enterPDB = new JMenuItem();
 123
 124   JMenuItem discoverPDB = new JMenuItem();
 125
 126   JMenu outputMenu = new JMenu();
 127
 128   JMenuItem sequenceFeature = new JMenuItem();
 129
 130   JMenuItem textColour = new JMenuItem();
 131
 132   JMenu jMenu1 = new JMenu();
 133
 134   JMenu structureMenu = new JMenu();
 135
 136   JMenu viewStructureMenu = new JMenu();
 137
 138   // JMenu colStructureMenu = new JMenu();
 139   JMenuItem editSequence = new JMenuItem();
 140
 141   // JMenuItem annotationMenuItem = new JMenuItem();
 142
 143   JMenu groupLinksMenu;
 144
 145   /**
 146    * Creates a new PopupMenu object.
 147    *
 148    * @param ap
 149    *          DOCUMENT ME!
 150    * @param seq
 151    *          DOCUMENT ME!
 152    */
 153   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 154   {
 155     this(ap, seq, links, null);
 156   }
 157
 158   /**
 159    *
 160    * @param ap
 161    * @param seq
 162    * @param links
 163    * @param groupLinks
 164    */
 165   public PopupMenu(final AlignmentPanel ap, final Sequence seq,
 166           final Vector links, final Vector groupLinks)
 167   {
 168     // /////////////////////////////////////////////////////////
 169     // If this is activated from the sequence panel, the user may want to
 170     // edit or annotate a particular residue. Therefore display the residue menu
 171     //
 172     // If from the IDPanel, we must display the sequence menu
 173     // ////////////////////////////////////////////////////////
 174     this.ap = ap;
 175     sequence = seq;
 176
 177     ButtonGroup colours = new ButtonGroup();
 178     colours.add(noColourmenuItem);
 179     colours.add(clustalColour);
 180     colours.add(zappoColour);
 181     colours.add(taylorColour);
 182     colours.add(hydrophobicityColour);
 183     colours.add(helixColour);
 184     colours.add(strandColour);
 185     colours.add(turnColour);
 186     colours.add(buriedColour);
 187     colours.add(abovePIDColour);
 188     colours.add(userDefinedColour);
 189     colours.add(PIDColour);
 190     colours.add(BLOSUM62Colour);
 191     colours.add(purinePyrimidineColour);
 192     // colours.add(covariationColour);
 193
 194     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 195     {
 196       JMenuItem item = new JMenuItem(
 197               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 198
 199       item.addActionListener(new java.awt.event.ActionListener()
 200       {
 201         public void actionPerformed(ActionEvent e)
 202         {
 203           outputText_actionPerformed(e);
 204         }
 205       });
 206
 207       outputMenu.add(item);
 208     }
 209
 210     try
 211     {
 212       jbInit();
 213     } catch (Exception e)
 214     {
 215       e.printStackTrace();
 216     }
 217
 218     if (seq != null)
 219     {
 220       sequenceMenu.setText(sequence.getName());
 221
 222       JMenuItem menuItem;
 223       if (seq.getDatasetSequence().getPDBId() != null
 224               && seq.getDatasetSequence().getPDBId().size() > 0)
 225       {
 226         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 227                 .elements();
 228
 229         while (e.hasMoreElements())
 230         {
 231           final PDBEntry pdb = (PDBEntry) e.nextElement();
 232
 233           menuItem = new JMenuItem();
 234           menuItem.setText(pdb.getId());
 235           menuItem.addActionListener(new java.awt.event.ActionListener()
 236           {
 237             public void actionPerformed(ActionEvent e)
 238             {
 239               // TODO re JAL-860: optionally open dialog or provide a menu entry
 240               // allowing user to open just one structure per sequence
 241               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 242               { pdb })[0], null, ap);
 243               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 244             }
 245
 246           });
 247           viewStructureMenu.add(menuItem);
 248
 249           /*
 250            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 251            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 252            * public void actionPerformed(ActionEvent e) {
 253            * colourByStructure(pdb.getId()); } });
 254            * colStructureMenu.add(menuItem);
 255            */
 256         }
 257       }
 258       else
 259       {
 260         if (ap.av.alignment.isNucleotide() == false)
 261         {
 262           structureMenu.remove(viewStructureMenu);
 263         }
 264         // structureMenu.remove(colStructureMenu);
 265       }
 266
 267       if (ap.av.alignment.isNucleotide() == true)
 268       {
 269         AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 270         for (int i = 0; i < aa.length; i++)
 271         {
 272           if (aa[i].getRNAStruc() != null)
 273           {
 274             final String rnastruc = aa[i].getRNAStruc();
 275
 276             menuItem = new JMenuItem();
 277             menuItem.setText("RNA structure - consensus");
 278             menuItem.addActionListener(new java.awt.event.ActionListener()
 279             {
 280               public void actionPerformed(ActionEvent e)
 281               {
 282                 new AppVarna(seq.getSequenceAsString(), rnastruc, seq
 283                         .getName(), ap);
 284               }
 285             });
 286             viewStructureMenu.add(menuItem);
 287           }
 288         }
 289
 290         // SequenceFeatures[] test = seq.getSequenceFeatures();
 291
 292         if (seq.getAnnotation() != null)
 293         {
 294           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 295           for (int i = 0; i < seqAnno.length; i++)
 296           {
 297             if (seqAnno[i].getRNAStruc() != null)
 298             {
 299               final String rnastruc = seqAnno[i].getRNAStruc();
 300
 301            // TODO: make rnastrucF a bit more nice
 302               menuItem = new JMenuItem();
 303               menuItem.setText("RNA structure - "+seq.getName());
 304               menuItem.addActionListener(new java.awt.event.ActionListener()
 305               {
 306                 public void actionPerformed(ActionEvent e)
 307                 {
 308                   // TODO: VARNA does'nt print gaps in the sequence
 309                   new AppVarna(seq.getSequenceAsString(), rnastruc, seq
 310                           .getName(), ap);
 311                 }
 312               });
 313               viewStructureMenu.add(menuItem);
 314             }
 315           }
 316         }
 317
 318
 319       }
 320
 321       menuItem = new JMenuItem("Hide Sequences");
 322       menuItem.addActionListener(new java.awt.event.ActionListener()
 323       {
 324         public void actionPerformed(ActionEvent e)
 325         {
 326           hideSequences(false);
 327         }
 328       });
 329       add(menuItem);
 330
 331       if (ap.av.getSelectionGroup() != null
 332               && ap.av.getSelectionGroup().getSize() > 1)
 333       {
 334         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 335         menuItem.addActionListener(new java.awt.event.ActionListener()
 336         {
 337           public void actionPerformed(ActionEvent e)
 338           {
 339             hideSequences(true);
 340           }
 341         });
 342         sequenceMenu.add(menuItem);
 343       }
 344
 345       if (ap.av.hasHiddenRows)
 346       {
 347         final int index = ap.av.alignment.findIndex(seq);
 348
 349         if (ap.av.adjustForHiddenSeqs(index)
 350                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 351         {
 352           menuItem = new JMenuItem("Reveal Sequences");
 353           menuItem.addActionListener(new ActionListener()
 354           {
 355             public void actionPerformed(ActionEvent e)
 356             {
