src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AAFrequency;
  24 import jalview.analysis.AlignmentAnnotationUtils;
  25 import jalview.analysis.Conservation;
  26 import jalview.commands.ChangeCaseCommand;
  27 import jalview.commands.EditCommand;
  28 import jalview.commands.EditCommand.Action;
  29 import jalview.datamodel.AlignmentAnnotation;
  30 import jalview.datamodel.AlignmentI;
  31 import jalview.datamodel.Annotation;
  32 import jalview.datamodel.ColumnSelection;
  33 import jalview.datamodel.DBRefEntry;
  34 import jalview.datamodel.PDBEntry;
  35 import jalview.datamodel.Sequence;
  36 import jalview.datamodel.SequenceFeature;
  37 import jalview.datamodel.SequenceGroup;
  38 import jalview.datamodel.SequenceI;
  39 import jalview.io.FormatAdapter;
  40 import jalview.io.SequenceAnnotationReport;
  41 import jalview.schemes.AnnotationColourGradient;
  42 import jalview.schemes.Blosum62ColourScheme;
  43 import jalview.schemes.BuriedColourScheme;
  44 import jalview.schemes.ClustalxColourScheme;
  45 import jalview.schemes.HelixColourScheme;
  46 import jalview.schemes.HydrophobicColourScheme;
  47 import jalview.schemes.NucleotideColourScheme;
  48 import jalview.schemes.PIDColourScheme;
  49 import jalview.schemes.PurinePyrimidineColourScheme;
  50 import jalview.schemes.ResidueProperties;
  51 import jalview.schemes.StrandColourScheme;
  52 import jalview.schemes.TaylorColourScheme;
  53 import jalview.schemes.TurnColourScheme;
  54 import jalview.schemes.UserColourScheme;
  55 import jalview.schemes.ZappoColourScheme;
  56 import jalview.util.GroupUrlLink;
  57 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  58 import jalview.util.MessageManager;
  59 import jalview.util.UrlLink;
  60
  61 import java.awt.Color;
  62 import java.awt.event.ActionEvent;
  63 import java.awt.event.ActionListener;
  64 import java.util.ArrayList;
  65 import java.util.Arrays;
  66 import java.util.Collection;
  67 import java.util.Collections;
  68 import java.util.Hashtable;
  69 import java.util.LinkedHashMap;
  70 import java.util.List;
  71 import java.util.Map;
  72 import java.util.TreeMap;
  73 import java.util.Vector;
  74
  75 import javax.swing.ButtonGroup;
  76 import javax.swing.JCheckBoxMenuItem;
  77 import javax.swing.JColorChooser;
  78 import javax.swing.JMenu;
  79 import javax.swing.JMenuItem;
  80 import javax.swing.JOptionPane;
  81 import javax.swing.JPopupMenu;
  82 import javax.swing.JRadioButtonMenuItem;
  83
  84 /**
  85  * DOCUMENT ME!
  86  *
  87  * @author $author$
  88  * @version $Revision: 1.118 $
  89  */
  90 public class PopupMenu extends JPopupMenu
  91 {
  92   private static final String ALL_ANNOTATIONS = "All";
  93
  94   private static final String COMMA = ",";
  95
  96   JMenu groupMenu = new JMenu();
  97
  98   JMenuItem groupName = new JMenuItem();
  99
 100   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
 101
 102   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 103
 104   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 105
 106   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
 107
 108   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 109
 110   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 111
 112   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 113
 114   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 115
 116   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
 117
 118   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
 119
 120   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
 121
 122   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 123
 124   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 125
 126   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 127
 128   // protected JRadioButtonMenuItem covariationColour = new
 129   // JRadioButtonMenuItem();
 130
 131   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 132
 133   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 134
 135   AlignmentPanel ap;
 136
 137   JMenu sequenceMenu = new JMenu();
 138
 139   JMenuItem sequenceName = new JMenuItem();
 140
 141   JMenuItem sequenceDetails = new JMenuItem();
 142
 143   JMenuItem sequenceSelDetails = new JMenuItem();
 144
 145   JMenuItem makeReferenceSeq = new JMenuItem();
 146
 147   JMenuItem chooseAnnotations = new JMenuItem();
 148
 149   SequenceI sequence;
 150
 151   JMenuItem createGroupMenuItem = new JMenuItem();
 152
 153   JMenuItem unGroupMenuItem = new JMenuItem();
 154
 155   JMenuItem outline = new JMenuItem();
 156
 157   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 158
 159   JMenu colourMenu = new JMenu();
 160
 161   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 162
 163   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 164
 165   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 166
 167   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 168
 169   JMenu editMenu = new JMenu();
 170
 171   JMenuItem cut = new JMenuItem();
 172
 173   JMenuItem copy = new JMenuItem();
 174
 175   JMenuItem upperCase = new JMenuItem();
 176
 177   JMenuItem lowerCase = new JMenuItem();
 178
 179   JMenuItem toggle = new JMenuItem();
 180
 181   JMenu pdbMenu = new JMenu();
 182
 183   JMenuItem pdbFromFile = new JMenuItem();
 184
 185   // JBPNote: Commented these out - Should add these services via the web
 186   // services menu system.
