src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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   SequenceI 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 SequenceI seq, Vector links,
 166           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     JMenuItem menuItem;
 219     if (seq != null)
 220     {
 221       sequenceMenu.setText(sequence.getName());
 222
 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 allowing user to open just one structure per sequence
 240               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
 241               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 242             }
 243
 244           });
 245           viewStructureMenu.add(menuItem);
 246
 247           /*
 248            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 249            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 250            * public void actionPerformed(ActionEvent e) {
 251            * colourByStructure(pdb.getId()); } });
 252            * colStructureMenu.add(menuItem);
 253            */
 254         }
 255       }
 256       else
 257       {
 258         if (ap.av.alignment.isNucleotide() == false)
 259         {
 260         structureMenu.remove(viewStructureMenu);
 261         }
 262         // structureMenu.remove(colStructureMenu);
 263       }
 264
 265       if (ap.av.alignment.isNucleotide() == true)
 266       {
 267         AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 268         for (int i = 0; i < aa.length; i++)
 269         {
 270           if (aa[i].getRNAStruc() != null)
 271           {
 272             final String rnastruc = aa[i].getRNAStruc();
 273
 274             menuItem = new JMenuItem();
 275             menuItem.setText("RNA structure - consensus");
 276             menuItem.addActionListener(new java.awt.event.ActionListener()
 277             {
 278               public void actionPerformed(ActionEvent e)
 279               {
 280                 new AppVarna(seq.getSequenceAsString(), rnastruc, seq
 281                         .getName(), ap);
 282               }
 283             });
 284             viewStructureMenu.add(menuItem);
 285           }
 286         }
 287
 288         // SequenceFeatures[] test = seq.getSequenceFeatures();
 289
 290         if (seq.getAnnotation() != null)
 291         {
 292           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 293           for (int i = 0; i < seqAnno.length; i++)
 294           {
 295             if (seqAnno[i].getRNAStruc() != null)
 296             {
 297               final String rnastruc = seqAnno[i].getRNAStruc();
 298
 299            // TODO: make rnastrucF a bit more nice
 300               menuItem = new JMenuItem();
 301               menuItem.setText("RNA structure - "+seq.getName());
 302               menuItem.addActionListener(new java.awt.event.ActionListener()
 303               {
 304                 public void actionPerformed(ActionEvent e)
 305                 {
 306                   // TODO: VARNA does'nt print gaps in the sequence
 307                   new AppVarna(seq.getSequenceAsString(), rnastruc, seq
 308                           .getName(), ap);
 309                 }
 310               });
 311               viewStructureMenu.add(menuItem);
 312             }
 313           }
 314         }
 315
 316
 317       }
 318
 319       menuItem = new JMenuItem("Hide Sequences");
 320       menuItem.addActionListener(new java.awt.event.ActionListener()
 321       {
 322         public void actionPerformed(ActionEvent e)
 323         {
 324           hideSequences(false);
 325         }
 326       });
 327       add(menuItem);
 328
 329       if (ap.av.getSelectionGroup() != null
 330               && ap.av.getSelectionGroup().getSize() > 1)
 331       {
 332         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 333         menuItem.addActionListener(new java.awt.event.ActionListener()
 334         {
 335           public void actionPerformed(ActionEvent e)
 336           {
 337             hideSequences(true);
 338           }
 339         });
 340         sequenceMenu.add(menuItem);
 341       }
 342
 343       if (ap.av.hasHiddenRows)
 344       {
 345         final int index = ap.av.alignment.findIndex(seq);
 346
 347         if (ap.av.adjustForHiddenSeqs(index)
 348                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 349         {
 350           menuItem = new JMenuItem("Reveal Sequences");
 351           menuItem.addActionListener(new ActionListener()
 352           {
 353             public void actionPerformed(ActionEvent e)
 354             {
 355               ap.av.showSequence(index);
 356               if (ap.overviewPanel != null)
 357               {
 358                 ap.overviewPanel.updateOverviewImage();
 359               }
 360             }
 361           });
 362           add(menuItem);
 363         }
 364       }
 365     }
 366     // for the case when no sequences are even visible
 367     if (ap.av.hasHiddenRows) {
 368       {
 369         menuItem = new JMenuItem("Reveal All");
 370         menuItem.addActionListener(new ActionListener()
 371         {
 372           public void actionPerformed(ActionEvent e)
 373           {
 374             ap.av.showAllHiddenSeqs();
 375             if (ap.overviewPanel != null)
 376             {
 377               ap.overviewPanel.updateOverviewImage();
 378             }
 379           }
 380         });
 381
 382         add(menuItem);
 383       }
 384
 385     }
 386
 387     SequenceGroup sg = ap.av.getSelectionGroup();
 388
 389     if (sg != null&& sg.getSize()>0)
 390     {
 391       groupName.setText("Name: "+sg.getName());
 392       groupName.setText("Edit name and description of current group.");
 393
 394       if (sg.cs instanceof ZappoColourScheme)
 395       {
 396         zappoColour.setSelected(true);
 397       }
 398       else if (sg.cs instanceof TaylorColourScheme)
 399       {
 400         taylorColour.setSelected(true);
 401       }
 402       else if (sg.cs instanceof PIDColourScheme)
 403       {
 404         PIDColour.setSelected(true);
 405       }
 406       else if (sg.cs instanceof Blosum62ColourScheme)
 407       {
 408         BLOSUM62Colour.setSelected(true);
 409       }
 410       else if (sg.cs instanceof UserColourScheme)
 411       {
 412         userDefinedColour.setSelected(true);
 413       }
 414       else if (sg.cs instanceof HydrophobicColourScheme)
 415       {
 416         hydrophobicityColour.setSelected(true);
 417       }
 418       else if (sg.cs instanceof HelixColourScheme)
 419       {
 420         helixColour.setSelected(true);
 421       }
 422       else if (sg.cs instanceof StrandColourScheme)
 423       {
 424         strandColour.setSelected(true);
 425       }
 426       else if (sg.cs instanceof TurnColourScheme)
 427       {
 428         turnColour.setSelected(true);
 429       }
 430       else if (sg.cs instanceof BuriedColourScheme)
 431       {
 432         buriedColour.setSelected(true);
 433       }
 434       else if (sg.cs instanceof ClustalxColourScheme)
 435       {
 436         clustalColour.setSelected(true);
 437       }
 438       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 439       {
 440         purinePyrimidineColour.setSelected(true);
 441       }
 442       /*
 443        * else if (sg.cs instanceof CovariationColourScheme) {