 357               ap.av.showSequence(index);
 358               if (ap.overviewPanel != null)
 359               {
 360                 ap.overviewPanel.updateOverviewImage();
 361               }
 362             }
 363           });
 364           add(menuItem);
 365         }
 366
 367         menuItem = new JMenuItem("Reveal All");
 368         menuItem.addActionListener(new ActionListener()
 369         {
 370           public void actionPerformed(ActionEvent e)
 371           {
 372             ap.av.showAllHiddenSeqs();
 373             if (ap.overviewPanel != null)
 374             {
 375               ap.overviewPanel.updateOverviewImage();
 376             }
 377           }
 378         });
 379
 380         add(menuItem);
 381       }
 382
 383     }
 384
 385     SequenceGroup sg = ap.av.getSelectionGroup();
 386
 387     if (sg != null)
 388     {
 389       groupName.setText("Name: " + sg.getName());
 390       groupName.setText("Edit name and description of current group.");
 391
 392       if (sg.cs instanceof ZappoColourScheme)
 393       {
 394         zappoColour.setSelected(true);
 395       }
 396       else if (sg.cs instanceof TaylorColourScheme)
 397       {
 398         taylorColour.setSelected(true);
 399       }
 400       else if (sg.cs instanceof PIDColourScheme)
 401       {
 402         PIDColour.setSelected(true);
 403       }
 404       else if (sg.cs instanceof Blosum62ColourScheme)
 405       {
 406         BLOSUM62Colour.setSelected(true);
 407       }
 408       else if (sg.cs instanceof UserColourScheme)
 409       {
 410         userDefinedColour.setSelected(true);
 411       }
 412       else if (sg.cs instanceof HydrophobicColourScheme)
 413       {
 414         hydrophobicityColour.setSelected(true);
 415       }
 416       else if (sg.cs instanceof HelixColourScheme)
 417       {
 418         helixColour.setSelected(true);
 419       }
 420       else if (sg.cs instanceof StrandColourScheme)
 421       {
 422         strandColour.setSelected(true);
 423       }
 424       else if (sg.cs instanceof TurnColourScheme)
 425       {
 426         turnColour.setSelected(true);
 427       }
 428       else if (sg.cs instanceof BuriedColourScheme)
 429       {
 430         buriedColour.setSelected(true);
 431       }
 432       else if (sg.cs instanceof ClustalxColourScheme)
 433       {
 434         clustalColour.setSelected(true);
 435       }
 436       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 437       {
 438         purinePyrimidineColour.setSelected(true);
 439       }
 440       /*
 441        * else if (sg.cs instanceof CovariationColourScheme) {
 442        * covariationColour.setSelected(true); }
 443        */
 444       else
 445       {
 446         noColourmenuItem.setSelected(true);
 447       }
 448
 449       if (sg.cs != null && sg.cs.conservationApplied())
 450       {
 451         conservationMenuItem.setSelected(true);
 452       }
 453       displayNonconserved.setSelected(sg.getShowNonconserved());
 454       showText.setSelected(sg.getDisplayText());
 455       showColourText.setSelected(sg.getColourText());
 456       showBoxes.setSelected(sg.getDisplayBoxes());
 457       // add any groupURLs to the groupURL submenu and make it visible
 458       if (groupLinks != null && groupLinks.size() > 0)
 459       {
 460         buildGroupURLMenu(sg, groupLinks);
 461       }
 462       // Add a 'show all structures' for the current selection
 463       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 464       for (SequenceI sq : ap.av.getSequenceSelection())
 465       {
 466         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 467                 .getPDBId();
 468         if (pes != null)
 469         {
 470           for (PDBEntry pe : pes)
 471           {
 472             pdbe.put(pe.getId(), pe);
 473           }
 474         }
 475       }
 476       if (pdbe.size() > 0)
 477       {
 478         final PDBEntry[] pe = pdbe.values().toArray(
 479                 new PDBEntry[pdbe.size()]);
 480         final JMenuItem gpdbview;
 481         structureMenu.add(gpdbview = new JMenuItem("View " + pdbe.size()
 482                 + " structures."));
 483         gpdbview
 484                 .setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 485         gpdbview.addActionListener(new ActionListener()
 486         {
 487
 488           @Override
 489           public void actionPerformed(ActionEvent e)
 490           {
 491             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 492           }
 493         });
 494       }
 495     }
 496     else
 497     {
 498       groupMenu.setVisible(false);
 499       editMenu.setVisible(false);
 500     }
 501
 502     if (!ap.av.alignment.getGroups().contains(sg))
 503     {
 504       unGroupMenuItem.setVisible(false);
 505     }
 506
 507     if (seq == null)
 508     {
 509       sequenceMenu.setVisible(false);
 510       structureMenu.setVisible(false);
 511     }
 512
 513     if (links != null && links.size() > 0)
 514     {
 515
 516       JMenu linkMenu = new JMenu("Link");
 517       Vector linkset = new Vector();
 518       for (int i = 0; i < links.size(); i++)
 519       {
 520         String link = links.elementAt(i).toString();
 521         UrlLink urlLink = null;
 522         try
 523         {
 524           urlLink = new UrlLink(link);
 525         } catch (Exception foo)
 526         {
 527           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 528                   + "'", foo);
 529           continue;
 530         }
 531         ;
 532         if (!urlLink.isValid())
 533         {
 534           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 535           continue;
 536         }
 537         final String label = urlLink.getLabel();
 538         if (urlLink.isDynamic())
 539         {
 540
 541           // collect matching db-refs
 542           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 543                   .getDBRef(), new String[]
 544           { urlLink.getTarget() });
 545           // collect id string too
 546           String id = seq.getName();
 547           String descr = seq.getDescription();
 548           if (descr != null && descr.length() < 1)
 549           {
 550             descr = null;
 551           }
 552
 553           if (dbr != null)
 554           {
 555             for (int r = 0; r < dbr.length; r++)
 556             {
 557               if (id != null && dbr[r].getAccessionId().equals(id))
 558               {
 559                 // suppress duplicate link creation for the bare sequence ID
 560                 // string with this link
 561                 id = null;
 562               }
 563               // create Bare ID link for this RUL
 564               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 565                       true);
 566               if (urls != null)
 567               {
 568                 for (int u = 0; u < urls.length; u += 2)
 569                 {
 570                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 571                   {
 572                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 573                     addshowLink(linkMenu, label + "|" + urls[u],
 574                             urls[u + 1]);
 575                   }
 576                 }
 577               }
 578             }
 579           }
 580           if (id != null)
 581           {
 582             // create Bare ID link for this RUL
 583             String[] urls = urlLink.makeUrls(id, true);
 584             if (urls != null)
 585             {
 586               for (int u = 0; u < urls.length; u += 2)
 587               {
 588                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 589                 {
 590                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 591                   addshowLink(linkMenu, label, urls[u + 1]);
