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 import javax.xml.parsers.ParserConfigurationException;
  27
  28 import org.xml.sax.SAXException;
  29
  30 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  31 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  32 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  33 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  34
  35 import MCview.*;
  36 import jalview.analysis.*;
  37 import jalview.commands.*;
  38 import jalview.datamodel.*;
  39 import jalview.io.*;
  40 import jalview.schemes.*;
  41 import jalview.util.GroupUrlLink;
  42 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  43 import jalview.util.UrlLink;
  44
  45 /**
  46  * DOCUMENT ME!
  47  *
  48  * @author $author$
  49  * @version $Revision: 1.118 $
  50  */
  51 public class PopupMenu extends JPopupMenu
  52 {
  53   JMenu groupMenu = new JMenu();
  54
  55   JMenuItem groupName = new JMenuItem();
  56
  57   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  62
  63   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  64
  65   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  66
  67   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  70
  71   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  72
  73   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  74
  75   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  76
  77   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  78
  79   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  80
  81   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  82   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  83
  84   // protected JRadioButtonMenuItem covariationColour = new
  85   // JRadioButtonMenuItem();
  86
  87   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  88
  89   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  90
  91   AlignmentPanel ap;
  92
  93   JMenu sequenceMenu = new JMenu();
  94
  95   JMenuItem sequenceName = new JMenuItem();
  96
  97   SequenceI sequence;
  98
  99   JMenuItem unGroupMenuItem = new JMenuItem();
 100
 101   JMenuItem outline = new JMenuItem();
 102
 103   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 104
 105   JMenu colourMenu = new JMenu();
 106
 107   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 108
 109   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 110
 111   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 112
 113   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 114
 115   JMenu editMenu = new JMenu();
 116
 117   JMenuItem cut = new JMenuItem();
 118
 119   JMenuItem copy = new JMenuItem();
 120
 121   JMenuItem upperCase = new JMenuItem();
 122
 123   JMenuItem lowerCase = new JMenuItem();
 124
 125   JMenuItem toggle = new JMenuItem();
 126
 127   JMenu pdbMenu = new JMenu();
 128
 129   JMenuItem pdbFromFile = new JMenuItem();
 130
 131   JMenuItem enterPDB = new JMenuItem();
 132
 133   JMenuItem discoverPDB = new JMenuItem();
 134
 135   JMenu outputMenu = new JMenu();
 136
 137   JMenuItem sequenceFeature = new JMenuItem();
 138
 139   JMenuItem textColour = new JMenuItem();
 140
 141   JMenu jMenu1 = new JMenu();
 142
 143   JMenu structureMenu = new JMenu();
 144
 145   JMenu viewStructureMenu = new JMenu();
 146
 147   // JMenu colStructureMenu = new JMenu();
 148   JMenuItem editSequence = new JMenuItem();
 149
 150   // JMenuItem annotationMenuItem = new JMenuItem();
 151
 152   JMenu groupLinksMenu;
 153
 154   /**
 155    * Creates a new PopupMenu object.
 156    *
 157    * @param ap
 158    *          DOCUMENT ME!
 159    * @param seq
 160    *          DOCUMENT ME!
 161    */
 162   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 163   {
 164     this(ap, seq, links, null);
 165   }
 166
 167   /**
 168    *
 169    * @param ap
 170    * @param seq
 171    * @param links
 172    * @param groupLinks
 173    */
 174   public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
 175           Vector groupLinks)
 176   {
 177     // /////////////////////////////////////////////////////////
 178     // If this is activated from the sequence panel, the user may want to
 179     // edit or annotate a particular residue. Therefore display the residue menu
 180     //
 181     // If from the IDPanel, we must display the sequence menu
 182     // ////////////////////////////////////////////////////////
 183     this.ap = ap;
 184     sequence = seq;
 185
 186     ButtonGroup colours = new ButtonGroup();
 187     colours.add(noColourmenuItem);
 188     colours.add(clustalColour);
 189     colours.add(zappoColour);
 190     colours.add(taylorColour);
 191     colours.add(hydrophobicityColour);
 192     colours.add(helixColour);
 193     colours.add(strandColour);
 194     colours.add(turnColour);
 195     colours.add(buriedColour);
 196     colours.add(abovePIDColour);
 197     colours.add(userDefinedColour);
 198     colours.add(PIDColour);
 199     colours.add(BLOSUM62Colour);
 200     colours.add(purinePyrimidineColour);
 201     colours.add(RNAInteractionColour);
 202     // colours.add(covariationColour);
 203
 204     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 205     {
 206       JMenuItem item = new JMenuItem(
 207               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 208
 209       item.addActionListener(new java.awt.event.ActionListener()
 210       {
 211         public void actionPerformed(ActionEvent e)
 212         {
 213           outputText_actionPerformed(e);
 214         }
 215       });
 216
 217       outputMenu.add(item);
 218     }
 219
 220     try
 221     {
 222       jbInit();
 223     } catch (Exception e)
 224     {
 225       e.printStackTrace();
 226     }
 227
 228     JMenuItem menuItem;
 229     if (seq != null)
 230     {
 231       sequenceMenu.setText(sequence.getName());
 232
 233       if (seq.getDatasetSequence().getPDBId() != null
 234               && seq.getDatasetSequence().getPDBId().size() > 0)
 235       {
 236         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 237                 .elements();
 238
 239         while (e.hasMoreElements())
 240         {
 241           final PDBEntry pdb = (PDBEntry) e.nextElement();
 242
 243           menuItem = new JMenuItem();
 244           menuItem.setText(pdb.getId());
 245           menuItem.addActionListener(new java.awt.event.ActionListener()
 246           {
 247             public void actionPerformed(ActionEvent e)
 248             {
 249                 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
 250               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
 251               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 252             }
 253
 254           });
 255           viewStructureMenu.add(menuItem);
 256
 257           /*
 258            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 259            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 260            * public void actionPerformed(ActionEvent e) {
 261            * colourByStructure(pdb.getId()); } });
 262            * colStructureMenu.add(menuItem);
 263            */
 264         }
 265       }
 266       else
 267       {
 268         if (ap.av.getAlignment().isNucleotide() == false)
 269         {
 270         structureMenu.remove(viewStructureMenu);
 271         }
 272         // structureMenu.remove(colStructureMenu);
 273       }
 274
 275       if (ap.av.getAlignment().isNucleotide() == true)
 276       {
 277         AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
 278         for (int i = 0; i < aa.length; i++)
 279         {
 280           if (aa[i].getRNAStruc() != null)
 281           {
 282             final String rnastruc = aa[i].getRNAStruc();
 283             final String structureLine=aa[i].label;
 284             menuItem = new JMenuItem();
 285             menuItem.setText("2D RNA "+structureLine);
 286             menuItem.addActionListener(new java.awt.event.ActionListener()
 287
 288             {
 289               public void actionPerformed(ActionEvent e)
 290               {
 291                         //System.out.println("1:"+structureLine);
 292                         System.out.println("1:sname"+seq.getName());
 293                         System.out.println("2:seq"+seq);
 294
 295                         //System.out.println("3:"+seq.getSequenceAsString());