 444        * covariationColour.setSelected(true); }
 445        */
 446       else
 447       {
 448         noColourmenuItem.setSelected(true);
 449       }
 450
 451       if (sg.cs != null && sg.cs.conservationApplied())
 452       {
 453         conservationMenuItem.setSelected(true);
 454       }
 455       displayNonconserved.setSelected(sg.getShowNonconserved());
 456       showText.setSelected(sg.getDisplayText());
 457       showColourText.setSelected(sg.getColourText());
 458       showBoxes.setSelected(sg.getDisplayBoxes());
 459       // add any groupURLs to the groupURL submenu and make it visible
 460       if (groupLinks != null && groupLinks.size() > 0)
 461       {
 462         buildGroupURLMenu(sg, groupLinks);
 463       }
 464       // Add a 'show all structures' for the current selection
 465       Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
 466       SequenceI sqass=null;
 467       for (SequenceI sq: ap.av.getSequenceSelection())
 468       {
 469         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
 470         if (pes!=null) {
 471           for (PDBEntry pe: pes)
 472           {
 473             pdbe.put(pe.getId(),  pe);
 474             if (sqass==null)
 475             {
 476               sqass = sq;
 477             }
 478           }
 479         }
 480       }
 481       if (pdbe.size()>0)
 482       {
 483         final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
 484         final JMenuItem gpdbview;
 485         if (pdbe.size()==1)
 486         {
 487           structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
 488         } else {
 489           structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
 490         }
 491         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 492         gpdbview.addActionListener(new ActionListener()
 493         {
 494
 495           @Override
 496           public void actionPerformed(ActionEvent e)
 497           {
 498             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 499           }
 500         });
 501       }
 502     }
 503     else
 504     {
 505       groupMenu.setVisible(false);
 506       editMenu.setVisible(false);
 507     }
 508
 509     if (!ap.av.alignment.getGroups().contains(sg))
 510     {
 511       unGroupMenuItem.setVisible(false);
 512     }
 513
 514     if (seq == null)
 515     {
 516       sequenceMenu.setVisible(false);
 517       structureMenu.setVisible(false);
 518     }
 519
 520     if (links != null && links.size() > 0)
 521     {
 522
 523       JMenu linkMenu = new JMenu("Link");
 524       Vector linkset = new Vector();
 525       for (int i = 0; i < links.size(); i++)
 526       {
 527         String link = links.elementAt(i).toString();
 528         UrlLink urlLink = null;
 529         try
 530         {
 531           urlLink = new UrlLink(link);
 532         } catch (Exception foo)
 533         {
 534           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 535                   + "'", foo);
 536           continue;
 537         }
 538         ;
 539         if (!urlLink.isValid())
 540         {
 541           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 542           continue;
 543         }
 544         final String label = urlLink.getLabel();
 545         if (seq!=null && urlLink.isDynamic())
 546         {
 547
 548           // collect matching db-refs
 549           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 550                   seq.getDBRef(), new String[]
 551                   { urlLink.getTarget() });
 552           // collect id string too
 553           String id = seq.getName();
 554           String descr = seq.getDescription();
 555           if (descr != null && descr.length() < 1)
 556           {
 557             descr = null;
 558           }
 559
 560           if (dbr != null)
 561           {
 562             for (int r = 0; r < dbr.length; r++)
 563             {
 564               if (id != null && dbr[r].getAccessionId().equals(id))
 565               {
 566                 // suppress duplicate link creation for the bare sequence ID
 567                 // string with this link
 568                 id = null;
 569               }
 570               // create Bare ID link for this RUL
 571               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 572                       true);
 573               if (urls != null)
 574               {
 575                 for (int u = 0; u < urls.length; u += 2)
 576                 {
 577                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 578                   {
 579                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 580                     addshowLink(linkMenu, label + "|" + urls[u],
 581                             urls[u + 1]);
 582                   }
 583                 }
 584               }
 585             }
 586           }
 587           if (id != null)
 588           {
 589             // create Bare ID link for this RUL
 590             String[] urls = urlLink.makeUrls(id, true);
 591             if (urls != null)
 592             {
 593               for (int u = 0; u < urls.length; u += 2)
 594               {
 595                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 596                 {
 597                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 598                   addshowLink(linkMenu, label, urls[u + 1]);
 599                 }
 600               }
 601             }
 602           }
 603           // Create urls from description but only for URL links which are regex
 604           // links
 605           if (descr != null && urlLink.getRegexReplace() != null)
 606           {
 607             // create link for this URL from description where regex matches
 608             String[] urls = urlLink.makeUrls(descr, true);
 609             if (urls != null)
 610             {
 611               for (int u = 0; u < urls.length; u += 2)
 612               {
 613                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 614                 {
 615                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 616                   addshowLink(linkMenu, label, urls[u + 1]);
 617                 }
 618               }
 619             }
 620           }
 621         }
 622         else
 623         {
 624           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 625           {
 626             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 627             // Add a non-dynamic link
 628             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 629           }
 630         }
 631       }
 632       if (sequence != null)
 633       {
 634         sequenceMenu.add(linkMenu);
 635       }
 636       else
 637       {
 638         add(linkMenu);
 639       }
 640     }
 641   }
 642
 643   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 644   {
 645
 646     // TODO: usability: thread off the generation of group url content so root
 647     // menu appears asap
 648     // sequence only URLs
 649     // ID/regex match URLs
 650     groupLinksMenu = new JMenu("Group Link");
 651     JMenu[] linkMenus = new JMenu[]
 652     { null, new JMenu("IDS"), new JMenu("Sequences"),
 653         new JMenu("IDS and Sequences") }; // three types of url that might be
 654                                           // created.