 592                 }
 593               }
 594             }
 595           }
 596           // Create urls from description but only for URL links which are regex
 597           // links
 598           if (descr != null && urlLink.getRegexReplace() != null)
 599           {
 600             // create link for this URL from description where regex matches
 601             String[] urls = urlLink.makeUrls(descr, true);
 602             if (urls != null)
 603             {
 604               for (int u = 0; u < urls.length; u += 2)
 605               {
 606                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 607                 {
 608                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 609                   addshowLink(linkMenu, label, urls[u + 1]);
 610                 }
 611               }
 612             }
 613           }
 614         }
 615         else
 616         {
 617           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 618           {
 619             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 620             // Add a non-dynamic link
 621             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 622           }
 623         }
 624       }
 625       if (sequence != null)
 626       {
 627         sequenceMenu.add(linkMenu);
 628       }
 629       else
 630       {
 631         add(linkMenu);
 632       }
 633     }
 634   }
 635
 636   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 637   {
 638
 639     // TODO: usability: thread off the generation of group url content so root
 640     // menu appears asap
 641     // sequence only URLs
 642     // ID/regex match URLs
 643     groupLinksMenu = new JMenu("Group Link");
 644     JMenu[] linkMenus = new JMenu[]
 645     { null, new JMenu("IDS"), new JMenu("Sequences"),
 646         new JMenu("IDS and Sequences") }; // three types of url that might be
 647     // created.
 648     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 649     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 650     Hashtable commonDbrefs = new Hashtable();
 651     for (int sq = 0; sq < seqs.length; sq++)
 652     {
 653
 654       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 655               .findPosition(sg.getEndRes());
 656       // just collect ids from dataset sequence
 657       // TODO: check if IDs collected from selecton group intersects with the
 658       // current selection, too
 659       SequenceI sqi = seqs[sq];
 660       while (sqi.getDatasetSequence() != null)
 661       {
 662         sqi = sqi.getDatasetSequence();
 663       }
 664       DBRefEntry[] dbr = sqi.getDBRef();
 665       if (dbr != null && dbr.length > 0)
 666       {
 667         for (int d = 0; d < dbr.length; d++)
 668         {
 669           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 670           Object[] sarray = (Object[]) commonDbrefs.get(src);
 671           if (sarray == null)
 672           {
 673             sarray = new Object[2];
 674             sarray[0] = new int[]
 675             { 0 };
 676             sarray[1] = new String[seqs.length];
 677
 678             commonDbrefs.put(src, sarray);
 679           }
 680
 681           if (((String[]) sarray[1])[sq] == null)
 682           {
 683             if (!dbr[d].hasMap()
 684                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 685             {
 686               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 687               ((int[]) sarray[0])[0]++;
 688             }
 689           }
 690         }
 691       }
 692     }
 693     // now create group links for all distinct ID/sequence sets.
 694     boolean addMenu = false; // indicates if there are any group links to give
 695     // to user
 696     for (int i = 0; i < groupLinks.size(); i++)
 697     {
 698       String link = groupLinks.elementAt(i).toString();
 699       GroupUrlLink urlLink = null;
 700       try
 701       {
 702         urlLink = new GroupUrlLink(link);
 703       } catch (Exception foo)
 704       {
 705         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 706                 + "'", foo);
 707         continue;
 708       }
 709       ;
 710       if (!urlLink.isValid())
 711       {
 712         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 713         continue;
 714       }
 715       final String label = urlLink.getLabel();
 716       boolean usingNames = false;
 717       // Now see which parts of the group apply for this URL
 718       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 719       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 720       String[] seqstr, ids; // input to makeUrl
 721       if (idset != null)
 722       {
 723         int numinput = ((int[]) idset[0])[0];
 724         String[] allids = ((String[]) idset[1]);
 725         seqstr = new String[numinput];
 726         ids = new String[numinput];
 727         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 728         {
 729           if (allids[sq] != null)
 730           {
 731             ids[idcount] = allids[sq];
 732             seqstr[idcount++] = idandseqs[1][sq];
 733           }
 734         }
 735       }
 736       else
 737       {
 738         // just use the id/seq set
 739         seqstr = idandseqs[1];
 740         ids = idandseqs[0];
 741         usingNames = true;
 742       }
 743       // and try and make the groupURL!
 744
 745       Object[] urlset = null;
 746       try
 747       {
 748         urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
 749                 + System.currentTimeMillis(), false);
 750       } catch (UrlStringTooLongException e)
 751       {
 752       }
 753       if (urlset != null)
 754       {
 755         int type = urlLink.getGroupURLType() & 3;
 756         // System.out.println(urlLink.getGroupURLType()
 757         // +" "+((String[])urlset[3])[0]);
 758         // first two bits ofurlLink type bitfield are sequenceids and sequences
 759         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 760         addshowLink(linkMenus[type], label
 761                 + (((type & 1) == 1) ? ("("
 762                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 763                 urlLink, urlset);
 764         addMenu = true;
 765       }
 766     }
 767     if (addMenu)
 768     {
 769       groupLinksMenu = new JMenu("Group Links");
 770       for (int m = 0; m < linkMenus.length; m++)
 771       {
 772         if (linkMenus[m] != null
 773                 && linkMenus[m].getMenuComponentCount() > 0)
 774         {
 775           groupLinksMenu.add(linkMenus[m]);
 776         }
 777       }
 778
 779       groupMenu.add(groupLinksMenu);
 780     }
 781   }
 782
 783   /**
 784    * add a show URL menu item to the given linkMenu
 785    *
 786    * @param linkMenu
 787    * @param label
 788    *          - menu label string
 789    * @param url
 790    *          - url to open
 791    */
 792   private void addshowLink(JMenu linkMenu, String label, final String url)
 793   {
 794     JMenuItem item = new JMenuItem(label);
 795     item.setToolTipText("open URL: " + url);
 796     item.addActionListener(new java.awt.event.ActionListener()
 797     {
 798       public void actionPerformed(ActionEvent e)
 799       {
 800         new Thread(new Runnable()
 801         {
 802
 803           public void run()
 804           {
 805             showLink(url);
 806           }
 807
 808         }).start();
 809       }
 810     });
 811
 812     linkMenu.add(item);
 813   }
 814
 815   /**
 816    * add a late bound groupURL item to the given linkMenu
 817    *
 818    * @param linkMenu
 819    * @param label
 820    *          - menu label string
 821    * @param urlgenerator
 822    *          GroupURLLink used to generate URL
 823    * @param urlstub
 824    *          Object array returned from the makeUrlStubs function.
