src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24
  25 import javax.swing.*;
  26 import javax.xml.parsers.ParserConfigurationException;
  27
  28 import org.xml.sax.SAXException;
  29
  30 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  31 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  32 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  33 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  34
  35 import jalview.analysis.*;
  36 import jalview.commands.*;
  37 import jalview.datamodel.*;
  38 import jalview.io.*;
  39 import jalview.schemes.*;
  40 import jalview.util.GroupUrlLink;
  41 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  42 import jalview.util.UrlLink;
  43
  44 /**
  45  * DOCUMENT ME!
  46  *
  47  * @author $author$
  48  * @version $Revision: 1.118 $
  49  */
  50 public class PopupMenu extends JPopupMenu
  51 {
  52   JMenu groupMenu = new JMenu();
  53
  54   JMenuItem groupName = new JMenuItem();
  55
  56   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  65
  66   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  71
  72   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  73
  74   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  75
  76   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  77
  78   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  79
  80   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  81   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  82
  83   // protected JRadioButtonMenuItem covariationColour = new
  84   // JRadioButtonMenuItem();
  85
  86   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  87
  88   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  89
  90   AlignmentPanel ap;
  91
  92   JMenu sequenceMenu = new JMenu();
  93
  94   JMenuItem sequenceName = new JMenuItem();
  95
  96   JMenuItem sequenceDetails = new JMenuItem();
  97
  98   JMenuItem sequenceSelDetails = new JMenuItem();
  99
 100   SequenceI sequence;
 101
 102   JMenuItem unGroupMenuItem = new JMenuItem();
 103
 104   JMenuItem outline = new JMenuItem();
 105
 106   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 107
 108   JMenu colourMenu = new JMenu();
 109
 110   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 111
 112   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 113
 114   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 115
 116   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 117
 118   JMenu editMenu = new JMenu();
 119
 120   JMenuItem cut = new JMenuItem();
 121
 122   JMenuItem copy = new JMenuItem();
 123
 124   JMenuItem upperCase = new JMenuItem();
 125
 126   JMenuItem lowerCase = new JMenuItem();
 127
 128   JMenuItem toggle = new JMenuItem();
 129
 130   JMenu pdbMenu = new JMenu();
 131
 132   JMenuItem pdbFromFile = new JMenuItem();
 133     // JBPNote: Commented these out - Should add these services via the web services menu system.
 134     // JMenuItem ContraFold = new JMenuItem();
 135
 136     // JMenuItem RNAFold = new JMenuItem();
 137
 138   JMenuItem enterPDB = new JMenuItem();
 139
 140   JMenuItem discoverPDB = new JMenuItem();
 141
 142   JMenu outputMenu = new JMenu();
 143
 144   JMenuItem sequenceFeature = new JMenuItem();
 145
 146   JMenuItem textColour = new JMenuItem();
 147
 148   JMenu jMenu1 = new JMenu();
 149
 150   JMenu structureMenu = new JMenu();
 151
 152   JMenu viewStructureMenu = new JMenu();
 153
 154   // JMenu colStructureMenu = new JMenu();
 155   JMenuItem editSequence = new JMenuItem();
 156
 157   // JMenuItem annotationMenuItem = new JMenuItem();
 158
 159   JMenu groupLinksMenu;
 160
 161   /**
 162    * Creates a new PopupMenu object.
 163    *
 164    * @param ap
 165    *          DOCUMENT ME!
 166    * @param seq
 167    *          DOCUMENT ME!
 168    */
 169   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 170   {
 171     this(ap, seq, links, null);
 172   }
 173
 174   /**
 175    *
 176    * @param ap
 177    * @param seq
 178    * @param links
 179    * @param groupLinks
 180    */
 181   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 182           Vector links, Vector groupLinks)
 183   {
 184     // /////////////////////////////////////////////////////////
 185     // If this is activated from the sequence panel, the user may want to
 186     // edit or annotate a particular residue. Therefore display the residue menu
 187     //
 188     // If from the IDPanel, we must display the sequence menu
 189     // ////////////////////////////////////////////////////////
 190     this.ap = ap;
 191     sequence = seq;
 192
 193     ButtonGroup colours = new ButtonGroup();
 194     colours.add(noColourmenuItem);
 195     colours.add(clustalColour);
 196     colours.add(zappoColour);
 197     colours.add(taylorColour);
 198     colours.add(hydrophobicityColour);
 199     colours.add(helixColour);
 200     colours.add(strandColour);
 201     colours.add(turnColour);
 202     colours.add(buriedColour);
 203     colours.add(abovePIDColour);
 204     colours.add(userDefinedColour);
 205     colours.add(PIDColour);
 206     colours.add(BLOSUM62Colour);
 207     colours.add(purinePyrimidineColour);
 208     colours.add(RNAInteractionColour);
 209     // colours.add(covariationColour);
 210
 211     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 212     {
 213       JMenuItem item = new JMenuItem(
 214               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 215
 216       item.addActionListener(new java.awt.event.ActionListener()
 217       {
 218         public void actionPerformed(ActionEvent e)
 219         {
 220           outputText_actionPerformed(e);
 221         }
 222       });
 223
 224       outputMenu.add(item);
 225     }
 226
 227     try
 228     {
 229       jbInit();
 230     } catch (Exception e)
 231     {
 232       e.printStackTrace();
 233     }
 234
 235     JMenuItem menuItem;
 236     if (seq != null)
 237     {
 238       sequenceMenu.setText(sequence.getName());
 239
 240       if (seq.getDatasetSequence().getPDBId() != null
 241               && seq.getDatasetSequence().getPDBId().size() > 0)
 242       {
 243         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 244                 .elements();
 245
 246         while (e.hasMoreElements())
 247         {
 248           final PDBEntry pdb = (PDBEntry) e.nextElement();
 249
 250           menuItem = new JMenuItem();
 251           menuItem.setText(pdb.getId());
 252           menuItem.addActionListener(new java.awt.event.ActionListener()
 253           {
 254             public void actionPerformed(ActionEvent e)
 255             {
 256               // TODO re JAL-860: optionally open dialog or provide a menu entry
 257               // allowing user to open just one structure per sequence
 258               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 259               { pdb })[0], null, ap);
 260               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 261             }
 262
 263           });
 264           viewStructureMenu.add(menuItem);
 265
 266           /*
 267            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 268            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 269            * public void actionPerformed(ActionEvent e) {
 270            * colourByStructure(pdb.getId()); } });
 271            * colStructureMenu.add(menuItem);
 272            */
 273         }
 274       }
 275       else
 276       {
 277         if (ap.av.getAlignment().isNucleotide() == false)
 278         {
 279           structureMenu.remove(viewStructureMenu);
 280         }
 281         // structureMenu.remove(colStructureMenu);
 282       }
 283
 284       if (ap.av.getAlignment().isNucleotide() == true)
 285       {
 286         AlignmentAnnotation[] aa = ap.av.getAlignment()
 287                 .getAlignmentAnnotation();
 288         for (int i = 0; i < aa.length; i++)
 289         {
 290           if (aa[i].getRNAStruc() != null)
 291           {
 292             final String rnastruc = aa[i].getRNAStruc();
 293             final String structureLine = aa[i].label;
 294             menuItem = new JMenuItem();
 295             menuItem.setText("2D RNA " + structureLine);
 296             menuItem.addActionListener(new java.awt.event.ActionListener()
 297
 298             {
 299               public void actionPerformed(ActionEvent e)
 300               {
 301                         //System.out.println("1:"+structureLine);
 302                         System.out.println("1:sname"+seq.getName());
 303                         System.out.println("2:seq"+seq);