 655     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 656     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 657     Hashtable commonDbrefs = new Hashtable();
 658     for (int sq = 0; sq < seqs.length; sq++)
 659     {
 660
 661       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 662               .findPosition(sg.getEndRes());
 663       // just collect ids from dataset sequence
 664       // TODO: check if IDs collected from selecton group intersects with the
 665       // current selection, too
 666       SequenceI sqi = seqs[sq];
 667       while (sqi.getDatasetSequence() != null)
 668       {
 669         sqi = sqi.getDatasetSequence();
 670       }
 671       DBRefEntry[] dbr = sqi.getDBRef();
 672       if (dbr != null && dbr.length > 0)
 673       {
 674         for (int d = 0; d < dbr.length; d++)
 675         {
 676           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 677           Object[] sarray = (Object[]) commonDbrefs.get(src);
 678           if (sarray == null)
 679           {
 680             sarray = new Object[2];
 681             sarray[0] = new int[]
 682             { 0 };
 683             sarray[1] = new String[seqs.length];
 684
 685             commonDbrefs.put(src, sarray);
 686           }
 687
 688           if (((String[]) sarray[1])[sq] == null)
 689           {
 690             if (!dbr[d].hasMap()
 691                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 692             {
 693               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 694               ((int[]) sarray[0])[0]++;
 695             }
 696           }
 697         }
 698       }
 699     }
 700     // now create group links for all distinct ID/sequence sets.
 701     boolean addMenu = false; // indicates if there are any group links to give
 702                              // to user
 703     for (int i = 0; i < groupLinks.size(); i++)
 704     {
 705       String link = groupLinks.elementAt(i).toString();
 706       GroupUrlLink urlLink = null;
 707       try
 708       {
 709         urlLink = new GroupUrlLink(link);
 710       } catch (Exception foo)
 711       {
 712         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 713                 + "'", foo);
 714         continue;
 715       }
 716       ;
 717       if (!urlLink.isValid())
 718       {
 719         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 720         continue;
 721       }
 722       final String label = urlLink.getLabel();
 723       boolean usingNames = false;
 724       // Now see which parts of the group apply for this URL
 725       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 726       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 727       String[] seqstr, ids; // input to makeUrl
 728       if (idset != null)
 729       {
 730         int numinput = ((int[]) idset[0])[0];
 731         String[] allids = ((String[]) idset[1]);
 732         seqstr = new String[numinput];
 733         ids = new String[numinput];
 734         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 735         {
 736           if (allids[sq] != null)
 737           {
 738             ids[idcount] = allids[sq];
 739             seqstr[idcount++] = idandseqs[1][sq];
 740           }
 741         }
 742       }
 743       else
 744       {
 745         // just use the id/seq set
 746         seqstr = idandseqs[1];
 747         ids = idandseqs[0];
 748         usingNames = true;
 749       }
 750       // and try and make the groupURL!
 751
 752       Object[] urlset = null;
 753       try
 754       {
 755         urlset = urlLink.makeUrlStubs(ids, seqstr,
 756                 "FromJalview" + System.currentTimeMillis(), false);
 757       } catch (UrlStringTooLongException e)
 758       {
 759       }
 760       if (urlset != null)
 761       {
 762         int type = urlLink.getGroupURLType() & 3;
 763         // System.out.println(urlLink.getGroupURLType()
 764         // +" "+((String[])urlset[3])[0]);
 765         // first two bits ofurlLink type bitfield are sequenceids and sequences
 766         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 767         addshowLink(linkMenus[type], label
 768                 + (((type & 1) == 1) ? ("("
 769                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 770                 urlLink, urlset);
 771         addMenu = true;
 772       }
 773     }
 774     if (addMenu)
 775     {
 776       groupLinksMenu = new JMenu("Group Links");
 777       for (int m = 0; m < linkMenus.length; m++)
 778       {
 779         if (linkMenus[m] != null
 780                 && linkMenus[m].getMenuComponentCount() > 0)
 781         {
 782           groupLinksMenu.add(linkMenus[m]);
 783         }
 784       }
 785
 786       groupMenu.add(groupLinksMenu);
 787     }
 788   }
 789
 790   /**
 791    * add a show URL menu item to the given linkMenu
 792    *
 793    * @param linkMenu
 794    * @param label
 795    *          - menu label string
 796    * @param url
 797    *          - url to open
 798    */
 799   private void addshowLink(JMenu linkMenu, String label, final String url)
 800   {
 801     JMenuItem item = new JMenuItem(label);
 802     item.setToolTipText("open URL: " + url);
 803     item.addActionListener(new java.awt.event.ActionListener()
 804     {
 805       public void actionPerformed(ActionEvent e)
 806       {
 807         new Thread(new Runnable()
 808         {
 809
 810           public void run()
 811           {
 812             showLink(url);
 813           }
 814
 815         }).start();
 816       }
 817     });
 818
 819     linkMenu.add(item);
 820   }
 821
 822   /**
 823    * add a late bound groupURL item to the given linkMenu
 824    *
 825    * @param linkMenu
 826    * @param label
 827    *          - menu label string
 828    * @param urlgenerator
 829    *          GroupURLLink used to generate URL
 830    * @param urlstub
 831    *          Object array returned from the makeUrlStubs function.
 832    */
 833   private void addshowLink(JMenu linkMenu, String label,
 834           final GroupUrlLink urlgenerator, final Object[] urlstub)
 835   {
 836     JMenuItem item = new JMenuItem(label);
 837     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 838             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 839                                                                              // put
 840                                                                              // in
 841                                                                              // info
 842                                                                              // about
 843                                                                              // what
 844                                                                              // is
 845                                                                              // being
 846                                                                              // sent.
 847     item.addActionListener(new java.awt.event.ActionListener()
 848     {
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         new Thread(new Runnable()
 852         {
 853
 854           public void run()
 855           {
 856             try
 857             {
 858               showLink(urlgenerator.constructFrom(urlstub));
 859             } catch (UrlStringTooLongException e)
 860             {
 861             }
 862           }
 863
 864         }).start();
 865       }
 866     });
 867
 868     linkMenu.add(item);
 869   }
 870
 871   /**
 872    * DOCUMENT ME!
 873    *
 874    * @throws Exception
 875    *           DOCUMENT ME!