 296                         System.out.println("3:strucseq"+rnastruc);
 297                         //System.out.println("4:struc"+seq.getRNA());
 298                         System.out.println("5:name"+seq.getName());
 299                         System.out.println("6:ap"+ap);
 300                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 301                             .getName(), ap);
 302                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 303                         System.out.println("end");
 304               }
 305             });
 306             viewStructureMenu.add(menuItem);
 307           }
 308         }
 309
 310         // SequenceFeatures[] test = seq.getSequenceFeatures();
 311
 312         if (seq.getAnnotation() != null)
 313         {
 314           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 315           for (int i = 0; i < seqAnno.length; i++)
 316           {
 317             if (seqAnno[i].getRNAStruc() != null)
 318             {
 319               final String rnastruc = seqAnno[i].getRNAStruc();
 320
 321            // TODO: make rnastrucF a bit more nice
 322               menuItem = new JMenuItem();
 323               menuItem.setText("2D RNA - "+seq.getName());
 324               menuItem.addActionListener(new java.awt.event.ActionListener()
 325               {
 326                 public void actionPerformed(ActionEvent e)
 327                 {
 328                   // TODO: VARNA does'nt print gaps in the sequence
 329
 330                   //new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 331                   new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
 332                           .getName(), ap);
 333                 }
 334               });
 335               viewStructureMenu.add(menuItem);
 336             }
 337           }
 338         }
 339
 340
 341       }
 342
 343       menuItem = new JMenuItem("Hide Sequences");
 344       menuItem.addActionListener(new java.awt.event.ActionListener()
 345       {
 346         public void actionPerformed(ActionEvent e)
 347         {
 348           hideSequences(false);
 349         }
 350       });
 351       add(menuItem);
 352
 353       if (ap.av.getSelectionGroup() != null
 354               && ap.av.getSelectionGroup().getSize() > 1)
 355       {
 356         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 357         menuItem.addActionListener(new java.awt.event.ActionListener()
 358         {
 359           public void actionPerformed(ActionEvent e)
 360           {
 361             hideSequences(true);
 362           }
 363         });
 364         sequenceMenu.add(menuItem);
 365       }
 366
 367       if (ap.av.hasHiddenRows())
 368       {
 369         final int index = ap.av.getAlignment().findIndex(seq);
 370
 371         if (ap.av.adjustForHiddenSeqs(index)
 372                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 373         {
 374           menuItem = new JMenuItem("Reveal Sequences");
 375           menuItem.addActionListener(new ActionListener()
 376           {
 377             public void actionPerformed(ActionEvent e)
 378             {
 379               ap.av.showSequence(index);
 380               if (ap.overviewPanel != null)
 381               {
 382                 ap.overviewPanel.updateOverviewImage();
 383               }
 384             }
 385           });
 386           add(menuItem);
 387         }
 388       }
 389     }
 390     // for the case when no sequences are even visible
 391     if (ap.av.hasHiddenRows()) {
 392       {
 393         menuItem = new JMenuItem("Reveal All");
 394         menuItem.addActionListener(new ActionListener()
 395         {
 396           public void actionPerformed(ActionEvent e)
 397           {
 398             ap.av.showAllHiddenSeqs();
 399             if (ap.overviewPanel != null)
 400             {
 401               ap.overviewPanel.updateOverviewImage();
 402             }
 403           }
 404         });
 405
 406         add(menuItem);
 407       }
 408
 409     }
 410
 411     SequenceGroup sg = ap.av.getSelectionGroup();
 412
 413     if (sg != null&& sg.getSize()>0)
 414     {
 415       groupName.setText("Name: "+sg.getName());
 416       groupName.setText("Edit name and description of current group.");
 417
 418       if (sg.cs instanceof ZappoColourScheme)
 419       {
 420         zappoColour.setSelected(true);
 421       }
 422       else if (sg.cs instanceof TaylorColourScheme)
 423       {
 424         taylorColour.setSelected(true);
 425       }
 426       else if (sg.cs instanceof PIDColourScheme)
 427       {
 428         PIDColour.setSelected(true);
 429       }
 430       else if (sg.cs instanceof Blosum62ColourScheme)
 431       {
 432         BLOSUM62Colour.setSelected(true);
 433       }
 434       else if (sg.cs instanceof UserColourScheme)
 435       {
 436         userDefinedColour.setSelected(true);
 437       }
 438       else if (sg.cs instanceof HydrophobicColourScheme)
 439       {
 440         hydrophobicityColour.setSelected(true);
 441       }
 442       else if (sg.cs instanceof HelixColourScheme)
 443       {
 444         helixColour.setSelected(true);
 445       }
 446       else if (sg.cs instanceof StrandColourScheme)
 447       {
 448         strandColour.setSelected(true);
 449       }
 450       else if (sg.cs instanceof TurnColourScheme)
 451       {
 452         turnColour.setSelected(true);
 453       }
 454       else if (sg.cs instanceof BuriedColourScheme)
 455       {
 456         buriedColour.setSelected(true);
 457       }
 458       else if (sg.cs instanceof ClustalxColourScheme)
 459       {
 460         clustalColour.setSelected(true);
 461       }
 462       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 463       {
 464         purinePyrimidineColour.setSelected(true);
 465       }
 466
 467       else if (sg.cs instanceof RNAInteractionColourScheme)
 468       {
 469         RNAInteractionColour.setSelected(true);
 470       }
 471       /*
 472        * else if (sg.cs instanceof CovariationColourScheme) {
 473        * covariationColour.setSelected(true); }
 474        */
 475       else
 476       {
 477         noColourmenuItem.setSelected(true);
 478       }
 479
 480       if (sg.cs != null && sg.cs.conservationApplied())
 481       {
 482         conservationMenuItem.setSelected(true);
 483       }
 484       displayNonconserved.setSelected(sg.getShowNonconserved());
 485       showText.setSelected(sg.getDisplayText());
 486       showColourText.setSelected(sg.getColourText());
 487       showBoxes.setSelected(sg.getDisplayBoxes());
 488       // add any groupURLs to the groupURL submenu and make it visible
 489       if (groupLinks != null && groupLinks.size() > 0)
 490       {
 491         buildGroupURLMenu(sg, groupLinks);
 492       }
 493       // Add a 'show all structures' for the current selection
 494       Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
 495       SequenceI sqass=null;
 496       for (SequenceI sq: ap.av.getSequenceSelection())
 497       {
 498         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
 499         if (pes!=null) {
 500           for (PDBEntry pe: pes)
 501           {
 502             pdbe.put(pe.getId(),  pe);
 503             if (sqass==null)
 504             {
 505               sqass = sq;
 506             }
 507           }
 508         }
 509       }
 510       if (pdbe.size()>0)
 511       {
 512         final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
 513         final JMenuItem gpdbview;
 514         if (pdbe.size()==1)
 515         {
 516           structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
 517         } else {
 518           structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
 519         }
 520         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 521         gpdbview.addActionListener(new ActionListener()
 522         {
 523
 524           @Override
 525           public void actionPerformed(ActionEvent e)
 526           {
 527             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 528           }
 529         });
 530       }
 531     }
 532     else
 533     {
 534       groupMenu.setVisible(false);
 535       editMenu.setVisible(false);
 536     }
 537