 187   // JMenuItem ContraFold = new JMenuItem();
 188
 189   // JMenuItem RNAFold = new JMenuItem();
 190
 191   JMenuItem enterPDB = new JMenuItem();
 192
 193   JMenuItem discoverPDB = new JMenuItem();
 194
 195   JMenu outputMenu = new JMenu();
 196
 197   JMenu seqShowAnnotationsMenu = new JMenu();
 198
 199   JMenu seqHideAnnotationsMenu = new JMenu();
 200
 201   JMenuItem seqAddReferenceAnnotations = new JMenuItem();
 202
 203   JMenu groupShowAnnotationsMenu = new JMenu();
 204
 205   JMenu groupHideAnnotationsMenu = new JMenu();
 206
 207   JMenuItem groupAddReferenceAnnotations = new JMenuItem();
 208
 209   JMenuItem sequenceFeature = new JMenuItem();
 210
 211   JMenuItem textColour = new JMenuItem();
 212
 213   JMenu jMenu1 = new JMenu();
 214
 215   JMenu structureMenu = new JMenu();
 216
 217   JMenu viewStructureMenu = new JMenu();
 218
 219   // JMenu colStructureMenu = new JMenu();
 220   JMenuItem editSequence = new JMenuItem();
 221
 222   // JMenuItem annotationMenuItem = new JMenuItem();
 223
 224   JMenu groupLinksMenu;
 225
 226   JMenuItem hideInsertions = new JMenuItem();
 227
 228   /**
 229    * Creates a new PopupMenu object.
 230    *
 231    * @param ap
 232    *          DOCUMENT ME!
 233    * @param seq
 234    *          DOCUMENT ME!
 235    */
 236   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 237   {
 238     this(ap, seq, links, null);
 239   }
 240
 241   /**
 242    *
 243    * @param ap
 244    * @param seq
 245    * @param links
 246    * @param groupLinks
 247    */
 248   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 249           Vector links, Vector groupLinks)
 250   {
 251     // /////////////////////////////////////////////////////////
 252     // If this is activated from the sequence panel, the user may want to
 253     // edit or annotate a particular residue. Therefore display the residue menu
 254     //
 255     // If from the IDPanel, we must display the sequence menu
 256     // ////////////////////////////////////////////////////////
 257     this.ap = ap;
 258     sequence = seq;
 259
 260     ButtonGroup colours = new ButtonGroup();
 261     colours.add(noColourmenuItem);
 262     colours.add(clustalColour);
 263     colours.add(zappoColour);
 264     colours.add(taylorColour);
 265     colours.add(hydrophobicityColour);
 266     colours.add(helixColour);
 267     colours.add(strandColour);
 268     colours.add(turnColour);
 269     colours.add(buriedColour);
 270     colours.add(abovePIDColour);
 271     colours.add(userDefinedColour);
 272     colours.add(PIDColour);
 273     colours.add(BLOSUM62Colour);
 274     colours.add(purinePyrimidineColour);
 275     colours.add(RNAInteractionColour);
 276     // colours.add(covariationColour);
 277
 278     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 279     {
 280       JMenuItem item = new JMenuItem(
 281               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 282
 283       item.addActionListener(new java.awt.event.ActionListener()
 284       {
 285         @Override
 286         public void actionPerformed(ActionEvent e)
 287         {
 288           outputText_actionPerformed(e);
 289         }
 290       });
 291
 292       outputMenu.add(item);
 293     }
 294
 295     /*
 296      * Build menus for annotation types that may be shown or hidden, and for
 297      * 'reference annotations' that may be added to the alignment. First for the
 298      * currently selected sequence (if there is one):
 299      */
 300     final List<SequenceI> selectedSequence = (seq == null ? Collections
 301             .<SequenceI> emptyList() : Arrays.asList(seq));
 302     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
 303             seqHideAnnotationsMenu, selectedSequence);
 304     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
 305             selectedSequence);
 306
 307     /*
 308      * And repeat for the current selection group (if there is one):
 309      */
 310     final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
 311             .<SequenceI> emptyList() : ap.av.getSelectionGroup()
 312             .getSequences());
 313     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
 314             groupHideAnnotationsMenu, selectedGroup);
 315     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
 316             selectedGroup);
 317
 318     try
 319     {
 320       jbInit();
 321     } catch (Exception e)
 322     {
 323       e.printStackTrace();
 324     }
 325
 326     JMenuItem menuItem;
 327     if (seq != null)
 328     {
 329       sequenceMenu.setText(sequence.getName());
 330       if (seq == ap.av.getAlignment().getSeqrep())
 331       {
 332         makeReferenceSeq.setText("Unmark representative");
 333       } else {