 876    */
 877   private void jbInit() throws Exception
 878   {
 879     groupMenu.setText("Group");
 880     groupMenu.setText("Selection");
 881     groupName.setText("Name");
 882     groupName.addActionListener(new java.awt.event.ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         groupName_actionPerformed();
 887       }
 888     });
 889     sequenceMenu.setText("Sequence");
 890     sequenceName.setText("Edit Name/Description");
 891     sequenceName.addActionListener(new java.awt.event.ActionListener()
 892     {
 893       public void actionPerformed(ActionEvent e)
 894       {
 895         sequenceName_actionPerformed();
 896       }
 897     });
 898     PIDColour.setFocusPainted(false);
 899     unGroupMenuItem.setText("Remove Group");
 900     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 901     {
 902       public void actionPerformed(ActionEvent e)
 903       {
 904         unGroupMenuItem_actionPerformed();
 905       }
 906     });
 907
 908     outline.setText("Border colour");
 909     outline.addActionListener(new java.awt.event.ActionListener()
 910     {
 911       public void actionPerformed(ActionEvent e)
 912       {
 913         outline_actionPerformed();
 914       }
 915     });
 916     nucleotideMenuItem.setText("Nucleotide");
 917     nucleotideMenuItem.addActionListener(new ActionListener()
 918     {
 919       public void actionPerformed(ActionEvent e)
 920       {
 921         nucleotideMenuItem_actionPerformed();
 922       }
 923     });
 924     colourMenu.setText("Group Colour");
 925     showBoxes.setText("Boxes");
 926     showBoxes.setState(true);
 927     showBoxes.addActionListener(new ActionListener()
 928     {
 929       public void actionPerformed(ActionEvent e)
 930       {
 931         showBoxes_actionPerformed();
 932       }
 933     });
 934     showText.setText("Text");
 935     showText.setState(true);
 936     showText.addActionListener(new ActionListener()
 937     {
 938       public void actionPerformed(ActionEvent e)
 939       {
 940         showText_actionPerformed();
 941       }
 942     });
 943     showColourText.setText("Colour Text");
 944     showColourText.addActionListener(new ActionListener()
 945     {
 946       public void actionPerformed(ActionEvent e)
 947       {
 948         showColourText_actionPerformed();
 949       }
 950     });
 951     displayNonconserved.setText("Show Nonconserved");
 952     displayNonconserved.setState(true);
 953     displayNonconserved.addActionListener(new ActionListener()
 954     {
 955       public void actionPerformed(ActionEvent e)
 956       {
 957         showNonconserved_actionPerformed();
 958       }
 959     });
 960     editMenu.setText("Edit");
 961     cut.setText("Cut");
 962     cut.addActionListener(new ActionListener()
 963     {
 964       public void actionPerformed(ActionEvent e)
 965       {
 966         cut_actionPerformed();
 967       }
 968     });
 969     upperCase.setText("To Upper Case");
 970     upperCase.addActionListener(new ActionListener()
 971     {
 972       public void actionPerformed(ActionEvent e)
 973       {
 974         changeCase(e);
 975       }
 976     });
 977     copy.setText("Copy");
 978     copy.addActionListener(new ActionListener()
 979     {
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         copy_actionPerformed();
 983       }
 984     });
 985     lowerCase.setText("To Lower Case");
 986     lowerCase.addActionListener(new ActionListener()
 987     {
 988       public void actionPerformed(ActionEvent e)
 989       {
 990         changeCase(e);
 991       }
 992     });
 993     toggle.setText("Toggle Case");
 994     toggle.addActionListener(new ActionListener()
 995     {
 996       public void actionPerformed(ActionEvent e)
 997       {
 998         changeCase(e);
 999       }
1000     });
1001     pdbMenu.setText("Associate Structure with Sequence");
1002     pdbFromFile.setText("From File");
1003     pdbFromFile.addActionListener(new ActionListener()
1004     {
1005       public void actionPerformed(ActionEvent e)
1006       {
1007         pdbFromFile_actionPerformed();
1008       }
1009     });
1010     enterPDB.setText("Enter PDB Id");
1011     enterPDB.addActionListener(new ActionListener()
1012     {
1013       public void actionPerformed(ActionEvent e)
1014       {
1015         enterPDB_actionPerformed();
1016       }
1017     });
1018     discoverPDB.setText("Discover PDB ids");
1019     discoverPDB.addActionListener(new ActionListener()
1020     {
1021       public void actionPerformed(ActionEvent e)
1022       {
1023         discoverPDB_actionPerformed();
1024       }
1025     });
1026     outputMenu.setText("Output to Textbox...");
1027     sequenceFeature.setText("Create Sequence Feature");
1028     sequenceFeature.addActionListener(new ActionListener()
1029     {
1030       public void actionPerformed(ActionEvent e)
1031       {
1032         sequenceFeature_actionPerformed();
1033       }
1034     });
1035     textColour.setText("Text Colour");
1036     textColour.addActionListener(new ActionListener()
1037     {
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         textColour_actionPerformed();
1041       }
1042     });
1043     jMenu1.setText("Group");
1044     structureMenu.setText("Structure");
1045     viewStructureMenu.setText("View Structure");
1046     // colStructureMenu.setText("Colour By Structure");
1047     editSequence.setText("Edit Sequence...");
1048     editSequence.addActionListener(new ActionListener()
1049     {
1050       public void actionPerformed(ActionEvent actionEvent)
1051       {
1052         editSequence_actionPerformed(actionEvent);
1053       }
1054     });
1055     /*
1056      * annotationMenuItem.setText("By Annotation");
1057      * annotationMenuItem.addActionListener(new ActionListener() { public void
1058      * actionPerformed(ActionEvent actionEvent) {
1059      * annotationMenuItem_actionPerformed(actionEvent); } });
1060      */
1061
1062     add(groupMenu);
1063
1064     add(sequenceMenu);
1065     this.add(structureMenu);
1066     groupMenu.add(editMenu);
1067     groupMenu.add(outputMenu);
1068     groupMenu.add(sequenceFeature);
1069     groupMenu.add(jMenu1);
1070     sequenceMenu.add(sequenceName);
1071     colourMenu.add(textColour);
1072     colourMenu.add(noColourmenuItem);
1073     colourMenu.add(clustalColour);
1074     colourMenu.add(BLOSUM62Colour);
1075     colourMenu.add(PIDColour);
1076     colourMenu.add(zappoColour);
1077     colourMenu.add(taylorColour);
1078     colourMenu.add(hydrophobicityColour);
1079     colourMenu.add(helixColour);
1080     colourMenu.add(strandColour);
1081     colourMenu.add(turnColour);