 304
 305                         //System.out.println("3:"+seq.getSequenceAsString());
 306                         System.out.println("3:strucseq"+rnastruc);
 307                         //System.out.println("4:struc"+seq.getRNA());
 308                         System.out.println("5:name"+seq.getName());
 309                         System.out.println("6:ap"+ap);
 310                         new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
 311                             .getName(), ap);
 312                         //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
 313                         System.out.println("end");
 314               }
 315             });
 316             viewStructureMenu.add(menuItem);
 317           }
 318         }
 319
 320         // SequenceFeatures[] test = seq.getSequenceFeatures();
 321
 322         if (seq.getAnnotation() != null)
 323         {
 324           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 325           for (int i = 0; i < seqAnno.length; i++)
 326           {
 327             if (seqAnno[i].getRNAStruc() != null)
 328             {
 329               final String rnastruc = seqAnno[i].getRNAStruc();
 330
 331               // TODO: make rnastrucF a bit more nice
 332               menuItem = new JMenuItem();
 333               menuItem.setText("2D RNA - " + seq.getName());
 334               menuItem.addActionListener(new java.awt.event.ActionListener()
 335               {
 336                 public void actionPerformed(ActionEvent e)
 337                 {
 338                   // TODO: VARNA does'nt print gaps in the sequence
 339
 340                   new AppVarna(seq.getName() + " structure", seq, seq
 341                           .getSequenceAsString(), rnastruc, seq.getName(),
 342                           ap);
 343                 }
 344               });
 345               viewStructureMenu.add(menuItem);
 346             }
 347           }
 348         }
 349
 350       }
 351
 352       menuItem = new JMenuItem("Hide Sequences");
 353       menuItem.addActionListener(new java.awt.event.ActionListener()
 354       {
 355         public void actionPerformed(ActionEvent e)
 356         {
 357           hideSequences(false);
 358         }
 359       });
 360       add(menuItem);
 361
 362       if (ap.av.getSelectionGroup() != null
 363               && ap.av.getSelectionGroup().getSize() > 1)
 364       {
 365         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 366         menuItem.addActionListener(new java.awt.event.ActionListener()
 367         {
 368           public void actionPerformed(ActionEvent e)
 369           {
 370             hideSequences(true);
 371           }
 372         });
 373         sequenceMenu.add(menuItem);
 374       }
 375
 376       if (ap.av.hasHiddenRows())
 377       {
 378         final int index = ap.av.getAlignment().findIndex(seq);
 379
 380         if (ap.av.adjustForHiddenSeqs(index)
 381                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 382         {
 383           menuItem = new JMenuItem("Reveal Sequences");
 384           menuItem.addActionListener(new ActionListener()
 385           {
 386             public void actionPerformed(ActionEvent e)
 387             {
 388               ap.av.showSequence(index);
 389               if (ap.overviewPanel != null)
 390               {
 391                 ap.overviewPanel.updateOverviewImage();
 392               }
 393             }
 394           });
 395           add(menuItem);
 396         }
 397       }
 398     }
 399     // for the case when no sequences are even visible
 400     if (ap.av.hasHiddenRows())
 401     {
 402       {
 403         menuItem = new JMenuItem("Reveal All");
 404         menuItem.addActionListener(new ActionListener()
 405         {
 406           public void actionPerformed(ActionEvent e)
 407           {
 408             ap.av.showAllHiddenSeqs();
 409             if (ap.overviewPanel != null)
 410             {
 411               ap.overviewPanel.updateOverviewImage();
 412             }
 413           }
 414         });
 415
 416         add(menuItem);
 417       }
 418
 419     }
 420
 421     SequenceGroup sg = ap.av.getSelectionGroup();
 422
 423     if (sg != null && sg.getSize() > 0)
 424     {
 425       groupName.setText("Name: " + sg.getName());
 426       groupName.setText("Edit name and description of current group.");
 427
 428       if (sg.cs instanceof ZappoColourScheme)
 429       {
 430         zappoColour.setSelected(true);
 431       }
 432       else if (sg.cs instanceof TaylorColourScheme)
 433       {
 434         taylorColour.setSelected(true);
 435       }
 436       else if (sg.cs instanceof PIDColourScheme)
 437       {
 438         PIDColour.setSelected(true);
 439       }
 440       else if (sg.cs instanceof Blosum62ColourScheme)
 441       {
 442         BLOSUM62Colour.setSelected(true);
 443       }
 444       else if (sg.cs instanceof UserColourScheme)
 445       {
 446         userDefinedColour.setSelected(true);
 447       }
 448       else if (sg.cs instanceof HydrophobicColourScheme)
 449       {
 450         hydrophobicityColour.setSelected(true);
 451       }
 452       else if (sg.cs instanceof HelixColourScheme)
 453       {
 454         helixColour.setSelected(true);
 455       }
 456       else if (sg.cs instanceof StrandColourScheme)
 457       {
 458         strandColour.setSelected(true);
 459       }
 460       else if (sg.cs instanceof TurnColourScheme)
 461       {
 462         turnColour.setSelected(true);
 463       }
 464       else if (sg.cs instanceof BuriedColourScheme)
 465       {
 466         buriedColour.setSelected(true);
 467       }
 468       else if (sg.cs instanceof ClustalxColourScheme)
 469       {
 470         clustalColour.setSelected(true);
 471       }
 472       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 473       {
 474         purinePyrimidineColour.setSelected(true);
 475       }
 476
 477
 478       /*
 479        * else if (sg.cs instanceof CovariationColourScheme) {
 480        * covariationColour.setSelected(true); }
 481        */
 482       else
 483       {
 484         noColourmenuItem.setSelected(true);
 485       }
 486
 487       if (sg.cs != null && sg.cs.conservationApplied())
 488       {
 489         conservationMenuItem.setSelected(true);
 490       }
 491       displayNonconserved.setSelected(sg.getShowNonconserved());
 492       showText.setSelected(sg.getDisplayText());
 493       showColourText.setSelected(sg.getColourText());
 494       showBoxes.setSelected(sg.getDisplayBoxes());
 495       // add any groupURLs to the groupURL submenu and make it visible
 496       if (groupLinks != null && groupLinks.size() > 0)
 497       {
 498         buildGroupURLMenu(sg, groupLinks);
 499       }
 500       // Add a 'show all structures' for the current selection
 501       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
 502       SequenceI sqass = null;
 503       for (SequenceI sq : ap.av.getSequenceSelection())
 504       {
 505         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 506                 .getPDBId();
 507         if (pes != null)
 508         {
 509           for (PDBEntry pe : pes)
 510           {
 511             pdbe.put(pe.getId(), pe);
 512             if (sqass == null)
 513             {
 514               sqass = sq;
 515             }
 516           }
 517         }
 518       }
 519       if (pdbe.size() > 0)
 520       {
 521         final PDBEntry[] pe = pdbe.values().toArray(
 522                 new PDBEntry[pdbe.size()]);
 523         final JMenuItem gpdbview;
 524         if (pdbe.size() == 1)
 525         {
 526           structureMenu.add(gpdbview = new JMenuItem("View structure for "
 527                   + sqass.getDisplayId(false)));
 528         }
 529         else
 530         {
 531           structureMenu.add(gpdbview = new JMenuItem("View all "
 532                   + pdbe.size() + " structures."));
 533         }
 534         gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
 535         gpdbview.addActionListener(new ActionListener()
 536         {
 537
 538           @Override
 539           public void actionPerformed(ActionEvent e)
 540           {
 541             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 542           }
 543         });
 544       }
 545     }
 546     else
 547     {
 548       groupMenu.setVisible(false);
 549       editMenu.setVisible(false);
 550     }
 551
 552     if (!ap.av.getAlignment().getGroups().contains(sg))
 553     {
 554       unGroupMenuItem.setVisible(false);