 538     if (!ap.av.getAlignment().getGroups().contains(sg))
 539     {
 540       unGroupMenuItem.setVisible(false);
 541     }
 542
 543     if (seq == null)
 544     {
 545       sequenceMenu.setVisible(false);
 546       structureMenu.setVisible(false);
 547     }
 548
 549     if (links != null && links.size() > 0)
 550     {
 551
 552       JMenu linkMenu = new JMenu("Link");
 553       Vector linkset = new Vector();
 554       for (int i = 0; i < links.size(); i++)
 555       {
 556         String link = links.elementAt(i).toString();
 557         UrlLink urlLink = null;
 558         try
 559         {
 560           urlLink = new UrlLink(link);
 561         } catch (Exception foo)
 562         {
 563           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 564                   + "'", foo);
 565           continue;
 566         }
 567         ;
 568         if (!urlLink.isValid())
 569         {
 570           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 571           continue;
 572         }
 573         final String label = urlLink.getLabel();
 574         if (seq!=null && urlLink.isDynamic())
 575         {
 576
 577           // collect matching db-refs
 578           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 579                   seq.getDBRef(), new String[]
 580                   { urlLink.getTarget() });
 581           // collect id string too
 582           String id = seq.getName();
 583           String descr = seq.getDescription();
 584           if (descr != null && descr.length() < 1)
 585           {
 586             descr = null;
 587           }
 588
 589           if (dbr != null)
 590           {
 591             for (int r = 0; r < dbr.length; r++)
 592             {
 593               if (id != null && dbr[r].getAccessionId().equals(id))
 594               {
 595                 // suppress duplicate link creation for the bare sequence ID
 596                 // string with this link
 597                 id = null;
 598               }
 599               // create Bare ID link for this RUL
 600               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 601                       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],
 610                             urls[u + 1]);
 611                   }
 612                 }
 613               }
 614             }
 615           }
 616           if (id != null)
 617           {
 618             // create Bare ID link for this RUL
 619             String[] urls = urlLink.makeUrls(id, true);
 620             if (urls != null)
 621             {
 622               for (int u = 0; u < urls.length; u += 2)
 623               {
 624                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 625                 {
 626                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 627                   addshowLink(linkMenu, label, urls[u + 1]);
 628                 }
 629               }
 630             }
 631           }
 632           // Create urls from description but only for URL links which are regex
 633           // links
 634           if (descr != null && urlLink.getRegexReplace() != null)
 635           {
 636             // create link for this URL from description where regex matches
 637             String[] urls = urlLink.makeUrls(descr, true);
 638             if (urls != null)
 639             {
 640               for (int u = 0; u < urls.length; u += 2)
 641               {
 642                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 643                 {
 644                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 645                   addshowLink(linkMenu, label, urls[u + 1]);
 646                 }
 647               }
 648             }
 649           }
 650         }
 651         else
 652         {
 653           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 654           {
 655             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 656             // Add a non-dynamic link
 657             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 658           }
 659         }
 660       }
 661       if (sequence != null)
 662       {
 663         sequenceMenu.add(linkMenu);
 664       }
 665       else
 666       {
 667         add(linkMenu);
 668       }
 669     }
 670   }
 671
 672   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 673   {
 674
 675     // TODO: usability: thread off the generation of group url content so root
 676     // menu appears asap
 677     // sequence only URLs
 678     // ID/regex match URLs
 679     groupLinksMenu = new JMenu("Group Link");
 680     JMenu[] linkMenus = new JMenu[]
 681     { null, new JMenu("IDS"), new JMenu("Sequences"),
 682         new JMenu("IDS and Sequences") }; // three types of url that might be
 683                                           // created.
 684     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 685     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 686     Hashtable commonDbrefs = new Hashtable();
 687     for (int sq = 0; sq < seqs.length; sq++)
 688     {
 689
 690       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 691               .findPosition(sg.getEndRes());
 692       // just collect ids from dataset sequence
 693       // TODO: check if IDs collected from selecton group intersects with the
 694       // current selection, too
 695       SequenceI sqi = seqs[sq];
 696       while (sqi.getDatasetSequence() != null)
 697       {
 698         sqi = sqi.getDatasetSequence();
 699       }
 700       DBRefEntry[] dbr = sqi.getDBRef();
 701       if (dbr != null && dbr.length > 0)
 702       {
 703         for (int d = 0; d < dbr.length; d++)
 704         {
 705           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 706           Object[] sarray = (Object[]) commonDbrefs.get(src);
 707           if (sarray == null)
 708           {
 709             sarray = new Object[2];
 710             sarray[0] = new int[]
 711             { 0 };
 712             sarray[1] = new String[seqs.length];
 713
 714             commonDbrefs.put(src, sarray);
 715           }
 716
 717           if (((String[]) sarray[1])[sq] == null)
 718           {
 719             if (!dbr[d].hasMap()
 720                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 721             {
 722               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 723               ((int[]) sarray[0])[0]++;
 724             }
 725           }
 726         }
 727       }
 728     }
 729     // now create group links for all distinct ID/sequence sets.
 730     boolean addMenu = false; // indicates if there are any group links to give
 731                              // to user
 732     for (int i = 0; i < groupLinks.size(); i++)
 733     {
 734       String link = groupLinks.elementAt(i).toString();
 735       GroupUrlLink urlLink = null;
 736       try
 737       {
 738         urlLink = new GroupUrlLink(link);
 739       } catch (Exception foo)
 740       {
 741         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 742                 + "'", foo);
 743         continue;
 744       }
 745       ;
 746       if (!urlLink.isValid())
 747       {
 748         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 749         continue;
 750       }
 751       final String label = urlLink.getLabel();
 752       boolean usingNames = false;
 753       // Now see which parts of the group apply for this URL
 754       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 755       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 756       String[] seqstr, ids; // input to makeUrl
 757       if (idset != null)
 758       {
 759         int numinput = ((int[]) idset[0])[0];
 760         String[] allids = ((String[]) idset[1]);
 761         seqstr = new String[numinput];
 762         ids = new String[numinput];
 763         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 764         {
 765           if (allids[sq] != null)
 766           {
 767             ids[idcount] = allids[sq];
 768             seqstr[idcount++] = idandseqs[1][sq];
 769           }
 770         }
 771       }
 772       else
 773       {
 774         // just use the id/seq set
 775         seqstr = idandseqs[1];
 776         ids = idandseqs[0];
 777         usingNames = true;
 778       }
 779       // and try and make the groupURL!