1082     colourMenu.add(buriedColour);
1083     colourMenu.add(nucleotideMenuItem);
1084     if (ap.getAlignment().isNucleotide()) {
1085         colourMenu.add(purinePyrimidineColour);
1086     }
1087     // colourMenu.add(covariationColour);
1088     colourMenu.add(userDefinedColour);
1089
1090     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1091     {
1092       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1093               .getUserColourSchemes().keys();
1094
1095       while (userColours.hasMoreElements())
1096       {
1097         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1098         item.addActionListener(new ActionListener()
1099         {
1100           public void actionPerformed(ActionEvent evt)
1101           {
1102             userDefinedColour_actionPerformed(evt);
1103           }
1104         });
1105         colourMenu.add(item);
1106       }
1107     }
1108
1109     colourMenu.addSeparator();
1110     colourMenu.add(abovePIDColour);
1111     colourMenu.add(conservationMenuItem);
1112     // colourMenu.add(annotationMenuItem);
1113     editMenu.add(copy);
1114     editMenu.add(cut);
1115     editMenu.add(editSequence);
1116     editMenu.add(upperCase);
1117     editMenu.add(lowerCase);
1118     editMenu.add(toggle);
1119     pdbMenu.add(pdbFromFile);
1120     pdbMenu.add(enterPDB);
1121     pdbMenu.add(discoverPDB);
1122     jMenu1.add(groupName);
1123     jMenu1.add(unGroupMenuItem);
1124     jMenu1.add(colourMenu);
1125     jMenu1.add(showBoxes);
1126     jMenu1.add(showText);
1127     jMenu1.add(showColourText);
1128     jMenu1.add(outline);
1129     jMenu1.add(displayNonconserved);
1130     structureMenu.add(pdbMenu);
1131     structureMenu.add(viewStructureMenu);
1132     // structureMenu.add(colStructureMenu);
1133     noColourmenuItem.setText("None");
1134     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1135     {
1136       public void actionPerformed(ActionEvent e)
1137       {
1138         noColourmenuItem_actionPerformed();
1139       }
1140     });
1141
1142     clustalColour.setText("Clustalx colours");
1143     clustalColour.addActionListener(new java.awt.event.ActionListener()
1144     {
1145       public void actionPerformed(ActionEvent e)
1146       {
1147         clustalColour_actionPerformed();
1148       }
1149     });
1150     zappoColour.setText("Zappo");
1151     zappoColour.addActionListener(new java.awt.event.ActionListener()
1152     {
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         zappoColour_actionPerformed();
1156       }
1157     });
1158     taylorColour.setText("Taylor");
1159     taylorColour.addActionListener(new java.awt.event.ActionListener()
1160     {
1161       public void actionPerformed(ActionEvent e)
1162       {
1163         taylorColour_actionPerformed();
1164       }
1165     });
1166     hydrophobicityColour.setText("Hydrophobicity");
1167     hydrophobicityColour
1168             .addActionListener(new java.awt.event.ActionListener()
1169             {
1170               public void actionPerformed(ActionEvent e)
1171               {
1172                 hydrophobicityColour_actionPerformed();
1173               }
1174             });
1175     helixColour.setText("Helix propensity");
1176     helixColour.addActionListener(new java.awt.event.ActionListener()
1177     {
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         helixColour_actionPerformed();
1181       }
1182     });
1183     strandColour.setText("Strand propensity");
1184     strandColour.addActionListener(new java.awt.event.ActionListener()
1185     {
1186       public void actionPerformed(ActionEvent e)
1187       {
1188         strandColour_actionPerformed();
1189       }
1190     });
1191     turnColour.setText("Turn propensity");
1192     turnColour.addActionListener(new java.awt.event.ActionListener()
1193     {
1194       public void actionPerformed(ActionEvent e)
1195       {
1196         turnColour_actionPerformed();
1197       }
1198     });
1199     buriedColour.setText("Buried Index");
1200     buriedColour.addActionListener(new java.awt.event.ActionListener()
1201     {
1202       public void actionPerformed(ActionEvent e)
1203       {
1204         buriedColour_actionPerformed();
1205       }
1206     });
1207     abovePIDColour.setText("Above % Identity");
1208     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1209     {
1210       public void actionPerformed(ActionEvent e)
1211       {
1212         abovePIDColour_actionPerformed();
1213       }
1214     });
1215     userDefinedColour.setText("User Defined...");
1216     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1217     {
1218       public void actionPerformed(ActionEvent e)
1219       {
1220         userDefinedColour_actionPerformed(e);
1221       }
1222     });
1223     PIDColour.setText("Percentage Identity");
1224     PIDColour.addActionListener(new java.awt.event.ActionListener()
1225     {
1226       public void actionPerformed(ActionEvent e)
1227       {
1228         PIDColour_actionPerformed();
1229       }
1230     });
1231     BLOSUM62Colour.setText("BLOSUM62");
1232     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1233     {
1234       public void actionPerformed(ActionEvent e)
1235       {
1236         BLOSUM62Colour_actionPerformed();
1237       }
1238     });
1239     purinePyrimidineColour.setText("Purine/Pyrimidine");
1240     purinePyrimidineColour
1241             .addActionListener(new java.awt.event.ActionListener()
1242             {
1243               public void actionPerformed(ActionEvent e)
1244               {
1245                 purinePyrimidineColour_actionPerformed();
1246               }
1247             });
1248     /*
1249      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1250      * public void actionPerformed(ActionEvent e) {
1251      * covariationColour_actionPerformed(); } });
1252      */
1253
1254     conservationMenuItem.setText("Conservation");
1255     conservationMenuItem
1256             .addActionListener(new java.awt.event.ActionListener()
1257             {
1258               public void actionPerformed(ActionEvent e)
1259               {
1260                 conservationMenuItem_actionPerformed();
1261               }
1262             });
1263   }
1264
1265   protected void showNonconserved_actionPerformed()
1266   {
1267     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1268     refresh();
1269   }
1270
1271   /**
1272    * call to refresh view after settings change
1273    */
1274   void refresh()
1275   {
1276     ap.updateAnnotation();
1277     ap.paintAlignment(true);
1278
1279     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1280   }
1281
1282   /**
1283    * DOCUMENT ME!