 555     }
 556
 557     if (seq == null)
 558     {
 559       sequenceMenu.setVisible(false);
 560       structureMenu.setVisible(false);
 561     }
 562
 563     if (links != null && links.size() > 0)
 564     {
 565
 566       JMenu linkMenu = new JMenu("Link");
 567       Vector linkset = new Vector();
 568       for (int i = 0; i < links.size(); i++)
 569       {
 570         String link = links.elementAt(i).toString();
 571         UrlLink urlLink = null;
 572         try
 573         {
 574           urlLink = new UrlLink(link);
 575         } catch (Exception foo)
 576         {
 577           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 578                   + "'", foo);
 579           continue;
 580         }
 581         ;
 582         if (!urlLink.isValid())
 583         {
 584           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 585           continue;
 586         }
 587         final String label = urlLink.getLabel();
 588         if (seq != null && urlLink.isDynamic())
 589         {
 590
 591           // collect matching db-refs
 592           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 593                   seq.getDBRef(), new String[]
 594                   { urlLink.getTarget() });
 595           // collect id string too
 596           String id = seq.getName();
 597           String descr = seq.getDescription();
 598           if (descr != null && descr.length() < 1)
 599           {
 600             descr = null;
 601           }
 602
 603           if (dbr != null)
 604           {
 605             for (int r = 0; r < dbr.length; r++)
 606             {
 607               if (id != null && dbr[r].getAccessionId().equals(id))
 608               {
 609                 // suppress duplicate link creation for the bare sequence ID
 610                 // string with this link
 611                 id = null;
 612               }
 613               // create Bare ID link for this RUL
 614               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 615                       true);
 616               if (urls != null)
 617               {
 618                 for (int u = 0; u < urls.length; u += 2)
 619                 {
 620                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 621                   {
 622                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 623                     addshowLink(linkMenu, label + "|" + urls[u],
 624                             urls[u + 1]);
 625                   }
 626                 }
 627               }
 628             }
 629           }
 630           if (id != null)
 631           {
 632             // create Bare ID link for this RUL
 633             String[] urls = urlLink.makeUrls(id, true);
 634             if (urls != null)
 635             {
 636               for (int u = 0; u < urls.length; u += 2)
 637               {
 638                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 639                 {
 640                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 641                   addshowLink(linkMenu, label, urls[u + 1]);
 642                 }
 643               }
 644             }
 645           }
 646           // Create urls from description but only for URL links which are regex
 647           // links
 648           if (descr != null && urlLink.getRegexReplace() != null)
 649           {
 650             // create link for this URL from description where regex matches
 651             String[] urls = urlLink.makeUrls(descr, true);
 652             if (urls != null)
 653             {
 654               for (int u = 0; u < urls.length; u += 2)
 655               {
 656                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 657                 {
 658                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 659                   addshowLink(linkMenu, label, urls[u + 1]);
 660                 }
 661               }
 662             }
 663           }
 664         }
 665         else
 666         {
 667           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 668           {
 669             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 670             // Add a non-dynamic link
 671             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 672           }
 673         }
 674       }
 675       if (sequence != null)
 676       {
 677         sequenceMenu.add(linkMenu);
 678       }
 679       else
 680       {
 681         add(linkMenu);
 682       }
 683     }
 684   }
 685
 686   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 687   {
 688
 689     // TODO: usability: thread off the generation of group url content so root
 690     // menu appears asap
 691     // sequence only URLs
 692     // ID/regex match URLs
 693     groupLinksMenu = new JMenu("Group Link");
 694     JMenu[] linkMenus = new JMenu[]
 695     { null, new JMenu("IDS"), new JMenu("Sequences"),
 696         new JMenu("IDS and Sequences") }; // three types of url that might be
 697                                           // created.
 698     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 699     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 700     Hashtable commonDbrefs = new Hashtable();
 701     for (int sq = 0; sq < seqs.length; sq++)
 702     {
 703
 704       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 705               .findPosition(sg.getEndRes());
 706       // just collect ids from dataset sequence
 707       // TODO: check if IDs collected from selecton group intersects with the
 708       // current selection, too
 709       SequenceI sqi = seqs[sq];
 710       while (sqi.getDatasetSequence() != null)
 711       {
 712         sqi = sqi.getDatasetSequence();
 713       }
 714       DBRefEntry[] dbr = sqi.getDBRef();
 715       if (dbr != null && dbr.length > 0)
 716       {
 717         for (int d = 0; d < dbr.length; d++)
 718         {
 719           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 720           Object[] sarray = (Object[]) commonDbrefs.get(src);
 721           if (sarray == null)
 722           {
 723             sarray = new Object[2];
 724             sarray[0] = new int[]
 725             { 0 };
 726             sarray[1] = new String[seqs.length];
 727
 728             commonDbrefs.put(src, sarray);
 729           }
 730
 731           if (((String[]) sarray[1])[sq] == null)
 732           {
 733             if (!dbr[d].hasMap()
 734                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 735             {
 736               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 737               ((int[]) sarray[0])[0]++;
 738             }
 739           }
 740         }
 741       }
 742     }
 743     // now create group links for all distinct ID/sequence sets.
 744     boolean addMenu = false; // indicates if there are any group links to give
 745                              // to user
 746     for (int i = 0; i < groupLinks.size(); i++)
 747     {
 748       String link = groupLinks.elementAt(i).toString();
 749       GroupUrlLink urlLink = null;
 750       try
 751       {
 752         urlLink = new GroupUrlLink(link);
 753       } catch (Exception foo)
 754       {
 755         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 756                 + "'", foo);
 757         continue;
 758       }
 759       ;
 760       if (!urlLink.isValid())
 761       {
 762         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 763         continue;
 764       }
 765       final String label = urlLink.getLabel();
 766       boolean usingNames = false;
 767       // Now see which parts of the group apply for this URL
 768       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 769       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 770       String[] seqstr, ids; // input to makeUrl
 771       if (idset != null)
 772       {
 773         int numinput = ((int[]) idset[0])[0];
 774         String[] allids = ((String[]) idset[1]);
 775         seqstr = new String[numinput];
 776         ids = new String[numinput];
 777         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 778         {
 779           if (allids[sq] != null)
 780           {
 781             ids[idcount] = allids[sq];
 782             seqstr[idcount++] = idandseqs[1][sq];
 783           }
 784         }
 785       }
 786       else
 787       {
 788         // just use the id/seq set
 789         seqstr = idandseqs[1];
 790         ids = idandseqs[0];
 791         usingNames = true;
 792       }
 793       // and try and make the groupURL!