 780
 781       Object[] urlset = null;
 782       try
 783       {
 784         urlset = urlLink.makeUrlStubs(ids, seqstr,
 785                 "FromJalview" + System.currentTimeMillis(), false);
 786       } catch (UrlStringTooLongException e)
 787       {
 788       }
 789       if (urlset != null)
 790       {
 791         int type = urlLink.getGroupURLType() & 3;
 792         // System.out.println(urlLink.getGroupURLType()
 793         // +" "+((String[])urlset[3])[0]);
 794         // first two bits ofurlLink type bitfield are sequenceids and sequences
 795         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 796         addshowLink(linkMenus[type], label
 797                 + (((type & 1) == 1) ? ("("
 798                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 799                 urlLink, urlset);
 800         addMenu = true;
 801       }
 802     }
 803     if (addMenu)
 804     {
 805       groupLinksMenu = new JMenu("Group Links");
 806       for (int m = 0; m < linkMenus.length; m++)
 807       {
 808         if (linkMenus[m] != null
 809                 && linkMenus[m].getMenuComponentCount() > 0)
 810         {
 811           groupLinksMenu.add(linkMenus[m]);
 812         }
 813       }
 814
 815       groupMenu.add(groupLinksMenu);
 816     }
 817   }
 818
 819   /**
 820    * add a show URL menu item to the given linkMenu
 821    *
 822    * @param linkMenu
 823    * @param label
 824    *          - menu label string
 825    * @param url
 826    *          - url to open
 827    */
 828   private void addshowLink(JMenu linkMenu, String label, final String url)
 829   {
 830     JMenuItem item = new JMenuItem(label);
 831     item.setToolTipText("open URL: " + url);
 832     item.addActionListener(new java.awt.event.ActionListener()
 833     {
 834       public void actionPerformed(ActionEvent e)
 835       {
 836         new Thread(new Runnable()
 837         {
 838
 839           public void run()
 840           {
 841             showLink(url);
 842           }
 843
 844         }).start();
 845       }
 846     });
 847
 848     linkMenu.add(item);
 849   }
 850
 851   /**
 852    * add a late bound groupURL item to the given linkMenu
 853    *
 854    * @param linkMenu
 855    * @param label
 856    *          - menu label string
 857    * @param urlgenerator
 858    *          GroupURLLink used to generate URL
 859    * @param urlstub
 860    *          Object array returned from the makeUrlStubs function.
 861    */
 862   private void addshowLink(JMenu linkMenu, String label,
 863           final GroupUrlLink urlgenerator, final Object[] urlstub)
 864   {
 865     JMenuItem item = new JMenuItem(label);
 866     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 867             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 868                                                                              // put
 869                                                                              // in
 870                                                                              // info
 871                                                                              // about
 872                                                                              // what
 873                                                                              // is
 874                                                                              // being
 875                                                                              // sent.
 876     item.addActionListener(new java.awt.event.ActionListener()
 877     {
 878       public void actionPerformed(ActionEvent e)
 879       {
 880         new Thread(new Runnable()
 881         {
 882
 883           public void run()
 884           {
 885             try
 886             {
 887               showLink(urlgenerator.constructFrom(urlstub));
 888             } catch (UrlStringTooLongException e)
 889             {
 890             }
 891           }
 892
 893         }).start();
 894       }
 895     });
 896
 897     linkMenu.add(item);
 898   }
 899
 900   /**
 901    * DOCUMENT ME!
 902    *
 903    * @throws Exception
 904    *           DOCUMENT ME!
 905    */
 906   private void jbInit() throws Exception
 907   {
 908     groupMenu.setText("Group");
 909     groupMenu.setText("Selection");
 910     groupName.setText("Name");
 911     groupName.addActionListener(new java.awt.event.ActionListener()
 912     {
 913       public void actionPerformed(ActionEvent e)
 914       {
 915         groupName_actionPerformed();
 916       }
 917     });
 918     sequenceMenu.setText("Sequence");
 919     sequenceName.setText("Edit Name/Description");
 920     sequenceName.addActionListener(new java.awt.event.ActionListener()
 921     {
 922       public void actionPerformed(ActionEvent e)
 923       {
 924         sequenceName_actionPerformed();
 925       }
 926     });
 927     PIDColour.setFocusPainted(false);
 928     unGroupMenuItem.setText("Remove Group");
 929     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 930     {
 931       public void actionPerformed(ActionEvent e)
 932       {
 933         unGroupMenuItem_actionPerformed();
 934       }
 935     });
 936
 937     outline.setText("Border colour");
 938     outline.addActionListener(new java.awt.event.ActionListener()
 939     {
 940       public void actionPerformed(ActionEvent e)
 941       {
 942         outline_actionPerformed();
 943       }
 944     });
 945     nucleotideMenuItem.setText("Nucleotide");
 946     nucleotideMenuItem.addActionListener(new ActionListener()
 947     {
 948       public void actionPerformed(ActionEvent e)
 949       {
 950         nucleotideMenuItem_actionPerformed();
 951       }
 952     });
 953     colourMenu.setText("Group Colour");
 954     showBoxes.setText("Boxes");
 955     showBoxes.setState(true);
 956     showBoxes.addActionListener(new ActionListener()
 957     {
 958       public void actionPerformed(ActionEvent e)
 959       {
 960         showBoxes_actionPerformed();
 961       }
 962     });
 963     showText.setText("Text");
 964     showText.setState(true);
 965     showText.addActionListener(new ActionListener()
 966     {
 967       public void actionPerformed(ActionEvent e)
 968       {
 969         showText_actionPerformed();
 970       }
 971     });
 972     showColourText.setText("Colour Text");
 973     showColourText.addActionListener(new ActionListener()
 974     {
 975       public void actionPerformed(ActionEvent e)
 976       {
 977         showColourText_actionPerformed();
 978       }
 979     });
 980     displayNonconserved.setText("Show Nonconserved");
 981     displayNonconserved.setState(true);
 982     displayNonconserved.addActionListener(new ActionListener()
 983     {
 984       public void actionPerformed(ActionEvent e)
 985       {
 986         showNonconserved_actionPerformed();
 987       }
 988     });
 989     editMenu.setText("Edit");
 990     cut.setText("Cut");
 991     cut.addActionListener(new ActionListener()
 992     {
 993       public void actionPerformed(ActionEvent e)
 994       {
 995         cut_actionPerformed();
 996       }
 997     });
 998     upperCase.setText("To Upper Case");
 999     upperCase.addActionListener(new ActionListener()
1000     {
1001       public void actionPerformed(ActionEvent e)
1002       {
1003         changeCase(e);
1004       }
1005     });
1006     copy.setText("Copy");
1007     copy.addActionListener(new ActionListener()
1008     {
1009       public void actionPerformed(ActionEvent e)
1010       {
1011         copy_actionPerformed();
1012       }
1013     });
1014     lowerCase.setText("To Lower Case");
1015     lowerCase.addActionListener(new ActionListener()