1284    *
1285    * @param e
1286    *          DOCUMENT ME!
1287    */
1288   protected void clustalColour_actionPerformed()
1289   {
1290     SequenceGroup sg = getGroup();
1291     sg.cs = new ClustalxColourScheme(
1292             sg.getSequences(ap.av.hiddenRepSequences),
1293             ap.av.alignment.getWidth());
1294     refresh();
1295   }
1296
1297   /**
1298    * DOCUMENT ME!
1299    *
1300    * @param e
1301    *          DOCUMENT ME!
1302    */
1303   protected void zappoColour_actionPerformed()
1304   {
1305     getGroup().cs = new ZappoColourScheme();
1306     refresh();
1307   }
1308
1309   /**
1310    * DOCUMENT ME!
1311    *
1312    * @param e
1313    *          DOCUMENT ME!
1314    */
1315   protected void taylorColour_actionPerformed()
1316   {
1317     getGroup().cs = new TaylorColourScheme();
1318     refresh();
1319   }
1320
1321   /**
1322    * DOCUMENT ME!
1323    *
1324    * @param e
1325    *          DOCUMENT ME!
1326    */
1327   protected void hydrophobicityColour_actionPerformed()
1328   {
1329     getGroup().cs = new HydrophobicColourScheme();
1330     refresh();
1331   }
1332
1333   /**
1334    * DOCUMENT ME!
1335    *
1336    * @param e
1337    *          DOCUMENT ME!
1338    */
1339   protected void helixColour_actionPerformed()
1340   {
1341     getGroup().cs = new HelixColourScheme();
1342     refresh();
1343   }
1344
1345   /**
1346    * DOCUMENT ME!
1347    *
1348    * @param e
1349    *          DOCUMENT ME!
1350    */
1351   protected void strandColour_actionPerformed()
1352   {
1353     getGroup().cs = new StrandColourScheme();
1354     refresh();
1355   }
1356
1357   /**
1358    * DOCUMENT ME!
1359    *
1360    * @param e
1361    *          DOCUMENT ME!
1362    */
1363   protected void turnColour_actionPerformed()
1364   {
1365     getGroup().cs = new TurnColourScheme();
1366     refresh();
1367   }
1368
1369   /**
1370    * DOCUMENT ME!
1371    *
1372    * @param e
1373    *          DOCUMENT ME!
1374    */
1375   protected void buriedColour_actionPerformed()
1376   {
1377     getGroup().cs = new BuriedColourScheme();
1378     refresh();
1379   }
1380
1381   /**
1382    * DOCUMENT ME!
1383    *
1384    * @param e
1385    *          DOCUMENT ME!
1386    */
1387   public void nucleotideMenuItem_actionPerformed()
1388   {
1389     getGroup().cs = new NucleotideColourScheme();
1390     refresh();
1391   }
1392
1393   protected void purinePyrimidineColour_actionPerformed()
1394   {
1395     getGroup().cs = new PurinePyrimidineColourScheme();
1396     refresh();
1397   }
1398
1399   /*
1400    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1401    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1402    */
1403   /**
1404    * DOCUMENT ME!
1405    *
1406    * @param e
1407    *          DOCUMENT ME!
1408    */
1409   protected void abovePIDColour_actionPerformed()
1410   {
1411     SequenceGroup sg = getGroup();
1412     if (sg.cs == null)
1413     {
1414       return;
1415     }
1416
1417     if (abovePIDColour.isSelected())
1418     {
1419       sg.cs.setConsensus(AAFrequency.calculate(
1420               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1421               sg.getEndRes() + 1));
1422
1423       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1424               .getName());
1425
1426       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1427
1428       SliderPanel.showPIDSlider();
1429     }
1430     else
1431     // remove PIDColouring
1432     {
1433       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1434     }
1435
1436     refresh();
1437   }
1438
1439   /**
1440    * DOCUMENT ME!
1441    *
1442    * @param e
1443    *          DOCUMENT ME!
1444    */
1445   protected void userDefinedColour_actionPerformed(ActionEvent e)
1446   {
1447     SequenceGroup sg = getGroup();
1448
1449     if (e.getActionCommand().equals("User Defined..."))
1450     {
1451       new UserDefinedColours(ap, sg);
1452     }
1453     else
1454     {
1455       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1456               .getUserColourSchemes().get(e.getActionCommand());
1457
1458       sg.cs = udc;
1459     }
1460     refresh();
1461   }
1462
1463   /**
1464    * DOCUMENT ME!
1465    *
1466    * @param e
1467    *          DOCUMENT ME!
1468    */
1469   protected void PIDColour_actionPerformed()
1470   {
1471     SequenceGroup sg = getGroup();
1472     sg.cs = new PIDColourScheme();
1473     sg.cs.setConsensus(AAFrequency.calculate(
1474             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1475             sg.getEndRes() + 1));
1476     refresh();
1477   }
1478
1479   /**
1480    * DOCUMENT ME!
1481    *
1482    * @param e
1483    *          DOCUMENT ME!
1484    */
1485   protected void BLOSUM62Colour_actionPerformed()
1486   {
1487     SequenceGroup sg = getGroup();
1488
1489     sg.cs = new Blosum62ColourScheme();
1490
1491     sg.cs.setConsensus(AAFrequency.calculate(
1492             sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1493             sg.getEndRes() + 1));
1494
1495     refresh();
1496   }
1497
1498   /**
1499    * DOCUMENT ME!
1500    *
1501    * @param e
1502    *          DOCUMENT ME!
1503    */
1504   protected void noColourmenuItem_actionPerformed()
1505   {
1506     getGroup().cs = null;
1507     refresh();
1508   }
1509
1510   /**
1511    * DOCUMENT ME!
1512    *
1513    * @param e
1514    *          DOCUMENT ME!