 825    */
 826   private void addshowLink(JMenu linkMenu, String label,
 827           final GroupUrlLink urlgenerator, final Object[] urlstub)
 828   {
 829     JMenuItem item = new JMenuItem(label);
 830     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 831             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 832     // put
 833     // in
 834     // info
 835     // about
 836     // what
 837     // is
 838     // being
 839     // sent.
 840     item.addActionListener(new java.awt.event.ActionListener()
 841     {
 842       public void actionPerformed(ActionEvent e)
 843       {
 844         new Thread(new Runnable()
 845         {
 846
 847           public void run()
 848           {
 849             try
 850             {
 851               showLink(urlgenerator.constructFrom(urlstub));
 852             } catch (UrlStringTooLongException e)
 853             {
 854             }
 855           }
 856
 857         }).start();
 858       }
 859     });
 860
 861     linkMenu.add(item);
 862   }
 863
 864   /**
 865    * DOCUMENT ME!
 866    *
 867    * @throws Exception
 868    *           DOCUMENT ME!
 869    */
 870   private void jbInit() throws Exception
 871   {
 872     groupMenu.setText("Group");
 873     groupMenu.setText("Selection");
 874     groupName.setText("Name");
 875     groupName.addActionListener(new java.awt.event.ActionListener()
 876     {
 877       public void actionPerformed(ActionEvent e)
 878       {
 879         groupName_actionPerformed();
 880       }
 881     });
 882     sequenceMenu.setText("Sequence");
 883     sequenceName.setText("Edit Name/Description");
 884     sequenceName.addActionListener(new java.awt.event.ActionListener()
 885     {
 886       public void actionPerformed(ActionEvent e)
 887       {
 888         sequenceName_actionPerformed();
 889       }
 890     });
 891     PIDColour.setFocusPainted(false);
 892     unGroupMenuItem.setText("Remove Group");
 893     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 894     {
 895       public void actionPerformed(ActionEvent e)
 896       {
 897         unGroupMenuItem_actionPerformed();
 898       }
 899     });
 900
 901     outline.setText("Border colour");
 902     outline.addActionListener(new java.awt.event.ActionListener()
 903     {
 904       public void actionPerformed(ActionEvent e)
 905       {
 906         outline_actionPerformed();
 907       }
 908     });
 909     nucleotideMenuItem.setText("Nucleotide");
 910     nucleotideMenuItem.addActionListener(new ActionListener()
 911     {
 912       public void actionPerformed(ActionEvent e)
 913       {
 914         nucleotideMenuItem_actionPerformed();
 915       }
 916     });
 917     colourMenu.setText("Group Colour");
 918     showBoxes.setText("Boxes");
 919     showBoxes.setState(true);
 920     showBoxes.addActionListener(new ActionListener()
 921     {
 922       public void actionPerformed(ActionEvent e)
 923       {
 924         showBoxes_actionPerformed();
 925       }
 926     });
 927     showText.setText("Text");
 928     showText.setState(true);
 929     showText.addActionListener(new ActionListener()
 930     {
 931       public void actionPerformed(ActionEvent e)
 932       {
 933         showText_actionPerformed();
 934       }
 935     });
 936     showColourText.setText("Colour Text");
 937     showColourText.addActionListener(new ActionListener()
 938     {
 939       public void actionPerformed(ActionEvent e)
 940       {
 941         showColourText_actionPerformed();
 942       }
 943     });
 944     displayNonconserved.setText("Show Nonconserved");
 945     displayNonconserved.setState(true);
 946     displayNonconserved.addActionListener(new ActionListener()
 947     {
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         showNonconserved_actionPerformed();
 951       }
 952     });
 953     editMenu.setText("Edit");
 954     cut.setText("Cut");
 955     cut.addActionListener(new ActionListener()
 956     {
 957       public void actionPerformed(ActionEvent e)
 958       {
 959         cut_actionPerformed();
 960       }
 961     });
 962     upperCase.setText("To Upper Case");
 963     upperCase.addActionListener(new ActionListener()
 964     {
 965       public void actionPerformed(ActionEvent e)
 966       {
 967         changeCase(e);
 968       }
 969     });
 970     copy.setText("Copy");
 971     copy.addActionListener(new ActionListener()
 972     {
 973       public void actionPerformed(ActionEvent e)
 974       {
 975         copy_actionPerformed();
 976       }
 977     });
 978     lowerCase.setText("To Lower Case");
 979     lowerCase.addActionListener(new ActionListener()
 980     {
 981       public void actionPerformed(ActionEvent e)
 982       {
 983         changeCase(e);
 984       }
 985     });
 986     toggle.setText("Toggle Case");
 987     toggle.addActionListener(new ActionListener()
 988     {
 989       public void actionPerformed(ActionEvent e)
 990       {
 991         changeCase(e);
 992       }
 993     });
 994     pdbMenu.setText("Associate Structure with Sequence");
 995     pdbFromFile.setText("From File");
 996     pdbFromFile.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         pdbFromFile_actionPerformed();
1001       }
1002     });
1003     enterPDB.setText("Enter PDB Id");
1004     enterPDB.addActionListener(new ActionListener()
1005     {
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         enterPDB_actionPerformed();
1009       }
1010     });
1011     discoverPDB.setText("Discover PDB ids");
1012     discoverPDB.addActionListener(new ActionListener()
1013     {
1014       public void actionPerformed(ActionEvent e)
1015       {
1016         discoverPDB_actionPerformed();
1017       }
1018     });
1019     outputMenu.setText("Output to Textbox...");
1020     sequenceFeature.setText("Create Sequence Feature");
1021     sequenceFeature.addActionListener(new ActionListener()
1022     {
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         sequenceFeature_actionPerformed();
1026       }
1027     });
1028     textColour.setText("Text Colour");
1029     textColour.addActionListener(new ActionListener()
1030     {
1031       public void actionPerformed(ActionEvent e)
1032       {
1033         textColour_actionPerformed();
1034       }
1035     });
1036     jMenu1.setText("Group");
1037     structureMenu.setText("Structure");
1038     viewStructureMenu.setText("View Structure");
1039     // colStructureMenu.setText("Colour By Structure");
1040     editSequence.setText("Edit Sequence...");
1041     editSequence.addActionListener(new ActionListener()
1042     {
1043       public void actionPerformed(ActionEvent actionEvent)
1044       {
1045         editSequence_actionPerformed(actionEvent);
1046       }
1047     });
1048     /*
1049      * annotationMenuItem.setText("By Annotation");
1050      * annotationMenuItem.addActionListener(new ActionListener() { public void
1051      * actionPerformed(ActionEvent actionEvent) {
1052      * annotationMenuItem_actionPerformed(actionEvent); } });
1053      */
1054
1055     add(groupMenu);
1056
1057     add(sequenceMenu);
1058     this.add(structureMenu);
1059     groupMenu.add(editMenu);