1016     {
1017       public void actionPerformed(ActionEvent e)
1018       {
1019         changeCase(e);
1020       }
1021     });
1022     toggle.setText("Toggle Case");
1023     toggle.addActionListener(new ActionListener()
1024     {
1025       public void actionPerformed(ActionEvent e)
1026       {
1027         changeCase(e);
1028       }
1029     });
1030     pdbMenu.setText("Associate Structure with Sequence");
1031     pdbFromFile.setText("From File");
1032     pdbFromFile.addActionListener(new ActionListener()
1033     {
1034       public void actionPerformed(ActionEvent e)
1035       {
1036         try {
1037                         pdbFromFile_actionPerformed();
1038                 } catch (ExceptionFileFormatOrSyntax e1) {
1039                         // TODO Auto-generated catch block
1040                         e1.printStackTrace();
1041                 } catch (ParserConfigurationException e1) {
1042                         // TODO Auto-generated catch block
1043                         e1.printStackTrace();
1044                 } catch (SAXException e1) {
1045                         // TODO Auto-generated catch block
1046                         e1.printStackTrace();
1047                 } catch (ExceptionPermissionDenied e1) {
1048                         // TODO Auto-generated catch block
1049                         e1.printStackTrace();
1050                 } catch (ExceptionLoadingFailed e1) {
1051                         // TODO Auto-generated catch block
1052                         e1.printStackTrace();
1053                 } catch (InterruptedException e1) {
1054                         // TODO Auto-generated catch block
1055                         e1.printStackTrace();
1056                 } catch (ExceptionUnmatchedClosingParentheses e1) {
1057                         // TODO Auto-generated catch block
1058                         e1.printStackTrace();
1059                 }
1060       }
1061     });
1062     enterPDB.setText("Enter PDB Id");
1063     enterPDB.addActionListener(new ActionListener()
1064     {
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         enterPDB_actionPerformed();
1068       }
1069     });
1070     discoverPDB.setText("Discover PDB ids");
1071     discoverPDB.addActionListener(new ActionListener()
1072     {
1073       public void actionPerformed(ActionEvent e)
1074       {
1075         discoverPDB_actionPerformed();
1076       }
1077     });
1078     outputMenu.setText("Output to Textbox...");
1079     sequenceFeature.setText("Create Sequence Feature");
1080     sequenceFeature.addActionListener(new ActionListener()
1081     {
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         sequenceFeature_actionPerformed();
1085       }
1086     });
1087     textColour.setText("Text Colour");
1088     textColour.addActionListener(new ActionListener()
1089     {
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         textColour_actionPerformed();
1093       }
1094     });
1095     jMenu1.setText("Group");
1096     structureMenu.setText("Structure");
1097     viewStructureMenu.setText("View Structure");
1098     // colStructureMenu.setText("Colour By Structure");
1099     editSequence.setText("Edit Sequence...");
1100     editSequence.addActionListener(new ActionListener()
1101     {
1102       public void actionPerformed(ActionEvent actionEvent)
1103       {
1104         editSequence_actionPerformed(actionEvent);
1105       }
1106     });
1107     /*
1108      * annotationMenuItem.setText("By Annotation");
1109      * annotationMenuItem.addActionListener(new ActionListener() { public void
1110      * actionPerformed(ActionEvent actionEvent) {
1111      * annotationMenuItem_actionPerformed(actionEvent); } });
1112      */
1113
1114     add(groupMenu);
1115
1116     add(sequenceMenu);
1117     this.add(structureMenu);
1118     groupMenu.add(editMenu);
1119     groupMenu.add(outputMenu);
1120     groupMenu.add(sequenceFeature);
1121     groupMenu.add(jMenu1);
1122     sequenceMenu.add(sequenceName);
1123     colourMenu.add(textColour);
1124     colourMenu.add(noColourmenuItem);
1125     colourMenu.add(clustalColour);
1126     colourMenu.add(BLOSUM62Colour);
1127     colourMenu.add(PIDColour);
1128     colourMenu.add(zappoColour);
1129     colourMenu.add(taylorColour);
1130     colourMenu.add(hydrophobicityColour);
1131     colourMenu.add(helixColour);
1132     colourMenu.add(strandColour);
1133     colourMenu.add(turnColour);
1134     colourMenu.add(buriedColour);
1135     colourMenu.add(nucleotideMenuItem);
1136     colourMenu.add(RNAInteractionColour);
1137     if (ap.getAlignment().isNucleotide()) {
1138         colourMenu.add(purinePyrimidineColour);
1139     }
1140     // colourMenu.add(covariationColour);
1141     colourMenu.add(userDefinedColour);
1142
1143     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1144     {
1145       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1146               .getUserColourSchemes().keys();
1147
1148       while (userColours.hasMoreElements())
1149       {
1150         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1151         item.addActionListener(new ActionListener()
1152         {
1153           public void actionPerformed(ActionEvent evt)
1154           {
1155             userDefinedColour_actionPerformed(evt);
1156           }
1157         });
1158         colourMenu.add(item);
1159       }
1160     }
1161
1162     colourMenu.addSeparator();
1163     colourMenu.add(abovePIDColour);
1164     colourMenu.add(conservationMenuItem);
1165     // colourMenu.add(annotationMenuItem);
1166     editMenu.add(copy);
1167     editMenu.add(cut);
1168     editMenu.add(editSequence);
1169     editMenu.add(upperCase);
1170     editMenu.add(lowerCase);
1171     editMenu.add(toggle);
1172     pdbMenu.add(pdbFromFile);
1173     pdbMenu.add(enterPDB);
1174     pdbMenu.add(discoverPDB);
1175     jMenu1.add(groupName);
1176     jMenu1.add(unGroupMenuItem);
1177     jMenu1.add(colourMenu);
1178     jMenu1.add(showBoxes);
1179     jMenu1.add(showText);
1180     jMenu1.add(showColourText);
1181     jMenu1.add(outline);
1182     jMenu1.add(displayNonconserved);
1183     structureMenu.add(pdbMenu);
1184     structureMenu.add(viewStructureMenu);
1185     // structureMenu.add(colStructureMenu);
1186     noColourmenuItem.setText("None");
1187     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1188     {
1189       public void actionPerformed(ActionEvent e)
1190       {
1191         noColourmenuItem_actionPerformed();
1192       }
1193     });
1194
1195     clustalColour.setText("Clustalx colours");
1196     clustalColour.addActionListener(new java.awt.event.ActionListener()
1197     {
1198       public void actionPerformed(ActionEvent e)
1199       {
1200         clustalColour_actionPerformed();
1201       }
1202     });
1203     zappoColour.setText("Zappo");
1204     zappoColour.addActionListener(new java.awt.event.ActionListener()
1205     {
1206       public void actionPerformed(ActionEvent e)
1207       {
1208         zappoColour_actionPerformed();
1209       }
1210     });
1211     taylorColour.setText("Taylor");
1212     taylorColour.addActionListener(new java.awt.event.ActionListener()
1213     {
1214       public void actionPerformed(ActionEvent e)
1215       {
1216         taylorColour_actionPerformed();
1217       }
1218     });
1219     hydrophobicityColour.setText("Hydrophobicity");
1220     hydrophobicityColour
1221             .addActionListener(new java.awt.event.ActionListener()
1222             {
1223               public void actionPerformed(ActionEvent e)
1224               {
1225                 hydrophobicityColour_actionPerformed();
1226               }
1227             });
1228     helixColour.setText("Helix propensity");