1515    */
1516   protected void conservationMenuItem_actionPerformed()
1517   {
1518     SequenceGroup sg = getGroup();
1519     if (sg.cs == null)
1520     {
1521       return;
1522     }
1523
1524     if (conservationMenuItem.isSelected())
1525     {
1526       Conservation c = new Conservation("Group",
1527               ResidueProperties.propHash, 3,
1528               sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1529               sg.getEndRes() + 1);
1530
1531       c.calculate();
1532       c.verdict(false, ap.av.ConsPercGaps);
1533
1534       sg.cs.setConservation(c);
1535
1536       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1537       SliderPanel.showConservationSlider();
1538     }
1539     else
1540     // remove ConservationColouring
1541     {
1542       sg.cs.setConservation(null);
1543     }
1544
1545     refresh();
1546   }
1547
1548   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1549   {
1550     SequenceGroup sg = getGroup();
1551     if (sg == null)
1552     {
1553       return;
1554     }
1555
1556     AnnotationColourGradient acg = new AnnotationColourGradient(
1557             sequence.getAnnotation()[0], null,
1558             AnnotationColourGradient.NO_THRESHOLD);
1559
1560     acg.predefinedColours = true;
1561     sg.cs = acg;
1562
1563     refresh();
1564   }
1565
1566   /**
1567    * DOCUMENT ME!
1568    *
1569    * @param e
1570    *          DOCUMENT ME!
1571    */
1572   protected void groupName_actionPerformed()
1573   {
1574
1575     SequenceGroup sg = getGroup();
1576     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1577             sg.getDescription(), "       Group Name ",
1578             "Group Description ", "Edit Group Name/Description",
1579             ap.alignFrame);
1580
1581     if (!dialog.accept)
1582     {
1583       return;
1584     }
1585
1586     sg.setName(dialog.getName());
1587     sg.setDescription(dialog.getDescription());
1588     refresh();
1589   }
1590
1591   /**
1592    * Get selection group - adding it to the alignment if necessary.
1593    *
1594    * @return sequence group to operate on
1595    */
1596   SequenceGroup getGroup()
1597   {
1598     SequenceGroup sg = ap.av.getSelectionGroup();
1599     // this method won't add a new group if it already exists
1600     if (sg != null)
1601     {
1602       ap.av.alignment.addGroup(sg);
1603     }
1604
1605     return sg;
1606   }
1607
1608   /**
1609    * DOCUMENT ME!
1610    *
1611    * @param e
1612    *          DOCUMENT ME!
1613    */
1614   void sequenceName_actionPerformed()
1615   {
1616     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1617             sequence.getDescription(), "       Sequence Name ",
1618             "Sequence Description ", "Edit Sequence Name/Description",
1619             ap.alignFrame);
1620
1621     if (!dialog.accept)
1622     {
1623       return;
1624     }
1625
1626     if (dialog.getName() != null)
1627     {
1628       if (dialog.getName().indexOf(" ") > -1)
1629       {
1630         JOptionPane.showMessageDialog(ap,
1631                 "Spaces have been converted to \"_\"",
1632                 "No spaces allowed in Sequence Name",
1633                 JOptionPane.WARNING_MESSAGE);
1634       }
1635
1636       sequence.setName(dialog.getName().replace(' ', '_'));
1637       ap.paintAlignment(false);
1638     }
1639
1640     sequence.setDescription(dialog.getDescription());
1641
1642     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1643             .getSequences());
1644
1645   }
1646
1647   /**
1648    * DOCUMENT ME!
1649    *
1650    * @param e
1651    *          DOCUMENT ME!
1652    */
1653   void unGroupMenuItem_actionPerformed()
1654   {
1655     SequenceGroup sg = ap.av.getSelectionGroup();
1656     ap.av.alignment.deleteGroup(sg);
1657     ap.av.setSelectionGroup(null);
1658     refresh();
1659   }
1660
1661   /**
1662    * DOCUMENT ME!
1663    *
1664    * @param e
1665    *          DOCUMENT ME!
1666    */
1667   protected void outline_actionPerformed()
1668   {
1669     SequenceGroup sg = getGroup();
1670     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1671             Color.BLUE);
1672
1673     if (col != null)
1674     {
1675       sg.setOutlineColour(col);
1676     }
1677
1678     refresh();
1679   }
1680
1681   /**
1682    * DOCUMENT ME!
1683    *
1684    * @param e
1685    *          DOCUMENT ME!
1686    */
1687   public void showBoxes_actionPerformed()
1688   {
1689     getGroup().setDisplayBoxes(showBoxes.isSelected());
1690     refresh();
1691   }
1692
1693   /**
1694    * DOCUMENT ME!
1695    *
1696    * @param e
1697    *          DOCUMENT ME!
1698    */
1699   public void showText_actionPerformed()
1700   {
1701     getGroup().setDisplayText(showText.isSelected());
1702     refresh();
1703   }
1704
1705   /**
1706    * DOCUMENT ME!
1707    *
1708    * @param e
1709    *          DOCUMENT ME!
1710    */
1711   public void showColourText_actionPerformed()
1712   {
1713     getGroup().setColourText(showColourText.isSelected());
1714     refresh();
1715   }
1716
1717   public void showLink(String url)
1718   {
1719     try
1720     {
1721       jalview.util.BrowserLauncher.openURL(url);
1722     } catch (Exception ex)
1723     {
1724       JOptionPane
1725               .showInternalMessageDialog(
1726                       Desktop.desktop,
1727                       "Unixers: Couldn't find default web browser."
1728                               + "\nAdd the full path to your browser in Preferences.",
1729                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1730
1731       ex.printStackTrace();
1732     }
1733   }
1734
1735   void hideSequences(boolean representGroup)
1736   {
1737     SequenceGroup sg = ap.av.getSelectionGroup();
1738     if (sg == null || sg.getSize() < 1)
1739     {
1740       ap.av.hideSequence(new SequenceI[]
1741       { sequence });
1742       return;
1743     }
1744
1745     ap.av.setSelectionGroup(null);
1746
1747     if (representGroup)
1748     {
1749       ap.av.hideRepSequences(sequence, sg);
1750
1751       return;
1752     }
1753
1754     int gsize = sg.getSize();
1755     SequenceI[] hseqs;
1756
1757     hseqs = new SequenceI[gsize];
1758
1759     int index = 0;
1760     for (int i = 0; i < gsize; i++)
1761     {
1762       hseqs[index++] = sg.getSequenceAt(i);
1763     }
1764
1765     ap.av.hideSequence(hseqs);
1766     // refresh(); TODO: ? needed ?