1060     groupMenu.add(outputMenu);
1061     groupMenu.add(sequenceFeature);
1062     groupMenu.add(jMenu1);
1063     sequenceMenu.add(sequenceName);
1064     colourMenu.add(textColour);
1065     colourMenu.add(noColourmenuItem);
1066     colourMenu.add(clustalColour);
1067     colourMenu.add(BLOSUM62Colour);
1068     colourMenu.add(PIDColour);
1069     colourMenu.add(zappoColour);
1070     colourMenu.add(taylorColour);
1071     colourMenu.add(hydrophobicityColour);
1072     colourMenu.add(helixColour);
1073     colourMenu.add(strandColour);
1074     colourMenu.add(turnColour);
1075     colourMenu.add(buriedColour);
1076     colourMenu.add(nucleotideMenuItem);
1077     colourMenu.add(purinePyrimidineColour);
1078     // colourMenu.add(covariationColour);
1079     colourMenu.add(userDefinedColour);
1080
1081     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1082     {
1083       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1084               .getUserColourSchemes().keys();
1085
1086       while (userColours.hasMoreElements())
1087       {
1088         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1089         item.addActionListener(new ActionListener()
1090         {
1091           public void actionPerformed(ActionEvent evt)
1092           {
1093             userDefinedColour_actionPerformed(evt);
1094           }
1095         });
1096         colourMenu.add(item);
1097       }
1098     }
1099
1100     colourMenu.addSeparator();
1101     colourMenu.add(abovePIDColour);
1102     colourMenu.add(conservationMenuItem);
1103     // colourMenu.add(annotationMenuItem);
1104     editMenu.add(copy);
1105     editMenu.add(cut);
1106     editMenu.add(editSequence);
1107     editMenu.add(upperCase);
1108     editMenu.add(lowerCase);
1109     editMenu.add(toggle);
1110     pdbMenu.add(pdbFromFile);
1111     pdbMenu.add(enterPDB);
1112     pdbMenu.add(discoverPDB);
1113     jMenu1.add(groupName);
1114     jMenu1.add(unGroupMenuItem);
1115     jMenu1.add(colourMenu);
1116     jMenu1.add(showBoxes);
1117     jMenu1.add(showText);
1118     jMenu1.add(showColourText);
1119     jMenu1.add(outline);
1120     jMenu1.add(displayNonconserved);
1121     structureMenu.add(pdbMenu);
1122     structureMenu.add(viewStructureMenu);
1123     // structureMenu.add(colStructureMenu);
1124     noColourmenuItem.setText("None");
1125     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1126     {
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         noColourmenuItem_actionPerformed();
1130       }
1131     });
1132
1133     clustalColour.setText("Clustalx colours");
1134     clustalColour.addActionListener(new java.awt.event.ActionListener()
1135     {
1136       public void actionPerformed(ActionEvent e)
1137       {
1138         clustalColour_actionPerformed();
1139       }
1140     });
1141     zappoColour.setText("Zappo");
1142     zappoColour.addActionListener(new java.awt.event.ActionListener()
1143     {
1144       public void actionPerformed(ActionEvent e)
1145       {
1146         zappoColour_actionPerformed();
1147       }
1148     });
1149     taylorColour.setText("Taylor");
1150     taylorColour.addActionListener(new java.awt.event.ActionListener()
1151     {
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         taylorColour_actionPerformed();
1155       }
1156     });
1157     hydrophobicityColour.setText("Hydrophobicity");
1158     hydrophobicityColour
1159             .addActionListener(new java.awt.event.ActionListener()
1160             {
1161               public void actionPerformed(ActionEvent e)
1162               {
1163                 hydrophobicityColour_actionPerformed();
1164               }
1165             });
1166     helixColour.setText("Helix propensity");
1167     helixColour.addActionListener(new java.awt.event.ActionListener()
1168     {
1169       public void actionPerformed(ActionEvent e)
1170       {
1171         helixColour_actionPerformed();
1172       }
1173     });
1174     strandColour.setText("Strand propensity");
1175     strandColour.addActionListener(new java.awt.event.ActionListener()
1176     {
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         strandColour_actionPerformed();
1180       }
1181     });
1182     turnColour.setText("Turn propensity");
1183     turnColour.addActionListener(new java.awt.event.ActionListener()
1184     {
1185       public void actionPerformed(ActionEvent e)
1186       {
1187         turnColour_actionPerformed();
1188       }
1189     });
1190     buriedColour.setText("Buried Index");
1191     buriedColour.addActionListener(new java.awt.event.ActionListener()
1192     {
1193       public void actionPerformed(ActionEvent e)
1194       {
1195         buriedColour_actionPerformed();
1196       }
1197     });
1198     abovePIDColour.setText("Above % Identity");
1199     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1200     {
1201       public void actionPerformed(ActionEvent e)
1202       {
1203         abovePIDColour_actionPerformed();
1204       }
1205     });
1206     userDefinedColour.setText("User Defined...");
1207     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1208     {
1209       public void actionPerformed(ActionEvent e)
1210       {
1211         userDefinedColour_actionPerformed(e);
1212       }
1213     });
1214     PIDColour.setText("Percentage Identity");
1215     PIDColour.addActionListener(new java.awt.event.ActionListener()
1216     {
1217       public void actionPerformed(ActionEvent e)
1218       {
1219         PIDColour_actionPerformed();
1220       }
1221     });
1222     BLOSUM62Colour.setText("BLOSUM62");
1223     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1224     {
1225       public void actionPerformed(ActionEvent e)
1226       {
1227         BLOSUM62Colour_actionPerformed();
1228       }
1229     });
1230     purinePyrimidineColour.setText("Purine/Pyrimidine");
1231     purinePyrimidineColour
1232             .addActionListener(new java.awt.event.ActionListener()
1233             {
1234               public void actionPerformed(ActionEvent e)
1235               {
1236                 purinePyrimidineColour_actionPerformed();
1237               }
1238             });
1239     /*
1240      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1241      * public void actionPerformed(ActionEvent e) {
1242      * covariationColour_actionPerformed(); } });
1243      */
1244
1245     conservationMenuItem.setText("Conservation");
1246     conservationMenuItem
1247             .addActionListener(new java.awt.event.ActionListener()
1248             {
1249               public void actionPerformed(ActionEvent e)
1250               {
1251                 conservationMenuItem_actionPerformed();
1252               }
1253             });
1254   }
1255
1256   protected void showNonconserved_actionPerformed()
1257   {
1258     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1259     refresh();
1260   }
1261
1262   /**
1263    * call to refresh view after settings change
1264    */
1265   void refresh()
1266   {
1267     ap.updateAnnotation();
1268     ap.paintAlignment(true);
1269
1270     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1271   }
1272
1273   /**
1274    * DOCUMENT ME!
