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