 794
 795       Object[] urlset = null;
 796       try
 797       {
 798         urlset = urlLink.makeUrlStubs(ids, seqstr,
 799                 "FromJalview" + System.currentTimeMillis(), false);
 800       } catch (UrlStringTooLongException e)
 801       {
 802       }
 803       if (urlset != null)
 804       {
 805         int type = urlLink.getGroupURLType() & 3;
 806         // System.out.println(urlLink.getGroupURLType()
 807         // +" "+((String[])urlset[3])[0]);
 808         // first two bits ofurlLink type bitfield are sequenceids and sequences
 809         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 810         addshowLink(linkMenus[type], label
 811                 + (((type & 1) == 1) ? ("("
 812                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 813                 urlLink, urlset);
 814         addMenu = true;
 815       }
 816     }
 817     if (addMenu)
 818     {
 819       groupLinksMenu = new JMenu("Group Links");
 820       for (int m = 0; m < linkMenus.length; m++)
 821       {
 822         if (linkMenus[m] != null
 823                 && linkMenus[m].getMenuComponentCount() > 0)
 824         {
 825           groupLinksMenu.add(linkMenus[m]);
 826         }
 827       }
 828
 829       groupMenu.add(groupLinksMenu);
 830     }
 831   }
 832
 833   /**
 834    * add a show URL menu item to the given linkMenu
 835    *
 836    * @param linkMenu
 837    * @param label
 838    *          - menu label string
 839    * @param url
 840    *          - url to open
 841    */
 842   private void addshowLink(JMenu linkMenu, String label, final String url)
 843   {
 844     JMenuItem item = new JMenuItem(label);
 845     item.setToolTipText("open URL: " + url);
 846     item.addActionListener(new java.awt.event.ActionListener()
 847     {
 848       public void actionPerformed(ActionEvent e)
 849       {
 850         new Thread(new Runnable()
 851         {
 852
 853           public void run()
 854           {
 855             showLink(url);
 856           }
 857
 858         }).start();
 859       }
 860     });
 861
 862     linkMenu.add(item);
 863   }
 864
 865   /**
 866    * add a late bound groupURL item to the given linkMenu
 867    *
 868    * @param linkMenu
 869    * @param label
 870    *          - menu label string
 871    * @param urlgenerator
 872    *          GroupURLLink used to generate URL
 873    * @param urlstub
 874    *          Object array returned from the makeUrlStubs function.
 875    */
 876   private void addshowLink(JMenu linkMenu, String label,
 877           final GroupUrlLink urlgenerator, final Object[] urlstub)
 878   {
 879     JMenuItem item = new JMenuItem(label);
 880     item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
 881             + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
 882                                                                              // put
 883                                                                              // in
 884                                                                              // info
 885                                                                              // about
 886                                                                              // what
 887                                                                              // is
 888                                                                              // being
 889                                                                              // sent.
 890     item.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         new Thread(new Runnable()
 895         {
 896
 897           public void run()
 898           {
 899             try
 900             {
 901               showLink(urlgenerator.constructFrom(urlstub));
 902             } catch (UrlStringTooLongException e)
 903             {
 904             }
 905           }
 906
 907         }).start();
 908       }
 909     });
 910
 911     linkMenu.add(item);
 912   }
 913
 914   /**
 915    * DOCUMENT ME!
 916    *
 917    * @throws Exception
 918    *           DOCUMENT ME!
 919    */
 920   private void jbInit() throws Exception
 921   {
 922     groupMenu.setText("Group");
 923     groupMenu.setText("Selection");
 924     groupName.setText("Name");
 925     groupName.addActionListener(new java.awt.event.ActionListener()
 926     {
 927       public void actionPerformed(ActionEvent e)
 928       {
 929         groupName_actionPerformed();
 930       }
 931     });
 932     sequenceMenu.setText("Sequence");
 933     sequenceName.setText("Edit Name/Description");
 934     sequenceName.addActionListener(new java.awt.event.ActionListener()
 935     {
 936       public void actionPerformed(ActionEvent e)
 937       {
 938         sequenceName_actionPerformed();
 939       }
 940     });
 941     sequenceDetails.setText("Sequence Details ...");
 942     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 943     {
 944       public void actionPerformed(ActionEvent e)
 945       {
 946         sequenceDetails_actionPerformed();
 947       }
 948     });
 949     sequenceSelDetails.setText("Sequence Details ...");
 950     sequenceSelDetails
 951             .addActionListener(new java.awt.event.ActionListener()
 952             {
 953               public void actionPerformed(ActionEvent e)
 954               {
 955                 sequenceSelectionDetails_actionPerformed();
 956               }
 957             });
 958     PIDColour.setFocusPainted(false);
 959     unGroupMenuItem.setText("Remove Group");
 960     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 961     {
 962       public void actionPerformed(ActionEvent e)
 963       {
 964         unGroupMenuItem_actionPerformed();
 965       }
 966     });
 967
 968     outline.setText("Border colour");
 969     outline.addActionListener(new java.awt.event.ActionListener()
 970     {
 971       public void actionPerformed(ActionEvent e)
 972       {
 973         outline_actionPerformed();
 974       }
 975     });
 976     nucleotideMenuItem.setText("Nucleotide");
 977     nucleotideMenuItem.addActionListener(new ActionListener()
 978     {
 979       public void actionPerformed(ActionEvent e)
 980       {
 981         nucleotideMenuItem_actionPerformed();
 982       }
 983     });
 984     colourMenu.setText("Group Colour");
 985     showBoxes.setText("Boxes");
 986     showBoxes.setState(true);
 987     showBoxes.addActionListener(new ActionListener()
 988     {
 989       public void actionPerformed(ActionEvent e)
 990       {
 991         showBoxes_actionPerformed();
 992       }
 993     });
 994     showText.setText("Text");
 995     showText.setState(true);
 996     showText.addActionListener(new ActionListener()
 997     {
 998       public void actionPerformed(ActionEvent e)
 999       {
1000         showText_actionPerformed();
1001       }
1002     });
1003     showColourText.setText("Colour Text");
1004     showColourText.addActionListener(new ActionListener()
1005     {
1006       public void actionPerformed(ActionEvent e)
1007       {
1008         showColourText_actionPerformed();
1009       }
1010     });
1011     displayNonconserved.setText("Show Nonconserved");
1012     displayNonconserved.setState(true);
1013     displayNonconserved.addActionListener(new ActionListener()
1014     {
1015       public void actionPerformed(ActionEvent e)
1016       {
1017         showNonconserved_actionPerformed();
1018       }
1019     });
1020     editMenu.setText("Edit");
1021     cut.setText("Cut");
1022     cut.addActionListener(new ActionListener()
1023     {
1024       public void actionPerformed(ActionEvent e)
1025       {
1026         cut_actionPerformed();
1027       }
1028     });
1029     upperCase.setText("To Upper Case");
1030     upperCase.addActionListener(new ActionListener()
1031     {
1032       public void actionPerformed(ActionEvent e)
1033       {
1034         changeCase(e);
1035       }
1036     });
1037     copy.setText("Copy");
1038     copy.addActionListener(new ActionListener()
1039     {
1040       public void actionPerformed(ActionEvent e)
1041       {
1042         copy_actionPerformed();
1043       }
1044     });
1045     lowerCase.setText("To Lower Case");
1046     lowerCase.addActionListener(new ActionListener()
1047     {
1048       public void actionPerformed(ActionEvent e)
1049       {
1050         changeCase(e);
1051       }
1052     });