1229     helixColour.addActionListener(new java.awt.event.ActionListener()
1230     {
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         helixColour_actionPerformed();
1234       }
1235     });
1236     strandColour.setText("Strand propensity");
1237     strandColour.addActionListener(new java.awt.event.ActionListener()
1238     {
1239       public void actionPerformed(ActionEvent e)
1240       {
1241         strandColour_actionPerformed();
1242       }
1243     });
1244     turnColour.setText("Turn propensity");
1245     turnColour.addActionListener(new java.awt.event.ActionListener()
1246     {
1247       public void actionPerformed(ActionEvent e)
1248       {
1249         turnColour_actionPerformed();
1250       }
1251     });
1252     buriedColour.setText("Buried Index");
1253     buriedColour.addActionListener(new java.awt.event.ActionListener()
1254     {
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         buriedColour_actionPerformed();
1258       }
1259     });
1260     abovePIDColour.setText("Above % Identity");
1261     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1262     {
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         abovePIDColour_actionPerformed();
1266       }
1267     });
1268     userDefinedColour.setText("User Defined...");
1269     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1270     {
1271       public void actionPerformed(ActionEvent e)
1272       {
1273         userDefinedColour_actionPerformed(e);
1274       }
1275     });
1276     PIDColour.setText("Percentage Identity");
1277     PIDColour.addActionListener(new java.awt.event.ActionListener()
1278     {
1279       public void actionPerformed(ActionEvent e)
1280       {
1281         PIDColour_actionPerformed();
1282       }
1283     });
1284     BLOSUM62Colour.setText("BLOSUM62");
1285     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1286     {
1287       public void actionPerformed(ActionEvent e)
1288       {
1289         BLOSUM62Colour_actionPerformed();
1290       }
1291     });
1292     purinePyrimidineColour.setText("Purine/Pyrimidine");
1293     purinePyrimidineColour
1294             .addActionListener(new java.awt.event.ActionListener()
1295             {
1296               public void actionPerformed(ActionEvent e)
1297               {
1298                 purinePyrimidineColour_actionPerformed();
1299               }
1300             });
1301
1302     RNAInteractionColour.setText("RNA Interaction type");
1303     RNAInteractionColour
1304             .addActionListener(new java.awt.event.ActionListener()
1305             {
1306               public void actionPerformed(ActionEvent e)
1307               {
1308                 RNAInteractionColour_actionPerformed();
1309               }
1310             });
1311     /*
1312      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1313      * public void actionPerformed(ActionEvent e) {
1314      * covariationColour_actionPerformed(); } });
1315      */
1316
1317     conservationMenuItem.setText("Conservation");
1318     conservationMenuItem
1319             .addActionListener(new java.awt.event.ActionListener()
1320             {
1321               public void actionPerformed(ActionEvent e)
1322               {
1323                 conservationMenuItem_actionPerformed();
1324               }
1325             });
1326   }
1327
1328   protected void showNonconserved_actionPerformed()
1329   {
1330     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1331     refresh();
1332   }
1333
1334   /**
1335    * call to refresh view after settings change
1336    */
1337   void refresh()
1338   {
1339     ap.updateAnnotation();
1340     ap.paintAlignment(true);
1341
1342     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1343   }
1344
1345   /**
1346    * DOCUMENT ME!
1347    *
1348    * @param e
1349    *          DOCUMENT ME!
1350    */
1351   protected void clustalColour_actionPerformed()
1352   {
1353     SequenceGroup sg = getGroup();
1354     sg.cs = new ClustalxColourScheme(
1355             sg,ap.av.getHiddenRepSequences());
1356     refresh();
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   protected void zappoColour_actionPerformed()
1366   {
1367     getGroup().cs = new ZappoColourScheme();
1368     refresh();
1369   }
1370
1371   /**
1372    * DOCUMENT ME!
1373    *
1374    * @param e
1375    *          DOCUMENT ME!
1376    */
1377   protected void taylorColour_actionPerformed()
1378   {
1379     getGroup().cs = new TaylorColourScheme();
1380     refresh();
1381   }
1382
1383   /**
1384    * DOCUMENT ME!
1385    *
1386    * @param e
1387    *          DOCUMENT ME!
1388    */
1389   protected void hydrophobicityColour_actionPerformed()
1390   {
1391     getGroup().cs = new HydrophobicColourScheme();
1392     refresh();
1393   }
1394
1395   /**
1396    * DOCUMENT ME!
1397    *
1398    * @param e
1399    *          DOCUMENT ME!
1400    */
1401   protected void helixColour_actionPerformed()
1402   {
1403     getGroup().cs = new HelixColourScheme();
1404     refresh();
1405   }
1406
1407   /**
1408    * DOCUMENT ME!
1409    *
1410    * @param e
1411    *          DOCUMENT ME!
1412    */
1413   protected void strandColour_actionPerformed()
1414   {
1415     getGroup().cs = new StrandColourScheme();
1416     refresh();
1417   }
1418
1419   /**
1420    * DOCUMENT ME!
1421    *
1422    * @param e
1423    *          DOCUMENT ME!
1424    */
1425   protected void turnColour_actionPerformed()
1426   {
1427     getGroup().cs = new TurnColourScheme();
1428     refresh();
1429   }
1430
1431   /**
1432    * DOCUMENT ME!
1433    *
1434    * @param e
1435    *          DOCUMENT ME!
1436    */
1437   protected void buriedColour_actionPerformed()
1438   {
1439     getGroup().cs = new BuriedColourScheme();
1440     refresh();
1441   }
1442
1443   /**
1444    * DOCUMENT ME!
1445    *
1446    * @param e
1447    *          DOCUMENT ME!
1448    */
1449   public void nucleotideMenuItem_actionPerformed()
1450   {
1451     getGroup().cs = new NucleotideColourScheme();
1452     refresh();
1453   }
1454
1455   protected void purinePyrimidineColour_actionPerformed()
1456   {
1457     getGroup().cs = new PurinePyrimidineColourScheme();
1458     refresh();
1459   }
1460
1461   protected void RNAInteractionColour_actionPerformed()
1462   {
1463     getGroup().cs = new RNAInteractionColourScheme();
1464     refresh();
1465   }
1466   /*
1467    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1468    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1469    */
1470   /**
1471    * DOCUMENT ME!
1472    *
1473    * @param e
1474    *          DOCUMENT ME!
1475    */
1476   protected void abovePIDColour_actionPerformed()
1477   {
1478     SequenceGroup sg = getGroup();
1479     if (sg.cs == null)
1480     {
1481       return;
1482     }
1483
1484     if (abovePIDColour.isSelected())
1485     {
1486       sg.cs.setConsensus(AAFrequency.calculate(
1487               sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1488               sg.getEndRes() + 1));
1489
1490       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1491               .getName());
1492
1493       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1494
1495       SliderPanel.showPIDSlider();
1496     }
1497     else
1498     // remove PIDColouring
1499     {
1500       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1501     }
1502
1503     refresh();
1504   }
1505
1506   /**
1507    * DOCUMENT ME!
1508    *
1509    * @param e
1510    *          DOCUMENT ME!
1511    */
1512   protected void userDefinedColour_actionPerformed(ActionEvent e)
1513   {
1514     SequenceGroup sg = getGroup();
1515
1516     if (e.getActionCommand().equals("User Defined..."))
