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