1053     toggle.setText("Toggle Case");
1054     toggle.addActionListener(new ActionListener()
1055     {
1056       public void actionPerformed(ActionEvent e)
1057       {
1058         changeCase(e);
1059       }
1060     });
1061     pdbMenu.setText("Associate Structure with Sequence");
1062     pdbFromFile.setText("From File");
1063     pdbFromFile.addActionListener(new ActionListener()
1064     {
1065       public void actionPerformed(ActionEvent e)
1066       {
1067         try {
1068                         pdbFromFile_actionPerformed();
1069                 } catch (Exception e1) {
1070                         // TODO Auto-generated catch block
1071                         e1.printStackTrace();
1072                 }
1073       }
1074     });
1075 //    RNAFold.setText("From RNA Fold with predict2D");
1076 //    RNAFold.addActionListener(new ActionListener()
1077 //    {
1078 //      public void actionPerformed(ActionEvent e)
1079 //      {
1080 //        try {
1081 //                      RNAFold_actionPerformed();
1082 //              } catch (Exception e1) {
1083 //                      // TODO Auto-generated catch block
1084 //                      e1.printStackTrace();
1085 //              }
1086 //      }
1087 //    });
1088 //    ContraFold.setText("From Contra Fold with predict2D");
1089 //    ContraFold.addActionListener(new ActionListener()
1090 //    {
1091 //      public void actionPerformed(ActionEvent e)
1092 //      {
1093 //        try {
1094 //                      ContraFold_actionPerformed();
1095 //              } catch (Exception e1) {
1096 //                      // TODO Auto-generated catch block
1097 //                      e1.printStackTrace();
1098 //              }
1099 //      }
1100 //    });
1101     enterPDB.setText("Enter PDB Id");
1102     enterPDB.addActionListener(new ActionListener()
1103     {
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         enterPDB_actionPerformed();
1107       }
1108     });
1109     discoverPDB.setText("Discover PDB ids");
1110     discoverPDB.addActionListener(new ActionListener()
1111     {
1112       public void actionPerformed(ActionEvent e)
1113       {
1114         discoverPDB_actionPerformed();
1115       }
1116     });
1117     outputMenu.setText("Output to Textbox...");
1118     sequenceFeature.setText("Create Sequence Feature");
1119     sequenceFeature.addActionListener(new ActionListener()
1120     {
1121       public void actionPerformed(ActionEvent e)
1122       {
1123         sequenceFeature_actionPerformed();
1124       }
1125     });
1126     textColour.setText("Text Colour");
1127     textColour.addActionListener(new ActionListener()
1128     {
1129       public void actionPerformed(ActionEvent e)
1130       {
1131         textColour_actionPerformed();
1132       }
1133     });
1134     jMenu1.setText("Group");
1135     structureMenu.setText("Structure");
1136     viewStructureMenu.setText("View Structure");
1137     // colStructureMenu.setText("Colour By Structure");
1138     editSequence.setText("Edit Sequence...");
1139     editSequence.addActionListener(new ActionListener()
1140     {
1141       public void actionPerformed(ActionEvent actionEvent)
1142       {
1143         editSequence_actionPerformed(actionEvent);
1144       }
1145     });
1146
1147     /*
1148      * annotationMenuItem.setText("By Annotation");
1149      * annotationMenuItem.addActionListener(new ActionListener() { public void
1150      * actionPerformed(ActionEvent actionEvent) {
1151      * annotationMenuItem_actionPerformed(actionEvent); } });
1152      */
1153     groupMenu.add(sequenceSelDetails);
1154     add(groupMenu);
1155     add(sequenceMenu);
1156     this.add(structureMenu);
1157     groupMenu.add(editMenu);
1158     groupMenu.add(outputMenu);
1159     groupMenu.add(sequenceFeature);
1160     groupMenu.add(jMenu1);
1161     sequenceMenu.add(sequenceName);
1162     sequenceMenu.add(sequenceDetails);
1163     colourMenu.add(textColour);
1164     colourMenu.add(noColourmenuItem);
1165     colourMenu.add(clustalColour);
1166     colourMenu.add(BLOSUM62Colour);
1167     colourMenu.add(PIDColour);
1168     colourMenu.add(zappoColour);
1169     colourMenu.add(taylorColour);
1170     colourMenu.add(hydrophobicityColour);
1171     colourMenu.add(helixColour);
1172     colourMenu.add(strandColour);
1173     colourMenu.add(turnColour);
1174     colourMenu.add(buriedColour);
1175     colourMenu.add(nucleotideMenuItem);
1176     if (ap.getAlignment().isNucleotide()) {
1177         // JBPNote - commented since the colourscheme isn't functional
1178         //  colourMenu.add(RNAInteractionColour);
1179         colourMenu.add(purinePyrimidineColour);
1180     }
1181     // colourMenu.add(covariationColour);
1182     colourMenu.add(userDefinedColour);
1183
1184     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1185     {
1186       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1187               .getUserColourSchemes().keys();
1188
1189       while (userColours.hasMoreElements())
1190       {
1191         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1192         item.addActionListener(new ActionListener()
1193         {
1194           public void actionPerformed(ActionEvent evt)
1195           {
1196             userDefinedColour_actionPerformed(evt);
1197           }
1198         });
1199         colourMenu.add(item);
1200       }
1201     }
1202
1203     colourMenu.addSeparator();
1204     colourMenu.add(abovePIDColour);
1205     colourMenu.add(conservationMenuItem);
1206     // colourMenu.add(annotationMenuItem);
1207     editMenu.add(copy);
1208     editMenu.add(cut);
1209     editMenu.add(editSequence);
1210     editMenu.add(upperCase);
1211     editMenu.add(lowerCase);
1212     editMenu.add(toggle);
1213     pdbMenu.add(pdbFromFile);
1214     // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1215     //    pdbMenu.add(RNAFold);
1216     //    pdbMenu.add(ContraFold);
1217     pdbMenu.add(enterPDB);
1218     pdbMenu.add(discoverPDB);
1219     jMenu1.add(groupName);
1220     jMenu1.add(unGroupMenuItem);
1221     jMenu1.add(colourMenu);
1222     jMenu1.add(showBoxes);
1223     jMenu1.add(showText);
1224     jMenu1.add(showColourText);
1225     jMenu1.add(outline);
1226     jMenu1.add(displayNonconserved);
1227     structureMenu.add(pdbMenu);
1228     structureMenu.add(viewStructureMenu);
1229     // structureMenu.add(colStructureMenu);
1230     noColourmenuItem.setText("None");
1231     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1232     {
1233       public void actionPerformed(ActionEvent e)
1234       {
1235         noColourmenuItem_actionPerformed();
1236       }
1237     });
1238
1239     clustalColour.setText("Clustalx colours");
1240     clustalColour.addActionListener(new java.awt.event.ActionListener()
1241     {
1242       public void actionPerformed(ActionEvent e)
1243       {
1244         clustalColour_actionPerformed();
1245       }
1246     });
1247     zappoColour.setText("Zappo");
1248     zappoColour.addActionListener(new java.awt.event.ActionListener()
1249     {
1250       public void actionPerformed(ActionEvent e)
1251       {
1252         zappoColour_actionPerformed();
1253       }
1254     });
1255     taylorColour.setText("Taylor");
1256     taylorColour.addActionListener(new java.awt.event.ActionListener()
1257     {
1258       public void actionPerformed(ActionEvent e)
1259       {
1260         taylorColour_actionPerformed();
1261       }
1262     });
1263     hydrophobicityColour.setText("Hydrophobicity");
1264     hydrophobicityColour
1265             .addActionListener(new java.awt.event.ActionListener()
1266             {
1267               public void actionPerformed(ActionEvent e)
1268               {
1269                 hydrophobicityColour_actionPerformed();
1270               }
1271             });
1272     helixColour.setText("Helix propensity");
1273     helixColour.addActionListener(new java.awt.event.ActionListener()
1274     {
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         helixColour_actionPerformed();
1278       }
1279     });
1280     strandColour.setText("Strand propensity");
1281     strandColour.addActionListener(new java.awt.event.ActionListener()
1282     {
1283       public void actionPerformed(ActionEvent e)
1284       {
1285         strandColour_actionPerformed();
1286       }
1287     });
1288     turnColour.setText("Turn propensity");