1517     {
1518       new UserDefinedColours(ap, sg);
1519     }
1520     else
1521     {
1522       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1523               .getUserColourSchemes().get(e.getActionCommand());
1524
1525       sg.cs = udc;
1526     }
1527     refresh();
1528   }
1529
1530   /**
1531    * DOCUMENT ME!
1532    *
1533    * @param e
1534    *          DOCUMENT ME!
1535    */
1536   protected void PIDColour_actionPerformed()
1537   {
1538     SequenceGroup sg = getGroup();
1539     sg.cs = new PIDColourScheme();
1540     sg.cs.setConsensus(AAFrequency.calculate(
1541             sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1542             sg.getEndRes() + 1));
1543     refresh();
1544   }
1545
1546   /**
1547    * DOCUMENT ME!
1548    *
1549    * @param e
1550    *          DOCUMENT ME!
1551    */
1552   protected void BLOSUM62Colour_actionPerformed()
1553   {
1554     SequenceGroup sg = getGroup();
1555
1556     sg.cs = new Blosum62ColourScheme();
1557
1558     sg.cs.setConsensus(AAFrequency.calculate(
1559             sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1560             sg.getEndRes() + 1));
1561
1562     refresh();
1563   }
1564
1565   /**
1566    * DOCUMENT ME!
1567    *
1568    * @param e
1569    *          DOCUMENT ME!
1570    */
1571   protected void noColourmenuItem_actionPerformed()
1572   {
1573     getGroup().cs = null;
1574     refresh();
1575   }
1576
1577   /**
1578    * DOCUMENT ME!
1579    *
1580    * @param e
1581    *          DOCUMENT ME!
1582    */
1583   protected void conservationMenuItem_actionPerformed()
1584   {
1585     SequenceGroup sg = getGroup();
1586     if (sg.cs == null)
1587     {
1588       return;
1589     }
1590
1591     if (conservationMenuItem.isSelected())
1592     {
1593       Conservation c = new Conservation("Group",
1594               ResidueProperties.propHash, 3,
1595               sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1596               sg.getEndRes() + 1);
1597
1598       c.calculate();
1599       c.verdict(false, ap.av.getConsPercGaps());
1600
1601       sg.cs.setConservation(c);
1602
1603       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1604       SliderPanel.showConservationSlider();
1605     }
1606     else
1607     // remove ConservationColouring
1608     {
1609       sg.cs.setConservation(null);
1610     }
1611
1612     refresh();
1613   }
1614
1615   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1616   {
1617     SequenceGroup sg = getGroup();
1618     if (sg == null)
1619     {
1620       return;
1621     }
1622
1623     AnnotationColourGradient acg = new AnnotationColourGradient(
1624             sequence.getAnnotation()[0], null,
1625             AnnotationColourGradient.NO_THRESHOLD);
1626
1627     acg.predefinedColours = true;
1628     sg.cs = acg;
1629
1630     refresh();
1631   }
1632
1633   /**
1634    * DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   protected void groupName_actionPerformed()
1640   {
1641
1642     SequenceGroup sg = getGroup();
1643     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1644             sg.getDescription(), "       Group Name ",
1645             "Group Description ", "Edit Group Name/Description",
1646             ap.alignFrame);
1647
1648     if (!dialog.accept)
1649     {
1650       return;
1651     }
1652
1653     sg.setName(dialog.getName());
1654     sg.setDescription(dialog.getDescription());
1655     refresh();
1656   }
1657
1658   /**
1659    * Get selection group - adding it to the alignment if necessary.
1660    *
1661    * @return sequence group to operate on
1662    */
1663   SequenceGroup getGroup()
1664   {
1665     SequenceGroup sg = ap.av.getSelectionGroup();
1666     // this method won't add a new group if it already exists
1667     if (sg != null)
1668     {
1669       ap.av.getAlignment().addGroup(sg);
1670     }
1671
1672     return sg;
1673   }
1674
1675   /**
1676    * DOCUMENT ME!
1677    *
1678    * @param e
1679    *          DOCUMENT ME!
1680    */
1681   void sequenceName_actionPerformed()
1682   {
1683     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1684             sequence.getDescription(), "       Sequence Name ",
1685             "Sequence Description ", "Edit Sequence Name/Description",
1686             ap.alignFrame);
1687
1688     if (!dialog.accept)
1689     {
1690       return;
1691     }
1692
1693     if (dialog.getName() != null)
1694     {
1695       if (dialog.getName().indexOf(" ") > -1)
1696       {
1697         JOptionPane.showMessageDialog(ap,
1698                 "Spaces have been converted to \"_\"",
1699                 "No spaces allowed in Sequence Name",
1700                 JOptionPane.WARNING_MESSAGE);
1701       }
1702
1703       sequence.setName(dialog.getName().replace(' ', '_'));
1704       ap.paintAlignment(false);
1705     }
1706
1707     sequence.setDescription(dialog.getDescription());
1708
1709     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1710             .getSequences());
1711
1712   }
1713
1714   /**
1715    * DOCUMENT ME!
1716    *
1717    * @param e
1718    *          DOCUMENT ME!
1719    */
1720   void unGroupMenuItem_actionPerformed()
1721   {
1722     SequenceGroup sg = ap.av.getSelectionGroup();
1723     ap.av.getAlignment().deleteGroup(sg);
1724     ap.av.setSelectionGroup(null);
1725     refresh();
1726   }
1727
1728   /**
1729    * DOCUMENT ME!
1730    *
1731    * @param e
1732    *          DOCUMENT ME!
1733    */
1734   protected void outline_actionPerformed()
1735   {
1736     SequenceGroup sg = getGroup();
1737     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1738             Color.BLUE);
1739
1740     if (col != null)
1741     {
1742       sg.setOutlineColour(col);
1743     }
1744
1745     refresh();
1746   }
1747
1748   /**
1749    * DOCUMENT ME!
1750    *
1751    * @param e
1752    *          DOCUMENT ME!
1753    */
1754   public void showBoxes_actionPerformed()
1755   {
1756     getGroup().setDisplayBoxes(showBoxes.isSelected());
1757     refresh();
1758   }
1759
1760   /**
1761    * DOCUMENT ME!
1762    *
1763    * @param e
1764    *          DOCUMENT ME!
1765    */
1766   public void showText_actionPerformed()
1767   {
1768     getGroup().setDisplayText(showText.isSelected());
1769     refresh();
1770   }
1771
1772   /**
1773    * DOCUMENT ME!
1774    *
1775    * @param e
1776    *          DOCUMENT ME!
1777    */
1778   public void showColourText_actionPerformed()
1779   {
1780     getGroup().setColourText(showColourText.isSelected());
1781     refresh();
1782   }
1783
1784   public void showLink(String url)
1785   {
1786     try
1787     {
1788       jalview.util.BrowserLauncher.openURL(url);
1789     } catch (Exception ex)
1790     {
1791       JOptionPane
1792               .showInternalMessageDialog(
1793                       Desktop.desktop,
1794                       "Unixers: Couldn't find default web browser."