 334         makeReferenceSeq.setText("Mark as representative");
 335       }
 336
 337       if (seq.getDatasetSequence().getPDBId() != null
 338               && seq.getDatasetSequence().getPDBId().size() > 0)
 339       {
 340         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 341                 .elements();
 342
 343         while (e.hasMoreElements())
 344         {
 345           final PDBEntry pdb = (PDBEntry) e.nextElement();
 346
 347           menuItem = new JMenuItem();
 348           menuItem.setText(pdb.getId());
 349           menuItem.addActionListener(new ActionListener()
 350           {
 351             @Override
 352             public void actionPerformed(ActionEvent e)
 353             {
 354               // TODO re JAL-860: optionally open dialog or provide a menu entry
 355               // allowing user to open just one structure per sequence
 356               // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 357               // { pdb })[0], null, ap);
 358               new StructureViewer(ap.getStructureSelectionManager())
 359                       .viewStructures(pdb,
 360                               ap.av.collateForPDB(new PDBEntry[]
 361                               { pdb })[0], null, ap);
 362             }
 363           });
 364           viewStructureMenu.add(menuItem);
 365
 366           /*
 367            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 368            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 369            * public void actionPerformed(ActionEvent e) {
 370            * colourByStructure(pdb.getId()); } });
 371            * colStructureMenu.add(menuItem);
 372            */
 373         }
 374       }
 375       else
 376       {
 377         if (ap.av.getAlignment().isNucleotide() == false)
 378         {
 379           structureMenu.remove(viewStructureMenu);
 380         }
 381         // structureMenu.remove(colStructureMenu);
 382       }
 383       if (ap.av.getAlignment().isNucleotide() == true)
 384       {
 385         AlignmentAnnotation[] aa = ap.av.getAlignment()
 386                 .getAlignmentAnnotation();
 387         for (int i = 0; aa != null && i < aa.length; i++)
 388         {
 389           if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
 390           {
 391             final String rnastruc = aa[i].getRNAStruc();
 392             final String structureLine = aa[i].label + " (alignment)";
 393             menuItem = new JMenuItem();
 394             menuItem.setText(MessageManager.formatMessage(
 395                     "label.2d_rna_structure_line", new String[]
 396                     { structureLine }));
 397             menuItem.addActionListener(new java.awt.event.ActionListener()
 398             {
 399               @Override
 400               public void actionPerformed(ActionEvent e)
 401               {
 402                 // // System.out.println("1:"+structureLine);
 403                 // System.out.println("1:sname" + seq.getName());
 404                 // System.out.println("2:seq" + seq);
 405                 //
 406                 // // System.out.println("3:"+seq.getSequenceAsString());
 407                 // System.out.println("3:strucseq" + rnastruc);
 408                 // // System.out.println("4:struc"+seq.getRNA());
 409                 // System.out.println("5:name" + seq.getName());
 410                 // System.out.println("6:ap" + ap);
 411                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
 412                         rnastruc, seq.getName(), ap);
 413                 // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
 414                 // seq.getName(), ap);
 415                 System.out.println("end");
 416               }
 417             });
 418             viewStructureMenu.add(menuItem);
 419           }
 420         }
 421
 422         // SequenceFeatures[] test = seq.getSequenceFeatures();
 423
 424         if (seq.getAnnotation() != null)
 425         {
 426           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 427           for (int i = 0; i < seqAnno.length; i++)
 428           {
 429             if (seqAnno[i].isValidStruc())
 430             {
 431               final String rnastruc = seqAnno[i].getRNAStruc();
 432
 433               // TODO: make rnastrucF a bit more nice
 434               menuItem = new JMenuItem();
 435               menuItem.setText(MessageManager.formatMessage(
 436                       "label.2d_rna_sequence_name", new String[]
 437                       { seq.getName() }));
 438               menuItem.addActionListener(new java.awt.event.ActionListener()
 439               {
 440                 @Override
 441                 public void actionPerformed(ActionEvent e)
 442                 {