1289     turnColour.addActionListener(new java.awt.event.ActionListener()
1290     {
1291       public void actionPerformed(ActionEvent e)
1292       {
1293         turnColour_actionPerformed();
1294       }
1295     });
1296     buriedColour.setText("Buried Index");
1297     buriedColour.addActionListener(new java.awt.event.ActionListener()
1298     {
1299       public void actionPerformed(ActionEvent e)
1300       {
1301         buriedColour_actionPerformed();
1302       }
1303     });
1304     abovePIDColour.setText("Above % Identity");
1305     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1306     {
1307       public void actionPerformed(ActionEvent e)
1308       {
1309         abovePIDColour_actionPerformed();
1310       }
1311     });
1312     userDefinedColour.setText("User Defined...");
1313     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1314     {
1315       public void actionPerformed(ActionEvent e)
1316       {
1317         userDefinedColour_actionPerformed(e);
1318       }
1319     });
1320     PIDColour.setText("Percentage Identity");
1321     PIDColour.addActionListener(new java.awt.event.ActionListener()
1322     {
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         PIDColour_actionPerformed();
1326       }
1327     });
1328     BLOSUM62Colour.setText("BLOSUM62");
1329     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1330     {
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         BLOSUM62Colour_actionPerformed();
1334       }
1335     });
1336     purinePyrimidineColour.setText("Purine/Pyrimidine");
1337     purinePyrimidineColour
1338             .addActionListener(new java.awt.event.ActionListener()
1339             {
1340               public void actionPerformed(ActionEvent e)
1341               {
1342                 purinePyrimidineColour_actionPerformed();
1343               }
1344             });
1345
1346
1347     /*
1348      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1349      * public void actionPerformed(ActionEvent e) {
1350      * covariationColour_actionPerformed(); } });
1351      */
1352
1353     conservationMenuItem.setText("Conservation");
1354     conservationMenuItem
1355             .addActionListener(new java.awt.event.ActionListener()
1356             {
1357               public void actionPerformed(ActionEvent e)
1358               {
1359                 conservationMenuItem_actionPerformed();
1360               }
1361             });
1362   }
1363
1364   protected void sequenceSelectionDetails_actionPerformed()
1365   {
1366     createSequenceDetailsReport(ap.av.getSequenceSelection());
1367   }
1368
1369   protected void sequenceDetails_actionPerformed()
1370   {
1371     createSequenceDetailsReport(new SequenceI[]
1372     { sequence });
1373   }
1374
1375   public void createSequenceDetailsReport(SequenceI[] sequences)
1376   {
1377     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1378     StringBuffer contents = new StringBuffer();
1379     for (SequenceI seq : sequences)
1380     {
1381       contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1382               + "</h2></p><p>");
1383       new SequenceAnnotationReport(null)
1384               .createSequenceAnnotationReport(
1385                       contents,
1386                       seq,
1387                       true,
1388                       true,
1389                       false,
1390                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1391                               : null);
1392       contents.append("</p>");
1393     }
1394     cap.setText("<html>" + contents.toString() + "</html>");
1395
1396     Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1397             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1398                     : "Selection"), 500, 400);
1399
1400   }
1401
1402   protected void showNonconserved_actionPerformed()
1403   {
1404     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1405     refresh();
1406   }
1407
1408   /**
1409    * call to refresh view after settings change
1410    */
1411   void refresh()
1412   {
1413     ap.updateAnnotation();
1414     ap.paintAlignment(true);
1415
1416     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1417   }
1418
1419   /**
1420    * DOCUMENT ME!
1421    *
1422    * @param e
1423    *          DOCUMENT ME!
1424    */
1425   protected void clustalColour_actionPerformed()
1426   {
1427     SequenceGroup sg = getGroup();
1428     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1429     refresh();
1430   }
1431
1432   /**
1433    * DOCUMENT ME!
1434    *
1435    * @param e
1436    *          DOCUMENT ME!
1437    */
1438   protected void zappoColour_actionPerformed()
1439   {
1440     getGroup().cs = new ZappoColourScheme();
1441     refresh();
1442   }
1443
1444   /**
1445    * DOCUMENT ME!
1446    *
1447    * @param e
1448    *          DOCUMENT ME!
1449    */
1450   protected void taylorColour_actionPerformed()
1451   {
1452     getGroup().cs = new TaylorColourScheme();
1453     refresh();
1454   }
1455
1456   /**
1457    * DOCUMENT ME!
1458    *
1459    * @param e
1460    *          DOCUMENT ME!
1461    */
1462   protected void hydrophobicityColour_actionPerformed()
1463   {
1464     getGroup().cs = new HydrophobicColourScheme();
1465     refresh();
1466   }
1467
1468   /**
1469    * DOCUMENT ME!
1470    *
1471    * @param e
1472    *          DOCUMENT ME!
1473    */
1474   protected void helixColour_actionPerformed()
1475   {
1476     getGroup().cs = new HelixColourScheme();
1477     refresh();
1478   }
1479
1480   /**
1481    * DOCUMENT ME!
1482    *
1483    * @param e
1484    *          DOCUMENT ME!
1485    */
1486   protected void strandColour_actionPerformed()
1487   {
1488     getGroup().cs = new StrandColourScheme();
1489     refresh();
1490   }
1491
1492   /**
1493    * DOCUMENT ME!
1494    *
1495    * @param e
1496    *          DOCUMENT ME!
1497    */
1498   protected void turnColour_actionPerformed()
1499   {
1500     getGroup().cs = new TurnColourScheme();
1501     refresh();
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    *
1507    * @param e
1508    *          DOCUMENT ME!
1509    */
1510   protected void buriedColour_actionPerformed()
1511   {
1512     getGroup().cs = new BuriedColourScheme();
1513     refresh();
1514   }
1515
1516   /**
1517    * DOCUMENT ME!
1518    *
1519    * @param e
1520    *          DOCUMENT ME!
1521    */
1522   public void nucleotideMenuItem_actionPerformed()
1523   {
1524     getGroup().cs = new NucleotideColourScheme();
1525     refresh();
1526   }
1527
1528   protected void purinePyrimidineColour_actionPerformed()
1529   {
1530     getGroup().cs = new PurinePyrimidineColourScheme();
1531     refresh();
1532   }
1533
1534
1535   /*
1536    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1537    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1538    */
1539   /**
1540    * DOCUMENT ME!
1541    *
1542    * @param e
1543    *          DOCUMENT ME!
1544    */
1545   protected void abovePIDColour_actionPerformed()
1546   {
1547     SequenceGroup sg = getGroup();
1548     if (sg.cs == null)
1549     {
1550       return;
1551     }
1552
1553     if (abovePIDColour.isSelected())
1554     {
1555       sg.cs.setConsensus(AAFrequency.calculate(
1556               sg.getSequences(ap.av.getHiddenRepSequences()),
1557               sg.getStartRes(), sg.getEndRes() + 1));
1558
1559       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1560               .getName());
1561
1562       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1563
1564       SliderPanel.showPIDSlider();
1565     }
1566     else
1567     // remove PIDColouring
1568     {
1569       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1570     }
1571
1572     refresh();
1573   }
1574
1575   /**
1576    * DOCUMENT ME!
1577    *
1578    * @param e
1579    *          DOCUMENT ME!
1580    */
1581   protected void userDefinedColour_actionPerformed(ActionEvent e)
1582   {
1583     SequenceGroup sg = getGroup();
1584
1585     if (e.getActionCommand().equals("User Defined..."))
1586     {
1587       new UserDefinedColours(ap, sg);
1588     }
1589     else
1590     {
1591       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1592               .getUserColourSchemes().get(e.getActionCommand());
1593
1594       sg.cs = udc;
1595     }
1596     refresh();
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    *
1602    * @param e
1603    *          DOCUMENT ME!