1767     ap.av.sendSelection();
1768   }
1769
1770   public void copy_actionPerformed()
1771   {
1772     ap.alignFrame.copy_actionPerformed(null);
1773   }
1774
1775   public void cut_actionPerformed()
1776   {
1777     ap.alignFrame.cut_actionPerformed(null);
1778   }
1779
1780   void changeCase(ActionEvent e)
1781   {
1782     Object source = e.getSource();
1783     SequenceGroup sg = ap.av.getSelectionGroup();
1784
1785     if (sg != null)
1786     {
1787       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1788               sg.getEndRes() + 1);
1789
1790       String description;
1791       int caseChange;
1792
1793       if (source == toggle)
1794       {
1795         description = "Toggle Case";
1796         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1797       }
1798       else if (source == upperCase)
1799       {
1800         description = "To Upper Case";
1801         caseChange = ChangeCaseCommand.TO_UPPER;
1802       }
1803       else
1804       {
1805         description = "To Lower Case";
1806         caseChange = ChangeCaseCommand.TO_LOWER;
1807       }
1808
1809       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1810               sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1811               caseChange);
1812
1813       ap.alignFrame.addHistoryItem(caseCommand);
1814
1815       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1816               .getSequences());
1817
1818     }
1819   }
1820
1821   public void outputText_actionPerformed(ActionEvent e)
1822   {
1823     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1824     cap.setForInput(null);
1825     Desktop.addInternalFrame(cap,
1826             "Alignment output - " + e.getActionCommand(), 600, 500);
1827
1828     String[] omitHidden = null;
1829
1830     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1831     // or we simply trust the user wants
1832     // wysiwig behaviour
1833     SequenceGroup sg = ap.av.getSelectionGroup();
1834     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1835     omitHidden = ap.av.getViewAsString(true);
1836     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1837     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1838     if (nala != null)
1839     {
1840       for (int i = 0; i < nala.length; i++)
1841       {
1842         AlignmentAnnotation na = nala[i];
1843         oal.addAnnotation(na);
1844       }
1845     }
1846     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1847             oal, omitHidden, csel, sg));
1848     oal = null;
1849   }
1850
1851   public void pdbFromFile_actionPerformed()
1852   {
1853     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1854             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1855     chooser.setFileView(new jalview.io.JalviewFileView());
1856     chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1857     chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1858
1859     int value = chooser.showOpenDialog(null);
1860
1861     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1862     {
1863       String choice = chooser.getSelectedFile().getPath();
1864       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1865       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1866     }
1867
1868   }
1869
1870   public void enterPDB_actionPerformed()
1871   {
1872     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1873             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1874
1875     if (id != null && id.length() > 0)
1876     {
1877       PDBEntry entry = new PDBEntry();
1878       entry.setId(id.toUpperCase());
1879       sequence.getDatasetSequence().addPDBId(entry);
1880     }
1881   }
1882
1883   public void discoverPDB_actionPerformed()
1884   {
1885
1886     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
1887     { sequence }
1888             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1889     Thread discpdb = new Thread(new Runnable()
1890     {
1891       public void run()
1892       {
1893
1894         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1895                 .fetchDBRefs(false);
1896       }
1897
1898     });
1899     discpdb.start();
1900   }
1901
1902   public void sequenceFeature_actionPerformed()
1903   {
1904     SequenceGroup sg = ap.av.getSelectionGroup();
1905     if (sg == null)
1906     {
1907       return;
1908     }
1909
1910     int rsize = 0, gSize = sg.getSize();
1911     SequenceI[] rseqs, seqs = new SequenceI[gSize];
1912     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1913
1914     for (int i = 0; i < gSize; i++)
1915     {
1916       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1917       int end = sg.findEndRes(sg.getSequenceAt(i));
1918       if (start <= end)
1919       {
1920         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1921         features[rsize] = new SequenceFeature(null, null, null, start, end,
1922                 "Jalview");
1923         rsize++;
1924       }
1925     }
1926     rseqs = new SequenceI[rsize];
1927     tfeatures = new SequenceFeature[rsize];
1928     System.arraycopy(seqs, 0, rseqs, 0, rsize);
1929     System.arraycopy(features, 0, tfeatures, 0, rsize);
1930     features = tfeatures;
1931     seqs = rseqs;
1932     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1933             features, true, ap))
1934     {
1935       ap.alignFrame.setShowSeqFeatures(true);
1936       ap.highlightSearchResults(null);
1937     }
1938   }
1939
1940   public void textColour_actionPerformed()
1941   {
1942     SequenceGroup sg = getGroup();
1943     if (sg != null)
1944     {
1945       new TextColourChooser().chooseColour(ap, sg);
1946     }
1947   }
1948
1949   public void colourByStructure(String pdbid)
1950   {
1951     Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
1952                     sequence, pdbid);
1953
1954     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1955             "Coloured by " + pdbid, anots);
1956
1957     ap.av.alignment.addAnnotation(an);
1958     an.createSequenceMapping(sequence, 0, true);
1959     // an.adjustForAlignment();
1960     ap.av.alignment.setAnnotationIndex(an, 0);
1961
1962     ap.adjustAnnotationHeight();
1963
1964     sequence.addAlignmentAnnotation(an);
1965
1966   }
1967
1968   public void editSequence_actionPerformed(ActionEvent actionEvent)
1969   {
1970     SequenceGroup sg = ap.av.getSelectionGroup();
1971
1972     if (sg != null)
1973     {
1974       if (sequence == null)
1975         sequence = (Sequence) sg.getSequenceAt(0);
1976
1977       EditNameDialog dialog = new EditNameDialog(
1978               sequence.getSequenceAsString(sg.getStartRes(),
1979                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
1980               "Edit Sequence", ap.alignFrame);
1981
1982       if (dialog.accept)
1983       {
1984         EditCommand editCommand = new EditCommand("Edit Sequences",
1985                 EditCommand.REPLACE, dialog.getName().replace(' ',
1986                         ap.av.getGapCharacter()),
1987                 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1988                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1989
1990         ap.alignFrame.addHistoryItem(editCommand);
1991
1992         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1993                 .getSequences());
1994       }
1995     }
1996   }
1997
1998 }