 443                   // TODO: VARNA does'nt print gaps in the sequence
 444
 445                   new AppVarna(seq.getName() + " structure", seq, seq
 446                           .getSequenceAsString(), rnastruc, seq.getName(),
 447                           ap);
 448                 }
 449               });
 450               viewStructureMenu.add(menuItem);
 451             }
 452           }
 453         }
 454       }
 455
 456       menuItem = new JMenuItem(
 457               MessageManager.getString("action.hide_sequences"));
 458       menuItem.addActionListener(new java.awt.event.ActionListener()
 459       {
 460         @Override
 461         public void actionPerformed(ActionEvent e)
 462         {
 463           hideSequences(false);
 464         }
 465       });
 466       add(menuItem);
 467
 468       if (ap.av.getSelectionGroup() != null
 469               && ap.av.getSelectionGroup().getSize() > 1)
 470       {
 471         menuItem = new JMenuItem(MessageManager.formatMessage(
 472                 "label.represent_group_with", new String[]
 473                 { seq.getName() }));
 474         menuItem.addActionListener(new java.awt.event.ActionListener()
 475         {
 476           @Override
 477           public void actionPerformed(ActionEvent e)
 478           {
 479             hideSequences(true);
 480           }
 481         });
 482         sequenceMenu.add(menuItem);
 483       }
 484
 485       if (ap.av.hasHiddenRows())
 486       {
 487         final int index = ap.av.getAlignment().findIndex(seq);
 488
 489         if (ap.av.adjustForHiddenSeqs(index)
 490                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 491         {
 492           menuItem = new JMenuItem(
 493                   MessageManager.getString("action.reveal_sequences"));
 494           menuItem.addActionListener(new ActionListener()
 495           {
 496             @Override
 497             public void actionPerformed(ActionEvent e)
 498             {
 499               ap.av.showSequence(index);
 500               if (ap.overviewPanel != null)
 501               {
 502                 ap.overviewPanel.updateOverviewImage();
 503               }
 504             }
 505           });
 506           add(menuItem);
 507         }
 508       }
 509     }
 510     // for the case when no sequences are even visible
 511     if (ap.av.hasHiddenRows())
 512     {
 513       {
 514         menuItem = new JMenuItem(
 515                 MessageManager.getString("action.reveal_all"));
 516         menuItem.addActionListener(new ActionListener()
 517         {
 518           @Override
 519           public void actionPerformed(ActionEvent e)
 520           {
 521             ap.av.showAllHiddenSeqs();
 522             if (ap.overviewPanel != null)
 523             {
 524               ap.overviewPanel.updateOverviewImage();
 525             }
 526           }
 527         });
 528
 529         add(menuItem);
 530       }
 531
 532     }
 533
 534     SequenceGroup sg = ap.av.getSelectionGroup();
 535     boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
 536             .getGroups().contains(sg) : false;
 537
 538     if (sg != null && sg.getSize() > 0)
 539     {
 540       groupName.setText(MessageManager.formatMessage("label.name_param",
 541               new String[]
 542               { sg.getName() }));
 543       groupName.setText(MessageManager
 544               .getString("label.edit_name_and_description_current_group"));
 545
 546       if (sg.cs instanceof ZappoColourScheme)
 547       {
 548         zappoColour.setSelected(true);
 549       }
 550       else if (sg.cs instanceof TaylorColourScheme)
 551       {
 552         taylorColour.setSelected(true);
 553       }
 554       else if (sg.cs instanceof PIDColourScheme)
 555       {
 556         PIDColour.setSelected(true);
 557       }
 558       else if (sg.cs instanceof Blosum62ColourScheme)
 559       {
 560         BLOSUM62Colour.setSelected(true);
 561       }
 562       else if (sg.cs instanceof UserColourScheme)
 563       {
 564         userDefinedColour.setSelected(true);
 565       }
 566       else if (sg.cs instanceof HydrophobicColourScheme)
 567       {
 568         hydrophobicityColour.setSelected(true);
 569       }
 570       else if (sg.cs instanceof HelixColourScheme)
 571       {
 572         helixColour.setSelected(true);
 573       }
 574       else if (sg.cs instanceof StrandColourScheme)
 575       {
 576         strandColour.setSelected(true);
 577       }
 578       else if (sg.cs instanceof TurnColourScheme)
 579       {
 580         turnColour.setSelected(true);
 581       }
 582       else if (sg.cs instanceof BuriedColourScheme)
 583       {
 584         buriedColour.setSelected(true);
 585       }
 586       else if (sg.cs instanceof ClustalxColourScheme)