1604    */
1605   protected void PIDColour_actionPerformed()
1606   {
1607     SequenceGroup sg = getGroup();
1608     sg.cs = new PIDColourScheme();
1609     sg.cs.setConsensus(AAFrequency.calculate(
1610             sg.getSequences(ap.av.getHiddenRepSequences()),
1611             sg.getStartRes(), sg.getEndRes() + 1));
1612     refresh();
1613   }
1614
1615   /**
1616    * DOCUMENT ME!
1617    *
1618    * @param e
1619    *          DOCUMENT ME!
1620    */
1621   protected void BLOSUM62Colour_actionPerformed()
1622   {
1623     SequenceGroup sg = getGroup();
1624
1625     sg.cs = new Blosum62ColourScheme();
1626
1627     sg.cs.setConsensus(AAFrequency.calculate(
1628             sg.getSequences(ap.av.getHiddenRepSequences()),
1629             sg.getStartRes(), sg.getEndRes() + 1));
1630
1631     refresh();
1632   }
1633
1634   /**
1635    * DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   protected void noColourmenuItem_actionPerformed()
1641   {
1642     getGroup().cs = null;
1643     refresh();
1644   }
1645
1646   /**
1647    * DOCUMENT ME!
1648    *
1649    * @param e
1650    *          DOCUMENT ME!
1651    */
1652   protected void conservationMenuItem_actionPerformed()
1653   {
1654     SequenceGroup sg = getGroup();
1655     if (sg.cs == null)
1656     {
1657       return;
1658     }
1659
1660     if (conservationMenuItem.isSelected())
1661     {
1662       Conservation c = new Conservation("Group",
1663               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1664                       .getHiddenRepSequences()), sg.getStartRes(),
1665               sg.getEndRes() + 1);
1666
1667       c.calculate();
1668       c.verdict(false, ap.av.getConsPercGaps());
1669
1670       sg.cs.setConservation(c);
1671
1672       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1673       SliderPanel.showConservationSlider();
1674     }
1675     else
1676     // remove ConservationColouring
1677     {
1678       sg.cs.setConservation(null);
1679     }
1680
1681     refresh();
1682   }
1683
1684   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1685   {
1686     SequenceGroup sg = getGroup();
1687     if (sg == null)
1688     {
1689       return;
1690     }
1691
1692     AnnotationColourGradient acg = new AnnotationColourGradient(
1693             sequence.getAnnotation()[0], null,
1694             AnnotationColourGradient.NO_THRESHOLD);
1695
1696     acg.predefinedColours = true;
1697     sg.cs = acg;
1698
1699     refresh();
1700   }
1701
1702   /**
1703    * DOCUMENT ME!
1704    *
1705    * @param e
1706    *          DOCUMENT ME!
1707    */
1708   protected void groupName_actionPerformed()
1709   {
1710
1711     SequenceGroup sg = getGroup();
1712     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1713             sg.getDescription(), "       Group Name ",
1714             "Group Description ", "Edit Group Name/Description",
1715             ap.alignFrame);
1716
1717     if (!dialog.accept)
1718     {
1719       return;
1720     }
1721
1722     sg.setName(dialog.getName());
1723     sg.setDescription(dialog.getDescription());
1724     refresh();
1725   }
1726
1727   /**
1728    * Get selection group - adding it to the alignment if necessary.
1729    *
1730    * @return sequence group to operate on
1731    */
1732   SequenceGroup getGroup()
1733   {
1734     SequenceGroup sg = ap.av.getSelectionGroup();
1735     // this method won't add a new group if it already exists
1736     if (sg != null)
1737     {
1738       ap.av.getAlignment().addGroup(sg);
1739     }
1740
1741     return sg;
1742   }
1743
1744   /**
1745    * DOCUMENT ME!
1746    *
1747    * @param e
1748    *          DOCUMENT ME!
1749    */
1750   void sequenceName_actionPerformed()
1751   {
1752     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1753             sequence.getDescription(), "       Sequence Name ",
1754             "Sequence Description ", "Edit Sequence Name/Description",
1755             ap.alignFrame);
1756
1757     if (!dialog.accept)
1758     {
1759       return;
1760     }
1761
1762     if (dialog.getName() != null)
1763     {
1764       if (dialog.getName().indexOf(" ") > -1)
1765       {
1766         JOptionPane.showMessageDialog(ap,
1767                 "Spaces have been converted to \"_\"",
1768                 "No spaces allowed in Sequence Name",
1769                 JOptionPane.WARNING_MESSAGE);
1770       }
1771
1772       sequence.setName(dialog.getName().replace(' ', '_'));
1773       ap.paintAlignment(false);
1774     }
1775
1776     sequence.setDescription(dialog.getDescription());
1777
1778     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1779             .getSequences());
1780
1781   }
1782
1783   /**
1784    * DOCUMENT ME!
1785    *
1786    * @param e
1787    *          DOCUMENT ME!
1788    */
1789   void unGroupMenuItem_actionPerformed()
1790   {
1791     SequenceGroup sg = ap.av.getSelectionGroup();
1792     ap.av.getAlignment().deleteGroup(sg);
1793     ap.av.setSelectionGroup(null);
1794     refresh();
1795   }
1796
1797   /**
1798    * DOCUMENT ME!
1799    *
1800    * @param e
1801    *          DOCUMENT ME!
1802    */
1803   protected void outline_actionPerformed()
1804   {
1805     SequenceGroup sg = getGroup();
1806     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1807             Color.BLUE);
1808
1809     if (col != null)
1810     {
1811       sg.setOutlineColour(col);
1812     }
1813
1814     refresh();
1815   }
1816
1817   /**
1818    * DOCUMENT ME!
1819    *
1820    * @param e
1821    *          DOCUMENT ME!
1822    */
1823   public void showBoxes_actionPerformed()
1824   {
1825     getGroup().setDisplayBoxes(showBoxes.isSelected());
1826     refresh();
1827   }
1828
1829   /**
1830    * DOCUMENT ME!
1831    *
1832    * @param e
1833    *          DOCUMENT ME!
1834    */
1835   public void showText_actionPerformed()
1836   {
1837     getGroup().setDisplayText(showText.isSelected());
1838     refresh();
1839   }
1840
1841   /**
1842    * DOCUMENT ME!
1843    *
1844    * @param e
1845    *          DOCUMENT ME!
1846    */
1847   public void showColourText_actionPerformed()
1848   {
1849     getGroup().setColourText(showColourText.isSelected());
1850     refresh();
1851   }
1852
1853   public void showLink(String url)
1854   {
1855     try
1856     {
1857       jalview.util.BrowserLauncher.openURL(url);
1858     } catch (Exception ex)
1859     {
1860       JOptionPane
1861               .showInternalMessageDialog(
1862                       Desktop.desktop,
1863                       "Unixers: Couldn't find default web browser."
1864                               + "\nAdd the full path to your browser in Preferences.",
1865                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1866
1867       ex.printStackTrace();
1868     }
1869   }
1870
1871   void hideSequences(boolean representGroup)
1872   {
1873     SequenceGroup sg = ap.av.getSelectionGroup();
1874     if (sg == null || sg.getSize() < 1)
1875     {
1876       ap.av.hideSequence(new SequenceI[]
1877       { sequence });
1878       return;
1879     }
1880
1881     ap.av.setSelectionGroup(null);
1882
1883     if (representGroup)
1884     {
1885       ap.av.hideRepSequences(sequence, sg);
1886
1887       return;
1888     }
1889
1890     int gsize = sg.getSize();
1891     SequenceI[] hseqs;
1892
1893     hseqs = new SequenceI[gsize];
1894
1895     int index = 0;
1896     for (int i = 0; i < gsize; i++)
1897     {
1898       hseqs[index++] = sg.getSequenceAt(i);
1899     }
1900
1901     ap.av.hideSequence(hseqs);
1902     // refresh(); TODO: ? needed ?