1795                               + "\nAdd the full path to your browser in Preferences.",
1796                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1797
1798       ex.printStackTrace();
1799     }
1800   }
1801
1802   void hideSequences(boolean representGroup)
1803   {
1804     SequenceGroup sg = ap.av.getSelectionGroup();
1805     if (sg == null || sg.getSize() < 1)
1806     {
1807       ap.av.hideSequence(new SequenceI[]
1808       { sequence });
1809       return;
1810     }
1811
1812     ap.av.setSelectionGroup(null);
1813
1814     if (representGroup)
1815     {
1816       ap.av.hideRepSequences(sequence, sg);
1817
1818       return;
1819     }
1820
1821     int gsize = sg.getSize();
1822     SequenceI[] hseqs;
1823
1824     hseqs = new SequenceI[gsize];
1825
1826     int index = 0;
1827     for (int i = 0; i < gsize; i++)
1828     {
1829       hseqs[index++] = sg.getSequenceAt(i);
1830     }
1831
1832     ap.av.hideSequence(hseqs);
1833     // refresh(); TODO: ? needed ?
1834     ap.av.sendSelection();
1835   }
1836
1837   public void copy_actionPerformed()
1838   {
1839     ap.alignFrame.copy_actionPerformed(null);
1840   }
1841
1842   public void cut_actionPerformed()
1843   {
1844     ap.alignFrame.cut_actionPerformed(null);
1845   }
1846
1847   void changeCase(ActionEvent e)
1848   {
1849     Object source = e.getSource();
1850     SequenceGroup sg = ap.av.getSelectionGroup();
1851
1852     if (sg != null)
1853     {
1854       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1855               sg.getEndRes() + 1);
1856
1857       String description;
1858       int caseChange;
1859
1860       if (source == toggle)
1861       {
1862         description = "Toggle Case";
1863         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1864       }
1865       else if (source == upperCase)
1866       {
1867         description = "To Upper Case";
1868         caseChange = ChangeCaseCommand.TO_UPPER;
1869       }
1870       else
1871       {
1872         description = "To Lower Case";
1873         caseChange = ChangeCaseCommand.TO_LOWER;
1874       }
1875
1876       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1877               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
1878               caseChange);
1879
1880       ap.alignFrame.addHistoryItem(caseCommand);
1881
1882       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1883               .getSequences());
1884
1885     }
1886   }
1887
1888   public void outputText_actionPerformed(ActionEvent e)
1889   {
1890     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1891     cap.setForInput(null);
1892     Desktop.addInternalFrame(cap,
1893             "Alignment output - " + e.getActionCommand(), 600, 500);
1894
1895     String[] omitHidden = null;
1896
1897     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1898     // or we simply trust the user wants
1899     // wysiwig behaviour
1900     SequenceGroup sg = ap.av.getSelectionGroup();
1901     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1902     omitHidden = ap.av.getViewAsString(true);
1903     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1904     AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation();
1905     if (nala != null)
1906     {
1907       for (int i = 0; i < nala.length; i++)
1908       {
1909         AlignmentAnnotation na = nala[i];
1910         oal.addAnnotation(na);
1911       }
1912     }
1913     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1914             oal, omitHidden, csel, sg));
1915     oal = null;
1916   }
1917
1918   public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
1919   {
1920     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1921             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1922     chooser.setFileView(new jalview.io.JalviewFileView());
1923     chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1924     chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1925
1926     int value = chooser.showOpenDialog(null);
1927
1928     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1929     {
1930       String choice = chooser.getSelectedFile().getPath();
1931       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1932       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1933     }
1934
1935   }
1936
1937   public void enterPDB_actionPerformed()
1938   {
1939     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1940             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1941
1942     if (id != null && id.length() > 0)
1943     {
1944       PDBEntry entry = new PDBEntry();
1945       entry.setId(id.toUpperCase());
1946       sequence.getDatasetSequence().addPDBId(entry);
1947     }
1948   }
1949
1950   public void discoverPDB_actionPerformed()
1951   {
1952
1953     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
1954     { sequence }
1955             : ap.av.getSequenceSelection());
1956     Thread discpdb = new Thread(new Runnable()
1957     {
1958       public void run()
1959       {
1960
1961         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1962                 .fetchDBRefs(false);
1963       }
1964
1965     });
1966     discpdb.start();
1967   }
1968
1969   public void sequenceFeature_actionPerformed()
1970   {
1971     SequenceGroup sg = ap.av.getSelectionGroup();
1972     if (sg == null)
1973     {
1974       return;
1975     }
1976
1977     int rsize = 0, gSize = sg.getSize();
1978     SequenceI[] rseqs, seqs = new SequenceI[gSize];
1979     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1980
1981     for (int i = 0; i < gSize; i++)
1982     {
1983       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1984       int end = sg.findEndRes(sg.getSequenceAt(i));
1985       if (start <= end)
1986       {
1987         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1988         features[rsize] = new SequenceFeature(null, null, null, start, end,
1989                 "Jalview");
1990         rsize++;
1991       }
1992     }
1993     rseqs = new SequenceI[rsize];
1994     tfeatures = new SequenceFeature[rsize];
1995     System.arraycopy(seqs, 0, rseqs, 0, rsize);
1996     System.arraycopy(features, 0, tfeatures, 0, rsize);
1997     features = tfeatures;
1998     seqs = rseqs;
1999     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2000             features, true, ap))
2001     {
2002       ap.alignFrame.setShowSeqFeatures(true);
2003       ap.highlightSearchResults(null);
2004     }
2005   }
2006
2007   public void textColour_actionPerformed()
2008   {
2009     SequenceGroup sg = getGroup();
2010     if (sg != null)
2011     {
2012       new TextColourChooser().chooseColour(ap, sg);
2013     }
2014   }
2015
2016   public void colourByStructure(String pdbid)
2017   {
2018     Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
2019                     sequence, pdbid);
2020
2021     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2022             "Coloured by " + pdbid, anots);
2023
2024     ap.av.getAlignment().addAnnotation(an);
2025     an.createSequenceMapping(sequence, 0, true);
2026     // an.adjustForAlignment();
2027     ap.av.getAlignment().setAnnotationIndex(an, 0);
2028
2029     ap.adjustAnnotationHeight();
2030
2031     sequence.addAlignmentAnnotation(an);
2032
2033   }
2034
2035   public void editSequence_actionPerformed(ActionEvent actionEvent)
2036   {
2037     SequenceGroup sg = ap.av.getSelectionGroup();
2038
2039     if (sg != null)
2040     {
2041       if (sequence == null)
2042         sequence = (Sequence) sg.getSequenceAt(0);
2043
2044       EditNameDialog dialog = new EditNameDialog(
2045               sequence.getSequenceAsString(sg.getStartRes(),
2046                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2047               "Edit Sequence", ap.alignFrame);
2048
2049       if (dialog.accept)
2050       {
2051         EditCommand editCommand = new EditCommand("Edit Sequences",
2052                 EditCommand.REPLACE, dialog.getName().replace(' ',
2053                         ap.av.getGapCharacter()),
2054                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2055                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2056
2057         ap.alignFrame.addHistoryItem(editCommand);
2058
2059         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2060                 .getSequences());
2061       }
2062     }
2063   }
2064
2065 }