 587       {
 588         clustalColour.setSelected(true);
 589       }
 590       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 591       {
 592         purinePyrimidineColour.setSelected(true);
 593       }
 594
 595       /*
 596        * else if (sg.cs instanceof CovariationColourScheme) {
 597        * covariationColour.setSelected(true); }
 598        */
 599       else
 600       {
 601         noColourmenuItem.setSelected(true);
 602       }
 603
 604       if (sg.cs != null && sg.cs.conservationApplied())
 605       {
 606         conservationMenuItem.setSelected(true);
 607       }
 608       displayNonconserved.setSelected(sg.getShowNonconserved());
 609       showText.setSelected(sg.getDisplayText());
 610       showColourText.setSelected(sg.getColourText());
 611       showBoxes.setSelected(sg.getDisplayBoxes());
 612       // add any groupURLs to the groupURL submenu and make it visible
 613       if (groupLinks != null && groupLinks.size() > 0)
 614       {
 615         buildGroupURLMenu(sg, groupLinks);
 616       }
 617       // Add a 'show all structures' for the current selection
 618       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
 619       SequenceI sqass = null;
 620       for (SequenceI sq : ap.av.getSequenceSelection())
 621       {
 622         Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
 623         if (pes != null && pes.size() > 0)
 624         {
 625           reppdb.put(pes.get(0).getId(), pes.get(0));
 626           for (PDBEntry pe : pes)
 627           {
 628             pdbe.put(pe.getId(), pe);
 629             if (sqass == null)
 630             {
 631               sqass = sq;
 632             }
 633           }
 634         }
 635       }
 636       if (pdbe.size() > 0)
 637       {
 638         final PDBEntry[] pe = pdbe.values().toArray(
 639                 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
 640                 new PDBEntry[reppdb.size()]);
 641         final JMenuItem gpdbview, rpdbview;
 642         if (pdbe.size() == 1)
 643         {
 644           structureMenu.add(gpdbview = new JMenuItem(MessageManager
 645                   .formatMessage("label.view_structure_for", new String[]
 646                   { sqass.getDisplayId(false) })));
 647         }
 648         else
 649         {
 650           structureMenu.add(gpdbview = new JMenuItem(MessageManager
 651                   .formatMessage("label.view_all_structures", new String[]
 652                   { new Integer(pdbe.size()).toString() })));
 653         }
 654         gpdbview.setToolTipText(MessageManager
 655                 .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
 656         gpdbview.addActionListener(new ActionListener()
 657         {
 658
 659           @Override
 660           public void actionPerformed(ActionEvent e)
 661           {
 662             new StructureViewer(ap.getStructureSelectionManager())
 663                     .viewStructures(ap, pe, ap.av.collateForPDB(pe));
 664           }
 665         });
 666         if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
 667         {
 668           structureMenu.add(rpdbview = new JMenuItem(MessageManager
 669                   .formatMessage(
 670                           "label.view_all_representative_structures",
 671                           new String[]
 672                           { new Integer(reppdb.size()).toString() })));
 673           rpdbview.setToolTipText(MessageManager
 674                   .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
 675           rpdbview.addActionListener(new ActionListener()
 676           {
 677
 678             @Override
 679             public void actionPerformed(ActionEvent e)
 680             {
 681               new StructureViewer(ap.getStructureSelectionManager())
 682                       .viewStructures(ap, pr, ap.av.collateForPDB(pr));
 683             }
 684           });
 685         }
 686       }
 687     }
 688     else
 689     {
 690       groupMenu.setVisible(false);
 691       editMenu.setVisible(false);
 692     }
 693
 694     if (!isDefinedGroup)
 695     {
 696       createGroupMenuItem.setVisible(true);
 697       unGroupMenuItem.setVisible(false);
 698       jMenu1.setText(MessageManager.getString("action.edit_new_group"));
 699     }
 700     else
 701     {
 702       createGroupMenuItem.setVisible(false);
 703       unGroupMenuItem.setVisible(true);
 704       jMenu1.setText(MessageManager.getString("action.edit_group"));
 705     }
 706
 707     if (seq == null)
 708     {
 709       sequenceMenu.setVisible(false);
 710       structureMenu.setVisible(false);
 711     }
 712
 713     if (links != null && links.size() > 0)
 714     {
 715
 716       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