1275    *
1276    * @param e
1277    *          DOCUMENT ME!
1278    */
1279   protected void clustalColour_actionPerformed()
1280   {
1281     SequenceGroup sg = getGroup();
1282     sg.cs = new ClustalxColourScheme(sg
1283             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
1284             .getWidth());
1285     refresh();
1286   }
1287
1288   /**
1289    * DOCUMENT ME!
1290    *
1291    * @param e
1292    *          DOCUMENT ME!
1293    */
1294   protected void zappoColour_actionPerformed()
1295   {
1296     getGroup().cs = new ZappoColourScheme();
1297     refresh();
1298   }
1299
1300   /**
1301    * DOCUMENT ME!
1302    *
1303    * @param e
1304    *          DOCUMENT ME!
1305    */
1306   protected void taylorColour_actionPerformed()
1307   {
1308     getGroup().cs = new TaylorColourScheme();
1309     refresh();
1310   }
1311
1312   /**
1313    * DOCUMENT ME!
1314    *
1315    * @param e
1316    *          DOCUMENT ME!
1317    */
1318   protected void hydrophobicityColour_actionPerformed()
1319   {
1320     getGroup().cs = new HydrophobicColourScheme();
1321     refresh();
1322   }
1323
1324   /**
1325    * DOCUMENT ME!
1326    *
1327    * @param e
1328    *          DOCUMENT ME!
1329    */
1330   protected void helixColour_actionPerformed()
1331   {
1332     getGroup().cs = new HelixColourScheme();
1333     refresh();
1334   }
1335
1336   /**
1337    * DOCUMENT ME!
1338    *
1339    * @param e
1340    *          DOCUMENT ME!
1341    */
1342   protected void strandColour_actionPerformed()
1343   {
1344     getGroup().cs = new StrandColourScheme();
1345     refresh();
1346   }
1347
1348   /**
1349    * DOCUMENT ME!
1350    *
1351    * @param e
1352    *          DOCUMENT ME!
1353    */
1354   protected void turnColour_actionPerformed()
1355   {
1356     getGroup().cs = new TurnColourScheme();
1357     refresh();
1358   }
1359
1360   /**
1361    * DOCUMENT ME!
1362    *
1363    * @param e
1364    *          DOCUMENT ME!
1365    */
1366   protected void buriedColour_actionPerformed()
1367   {
1368     getGroup().cs = new BuriedColourScheme();
1369     refresh();
1370   }
1371
1372   /**
1373    * DOCUMENT ME!
1374    *
1375    * @param e
1376    *          DOCUMENT ME!
1377    */
1378   public void nucleotideMenuItem_actionPerformed()
1379   {
1380     getGroup().cs = new NucleotideColourScheme();
1381     refresh();
1382   }
1383
1384   protected void purinePyrimidineColour_actionPerformed()
1385   {
1386     getGroup().cs = new PurinePyrimidineColourScheme();
1387     refresh();
1388   }
1389
1390   /*
1391    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1392    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1393    */
1394   /**
1395    * DOCUMENT ME!
1396    *
1397    * @param e
1398    *          DOCUMENT ME!
1399    */
1400   protected void abovePIDColour_actionPerformed()
1401   {
1402     SequenceGroup sg = getGroup();
1403     if (sg.cs == null)
1404     {
1405       return;
1406     }
1407
1408     if (abovePIDColour.isSelected())
1409     {
1410       sg.cs.setConsensus(AAFrequency.calculate(sg
1411               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1412               .getEndRes() + 1));
1413
1414       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1415               .getName());
1416
1417       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1418
1419       SliderPanel.showPIDSlider();
1420     }
1421     else
1422     // remove PIDColouring
1423     {
1424       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1425     }
1426
1427     refresh();
1428   }
1429
1430   /**
1431    * DOCUMENT ME!
1432    *
1433    * @param e
1434    *          DOCUMENT ME!
1435    */
1436   protected void userDefinedColour_actionPerformed(ActionEvent e)
1437   {
1438     SequenceGroup sg = getGroup();
1439
1440     if (e.getActionCommand().equals("User Defined..."))
1441     {
1442       new UserDefinedColours(ap, sg);
1443     }
1444     else
1445     {
1446       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1447               .getUserColourSchemes().get(e.getActionCommand());
1448
1449       sg.cs = udc;
1450     }
1451     refresh();
1452   }
1453
1454   /**
1455    * DOCUMENT ME!
1456    *
1457    * @param e
1458    *          DOCUMENT ME!
1459    */
1460   protected void PIDColour_actionPerformed()
1461   {
1462     SequenceGroup sg = getGroup();
1463     sg.cs = new PIDColourScheme();
1464     sg.cs.setConsensus(AAFrequency.calculate(sg
1465             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1466             .getEndRes() + 1));
1467     refresh();
1468   }
1469
1470   /**
1471    * DOCUMENT ME!
1472    *
1473    * @param e
1474    *          DOCUMENT ME!
1475    */
1476   protected void BLOSUM62Colour_actionPerformed()
1477   {
1478     SequenceGroup sg = getGroup();
1479
1480     sg.cs = new Blosum62ColourScheme();
1481
1482     sg.cs.setConsensus(AAFrequency.calculate(sg
1483             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1484             .getEndRes() + 1));
1485
1486     refresh();
1487   }
1488
1489   /**
1490    * DOCUMENT ME!
1491    *
1492    * @param e
1493    *          DOCUMENT ME!