1903     ap.av.sendSelection();
1904   }
1905
1906   public void copy_actionPerformed()
1907   {
1908     ap.alignFrame.copy_actionPerformed(null);
1909   }
1910
1911   public void cut_actionPerformed()
1912   {
1913     ap.alignFrame.cut_actionPerformed(null);
1914   }
1915
1916   void changeCase(ActionEvent e)
1917   {
1918     Object source = e.getSource();
1919     SequenceGroup sg = ap.av.getSelectionGroup();
1920
1921     if (sg != null)
1922     {
1923       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1924               sg.getEndRes() + 1);
1925
1926       String description;
1927       int caseChange;
1928
1929       if (source == toggle)
1930       {
1931         description = "Toggle Case";
1932         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1933       }
1934       else if (source == upperCase)
1935       {
1936         description = "To Upper Case";
1937         caseChange = ChangeCaseCommand.TO_UPPER;
1938       }
1939       else
1940       {
1941         description = "To Lower Case";
1942         caseChange = ChangeCaseCommand.TO_LOWER;
1943       }
1944
1945       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1946               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1947               startEnd, caseChange);
1948
1949       ap.alignFrame.addHistoryItem(caseCommand);
1950
1951       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1952               .getSequences());
1953
1954     }
1955   }
1956
1957   public void outputText_actionPerformed(ActionEvent e)
1958   {
1959     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1960     cap.setForInput(null);
1961     Desktop.addInternalFrame(cap,
1962             "Alignment output - " + e.getActionCommand(), 600, 500);
1963
1964     String[] omitHidden = null;
1965
1966     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1967     // or we simply trust the user wants
1968     // wysiwig behaviour
1969     SequenceGroup sg = ap.av.getSelectionGroup();
1970     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1971     omitHidden = ap.av.getViewAsString(true);
1972     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1973     AlignmentAnnotation[] nala = ap.av.getAlignment()
1974             .getAlignmentAnnotation();
1975     if (nala != null)
1976     {
1977       for (int i = 0; i < nala.length; i++)
1978       {
1979         AlignmentAnnotation na = nala[i];
1980         oal.addAnnotation(na);
1981       }
1982     }
1983     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1984             oal, omitHidden, csel, sg));
1985     oal = null;
1986   }
1987
1988   public void pdbFromFile_actionPerformed() throws Exception
1989   {
1990     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1991             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1992     chooser.setFileView(new jalview.io.JalviewFileView());
1993     chooser.setDialogTitle("Select a PDB file for "
1994             + sequence.getDisplayId(false));
1995     chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1996             + sequence.getDisplayId(false) + "'");
1997
1998     int value = chooser.showOpenDialog(null);
1999
2000     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2001     {
2002       String choice = chooser.getSelectedFile().getPath();
2003       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2004       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2005               jalview.io.AppletFormatAdapter.FILE, sequence, true);
2006     }
2007
2008   }
2009     // JBNote: commented out - these won't be instantiated here...!
2010 //  public void RNAFold_actionPerformed() throws Exception
2011 //  {
2012 //        Predict2D P2D = new Predict2D();
2013 //        P2D.getStructure2DFromRNAFold("toto");
2014 //  }
2015 //
2016 //  public void ContraFold_actionPerformed() throws Exception
2017 //  {
2018 //        Predict2D P2D = new Predict2D();
2019 //        P2D.getStructure2DFromContraFold("toto");
2020 //  }
2021   public void enterPDB_actionPerformed()
2022   {
2023     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2024             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
2025
2026     if (id != null && id.length() > 0)
2027     {
2028       PDBEntry entry = new PDBEntry();
2029       entry.setId(id.toUpperCase());
2030       sequence.getDatasetSequence().addPDBId(entry);
2031     }
2032   }
2033
2034   public void discoverPDB_actionPerformed()
2035   {
2036
2037     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2038     { sequence }
2039             : ap.av.getSequenceSelection());
2040     Thread discpdb = new Thread(new Runnable()
2041     {
2042       public void run()
2043       {
2044
2045         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2046                 .fetchDBRefs(false);
2047       }
2048
2049     });
2050     discpdb.start();
2051   }
2052
2053   public void sequenceFeature_actionPerformed()
2054   {
2055     SequenceGroup sg = ap.av.getSelectionGroup();
2056     if (sg == null)
2057     {
2058       return;
2059     }
2060
2061     int rsize = 0, gSize = sg.getSize();
2062     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2063     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2064
2065     for (int i = 0; i < gSize; i++)
2066     {
2067       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2068       int end = sg.findEndRes(sg.getSequenceAt(i));
2069       if (start <= end)
2070       {
2071         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2072         features[rsize] = new SequenceFeature(null, null, null, start, end,
2073                 "Jalview");
2074         rsize++;
2075       }
2076     }
2077     rseqs = new SequenceI[rsize];
2078     tfeatures = new SequenceFeature[rsize];
2079     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2080     System.arraycopy(features, 0, tfeatures, 0, rsize);
2081     features = tfeatures;
2082     seqs = rseqs;
2083     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2084             features, true, ap))
2085     {
2086       ap.alignFrame.setShowSeqFeatures(true);
2087       ap.highlightSearchResults(null);
2088     }
2089   }
2090
2091   public void textColour_actionPerformed()
2092   {
2093     SequenceGroup sg = getGroup();
2094     if (sg != null)
2095     {
2096       new TextColourChooser().chooseColour(ap, sg);
2097     }
2098   }
2099
2100   public void colourByStructure(String pdbid)
2101   {
2102     Annotation[] anots = ap.av.getStructureSelectionManager()
2103             .colourSequenceFromStructure(sequence, pdbid);
2104
2105     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2106             "Coloured by " + pdbid, anots);
2107
2108     ap.av.getAlignment().addAnnotation(an);
2109     an.createSequenceMapping(sequence, 0, true);
2110     // an.adjustForAlignment();
2111     ap.av.getAlignment().setAnnotationIndex(an, 0);
2112
2113     ap.adjustAnnotationHeight();
2114
2115     sequence.addAlignmentAnnotation(an);
2116
2117   }
2118
2119   public void editSequence_actionPerformed(ActionEvent actionEvent)
2120   {
2121     SequenceGroup sg = ap.av.getSelectionGroup();
2122
2123     if (sg != null)
2124     {
2125       if (sequence == null)
2126         sequence = (Sequence) sg.getSequenceAt(0);
2127
2128       EditNameDialog dialog = new EditNameDialog(
2129               sequence.getSequenceAsString(sg.getStartRes(),
2130                       sg.getEndRes() + 1), null, "Edit Sequence ", null,
2131               "Edit Sequence", ap.alignFrame);
2132
2133       if (dialog.accept)
2134       {
2135         EditCommand editCommand = new EditCommand("Edit Sequences",
2136                 EditCommand.REPLACE, dialog.getName().replace(' ',
2137                         ap.av.getGapCharacter()),
2138                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2139                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2140
2141         ap.alignFrame.addHistoryItem(editCommand);
2142
2143         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2144                 .getSequences());
2145       }
2146     }
2147   }
2148
2149 }