src/jalview/gui/PopupMenu.java

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