1494    */
1495   protected void noColourmenuItem_actionPerformed()
1496   {
1497     getGroup().cs = null;
1498     refresh();
1499   }
1500
1501   /**
1502    * DOCUMENT ME!
1503    *
1504    * @param e
1505    *          DOCUMENT ME!
1506    */
1507   protected void conservationMenuItem_actionPerformed()
1508   {
1509     SequenceGroup sg = getGroup();
1510     if (sg.cs == null)
1511     {
1512       return;
1513     }
1514
1515     if (conservationMenuItem.isSelected())
1516     {
1517       Conservation c = new Conservation("Group",
1518               ResidueProperties.propHash, 3, sg
1519                       .getSequences(ap.av.hiddenRepSequences), sg
1520                       .getStartRes(), sg.getEndRes() + 1);
1521
1522       c.calculate();
1523       c.verdict(false, ap.av.ConsPercGaps);
1524
1525       sg.cs.setConservation(c);
1526
1527       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1528       SliderPanel.showConservationSlider();
1529     }
1530     else
1531     // remove ConservationColouring
1532     {
1533       sg.cs.setConservation(null);
1534     }
1535
1536     refresh();
1537   }
1538
1539   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1540   {
1541     SequenceGroup sg = getGroup();
1542     if (sg == null)
1543     {
1544       return;
1545     }
1546
1547     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1548             .getAnnotation()[0], null,
1549             AnnotationColourGradient.NO_THRESHOLD);
1550
1551     acg.predefinedColours = true;
1552     sg.cs = acg;
1553
1554     refresh();
1555   }
1556
1557   /**
1558    * DOCUMENT ME!
1559    *
1560    * @param e
1561    *          DOCUMENT ME!
1562    */
1563   protected void groupName_actionPerformed()
1564   {
1565
1566     SequenceGroup sg = getGroup();
1567     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1568             .getDescription(), "       Group Name ", "Group Description ",
1569             "Edit Group Name/Description", ap.alignFrame);
1570
1571     if (!dialog.accept)
1572     {
1573       return;
1574     }
1575
1576     sg.setName(dialog.getName());
1577     sg.setDescription(dialog.getDescription());
1578     refresh();
1579   }
1580
1581   /**
1582    * Get selection group - adding it to the alignment if necessary.
1583    *
1584    * @return sequence group to operate on
1585    */
1586   SequenceGroup getGroup()
1587   {
1588     SequenceGroup sg = ap.av.getSelectionGroup();
1589     // this method won't add a new group if it already exists
1590     if (sg != null)
1591     {
1592       ap.av.alignment.addGroup(sg);
1593     }
1594
1595     return sg;
1596   }
1597
1598   /**
1599    * DOCUMENT ME!
1600    *
1601    * @param e
1602    *          DOCUMENT ME!
1603    */
1604   void sequenceName_actionPerformed()
1605   {
1606     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1607             .getDescription(), "       Sequence Name ",
1608             "Sequence Description ", "Edit Sequence Name/Description",
1609             ap.alignFrame);
1610
1611     if (!dialog.accept)
1612     {
1613       return;
1614     }
1615
1616     if (dialog.getName() != null)
1617     {
1618       if (dialog.getName().indexOf(" ") > -1)
1619       {
1620         JOptionPane.showMessageDialog(ap,
1621                 "Spaces have been converted to \"_\"",
1622                 "No spaces allowed in Sequence Name",
1623                 JOptionPane.WARNING_MESSAGE);
1624       }
1625
1626       sequence.setName(dialog.getName().replace(' ', '_'));
1627       ap.paintAlignment(false);
1628     }
1629
1630     sequence.setDescription(dialog.getDescription());
1631
1632     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1633             .getSequences());
1634
1635   }
1636
1637   /**
1638    * DOCUMENT ME!
1639    *
1640    * @param e
1641    *          DOCUMENT ME!
1642    */
1643   void unGroupMenuItem_actionPerformed()
1644   {
1645     SequenceGroup sg = ap.av.getSelectionGroup();
1646     ap.av.alignment.deleteGroup(sg);
1647     ap.av.setSelectionGroup(null);
1648     refresh();
1649   }
1650
1651   /**
1652    * DOCUMENT ME!
1653    *
1654    * @param e
1655    *          DOCUMENT ME!
1656    */
1657   protected void outline_actionPerformed()
1658   {
1659     SequenceGroup sg = getGroup();
1660     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1661             Color.BLUE);
1662
1663     if (col != null)
1664     {
1665       sg.setOutlineColour(col);
1666     }
1667
1668     refresh();
1669   }
1670
1671   /**
1672    * DOCUMENT ME!
1673    *
1674    * @param e
1675    *          DOCUMENT ME!
1676    */
1677   public void showBoxes_actionPerformed()
1678   {
1679     getGroup().setDisplayBoxes(showBoxes.isSelected());
1680     refresh();
1681   }
1682
1683   /**
1684    * DOCUMENT ME!
1685    *
1686    * @param e
1687    *          DOCUMENT ME!
1688    */
1689   public void showText_actionPerformed()
1690   {
1691     getGroup().setDisplayText(showText.isSelected());
1692     refresh();
1693   }
1694
1695   /**
1696    * DOCUMENT ME!
1697    *
1698    * @param e
1699    *          DOCUMENT ME!
1700    */
1701   public void showColourText_actionPerformed()
1702   {
1703     getGroup().setColourText(showColourText.isSelected());
1704     refresh();
1705   }
1706
1707   public void showLink(String url)
1708   {
1709     try
1710     {
1711       jalview.util.BrowserLauncher.openURL(url);
1712     } catch (Exception ex)
1713     {
1714       JOptionPane
1715               .showInternalMessageDialog(
1716                       Desktop.desktop,
1717                       "Unixers: Couldn't find default web browser."
1718                               + "\nAdd the full path to your browser in Preferences.",
1719                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1720
1721       ex.printStackTrace();
1722     }
1723   }
1724
1725   void hideSequences(boolean representGroup)
1726   {
1727     SequenceGroup sg = ap.av.getSelectionGroup();
1728     if (sg == null || sg.getSize() < 1)
1729     {
1730       ap.av.hideSequence(new SequenceI[]
1731       { sequence });
1732       return;
1733     }
1734
1735     ap.av.setSelectionGroup(null);
1736
1737     if (representGroup)
1738     {
1739       ap.av.hideRepSequences(sequence, sg);
1740
1741       return;
1742     }
1743
1744     int gsize = sg.getSize();
1745     SequenceI[] hseqs;
1746
1747     hseqs = new SequenceI[gsize];
1748
1749     int index = 0;
1750     for (int i = 0; i < gsize; i++)
1751     {
1752       hseqs[index++] = sg.getSequenceAt(i);
1753     }
1754
1755     ap.av.hideSequence(hseqs);
1756     // refresh(); TODO: ? needed ?
1757     ap.av.sendSelection();
1758   }
1759
1760   public void copy_actionPerformed()
1761   {
1762     ap.alignFrame.copy_actionPerformed(null);
1763   }
1764
1765   public void cut_actionPerformed()
1766   {
1767     ap.alignFrame.cut_actionPerformed(null);
1768   }
1769
1770   void changeCase(ActionEvent e)
1771   {
1772     Object source = e.getSource();
1773     SequenceGroup sg = ap.av.getSelectionGroup();
1774
1775     if (sg != null)
1776     {
1777       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1778               sg.getEndRes() + 1);
1779
1780       String description;
1781       int caseChange;
1782
1783       if (source == toggle)
1784       {
1785         description = "Toggle Case";
1786         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1787       }
1788       else if (source == upperCase)
1789       {
1790         description = "To Upper Case";
1791         caseChange = ChangeCaseCommand.TO_UPPER;
1792       }
1793       else
1794       {
1795         description = "To Lower Case";
1796         caseChange = ChangeCaseCommand.TO_LOWER;
1797       }
1798
1799       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1800               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1801               caseChange);
1802
1803       ap.alignFrame.addHistoryItem(caseCommand);
1804
1805       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1806               .getSequences());
1807
1808     }
1809   }
1810
1811   public void outputText_actionPerformed(ActionEvent e)
1812   {
1813     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1814     cap.setForInput(null);
1815     Desktop.addInternalFrame(cap, "Alignment output - "
1816             + e.getActionCommand(), 600, 500);
1817
1818     String[] omitHidden = null;
1819
1820     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1821     // or we simply trust the user wants
1822     // wysiwig behaviour
1823     SequenceGroup sg = ap.av.getSelectionGroup();
1824     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1825     omitHidden = ap.av.getViewAsString(true);
1826     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1827     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1828     if (nala != null)
1829     {
1830       for (int i = 0; i < nala.length; i++)
1831       {
1832         AlignmentAnnotation na = nala[i];
1833         oal.addAnnotation(na);
1834       }
1835     }
1836     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1837             oal, omitHidden, csel, sg));
1838     oal = null;
1839   }
1840
1841   public void pdbFromFile_actionPerformed()
1842   {
1843     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1844             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1845     chooser.setFileView(new jalview.io.JalviewFileView());
1846     chooser.setDialogTitle("Select a PDB file for "
1847             + sequence.getDisplayId(false));
1848     chooser
1849             .setToolTipText("Load a PDB file and associate it with sequence '"
1850                     + sequence.getDisplayId(false) + "'");
1851
1852     int value = chooser.showOpenDialog(null);
1853
1854     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1855     {
1856       String choice = chooser.getSelectedFile().getPath();
1857       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1858       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1859               jalview.io.AppletFormatAdapter.FILE, sequence, true);
1860     }
1861
1862   }
1863
1864   public void enterPDB_actionPerformed()
1865   {
1866     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1867             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1868
1869     if (id != null && id.length() > 0)
1870     {
1871       PDBEntry entry = new PDBEntry();
1872       entry.setId(id.toUpperCase());
1873       sequence.getDatasetSequence().addPDBId(entry);
1874     }
1875   }
1876
1877   public void discoverPDB_actionPerformed()
1878   {
1879
1880     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1881     { sequence }
1882             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1883     Thread discpdb = new Thread(new Runnable()
1884     {
1885       public void run()
1886       {
1887
1888         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1889                 .fetchDBRefs(false);
1890       }
1891
1892     });
1893     discpdb.start();
1894   }
1895
1896   public void sequenceFeature_actionPerformed()
1897   {
1898     SequenceGroup sg = ap.av.getSelectionGroup();
1899     if (sg == null)
1900     {
1901       return;
1902     }
1903
1904     int rsize = 0, gSize = sg.getSize();
1905     SequenceI[] rseqs, seqs = new SequenceI[gSize];
1906     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1907
1908     for (int i = 0; i < gSize; i++)
1909     {
1910       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1911       int end = sg.findEndRes(sg.getSequenceAt(i));
1912       if (start <= end)
1913       {
1914         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1915         features[rsize] = new SequenceFeature(null, null, null, start, end,
1916                 "Jalview");
1917         rsize++;
1918       }
1919     }
1920     rseqs = new SequenceI[rsize];
1921     tfeatures = new SequenceFeature[rsize];
1922     System.arraycopy(seqs, 0, rseqs, 0, rsize);
1923     System.arraycopy(features, 0, tfeatures, 0, rsize);
1924     features = tfeatures;
1925     seqs = rseqs;
1926     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1927             features, true, ap))
1928     {
1929       ap.alignFrame.setShowSeqFeatures(true);
1930       ap.highlightSearchResults(null);
1931     }
1932   }
1933
1934   public void textColour_actionPerformed()
1935   {
1936     SequenceGroup sg = getGroup();
1937     if (sg != null)
1938     {
1939       new TextColourChooser().chooseColour(ap, sg);
1940     }
1941   }
1942
1943   public void colourByStructure(String pdbid)
1944   {
1945     Annotation[] anots = ap.av.getStructureSelectionManager()
1946             .colourSequenceFromStructure(sequence, pdbid);
1947
1948     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1949             "Coloured by " + pdbid, anots);
1950
1951     ap.av.alignment.addAnnotation(an);
1952     an.createSequenceMapping(sequence, 0, true);
1953     // an.adjustForAlignment();
1954     ap.av.alignment.setAnnotationIndex(an, 0);
1955
1956     ap.adjustAnnotationHeight();
1957
1958     sequence.addAlignmentAnnotation(an);
1959
1960   }
1961
1962   public void editSequence_actionPerformed(ActionEvent actionEvent)
1963   {
1964     SequenceGroup sg = ap.av.getSelectionGroup();
1965
1966     if (sg != null)
1967     {
1968       if (sequence == null)
1969         sequence = (Sequence) sg.getSequenceAt(0);
1970
1971       EditNameDialog dialog = new EditNameDialog(sequence
1972               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1973               null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame);
1974
1975       if (dialog.accept)
1976       {
1977         EditCommand editCommand = new EditCommand("Edit Sequences",
1978                 EditCommand.REPLACE, dialog.getName().replace(' ',
1979                         ap.av.getGapCharacter()), sg
1980                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1981                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1982
1983         ap.alignFrame.addHistoryItem(editCommand);
1984
1985         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1986                 .getSequences());
1987       }
1988     }
1989   }
1990
1991 }