 717       Vector linkset = new Vector();
 718       for (int i = 0; i < links.size(); i++)
 719       {
 720         String link = links.elementAt(i).toString();
 721         UrlLink urlLink = null;
 722         try
 723         {
 724           urlLink = new UrlLink(link);
 725         } catch (Exception foo)
 726         {
 727           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 728                   + "'", foo);
 729           continue;
 730         }
 731         ;
 732         if (!urlLink.isValid())
 733         {
 734           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 735           continue;
 736         }
 737         final String label = urlLink.getLabel();
 738         if (seq != null && urlLink.isDynamic())
 739         {
 740
 741           // collect matching db-refs
 742           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 743                   seq.getDBRef(), new String[]
 744                   { urlLink.getTarget() });
 745           // collect id string too
 746           String id = seq.getName();
 747           String descr = seq.getDescription();
 748           if (descr != null && descr.length() < 1)
 749           {
 750             descr = null;
 751           }
 752
 753           if (dbr != null)
 754           {
 755             for (int r = 0; r < dbr.length; r++)
 756             {
 757               if (id != null && dbr[r].getAccessionId().equals(id))
 758               {
 759                 // suppress duplicate link creation for the bare sequence ID
 760                 // string with this link
 761                 id = null;
 762               }
 763               // create Bare ID link for this RUL
 764               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 765                       true);
 766               if (urls != null)
 767               {
 768                 for (int u = 0; u < urls.length; u += 2)
 769                 {
 770                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 771                   {
 772                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 773                     addshowLink(linkMenu, label + "|" + urls[u],
 774                             urls[u + 1]);
 775                   }
 776                 }
 777               }
 778             }
 779           }
 780           if (id != null)
 781           {
 782             // create Bare ID link for this RUL
 783             String[] urls = urlLink.makeUrls(id, true);
 784             if (urls != null)
 785             {
 786               for (int u = 0; u < urls.length; u += 2)
 787               {
 788                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 789                 {
 790                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 791                   addshowLink(linkMenu, label, urls[u + 1]);
 792                 }
 793               }
 794             }
 795           }
 796           // Create urls from description but only for URL links which are regex
 797           // links
 798           if (descr != null && urlLink.getRegexReplace() != null)
 799           {
 800             // create link for this URL from description where regex matches
 801             String[] urls = urlLink.makeUrls(descr, true);
 802             if (urls != null)
 803             {
 804               for (int u = 0; u < urls.length; u += 2)
 805               {
 806                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 807                 {
 808                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 809                   addshowLink(linkMenu, label, urls[u + 1]);
 810                 }
 811               }
 812             }
 813           }
 814         }
 815         else
 816         {
 817           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 818           {
 819             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 820             // Add a non-dynamic link
 821             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 822           }
 823         }
 824       }
 825       if (sequence != null)
 826       {
 827         sequenceMenu.add(linkMenu);
 828       }
 829       else
 830       {
 831         add(linkMenu);
 832       }
 833     }
 834   }
 835
 836   /**
 837    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
 838    * "All" is added first, followed by a separator. Then add any annotation
 839    * types associated with the current selection. Separate menus are built for
 840    * the selected sequence group (if any), and the selected sequence.
 841    * <p>
 842    * Some annotation rows are always rendered together - these can be identified
 843    * by a common graphGroup property > -1. Only one of each group will be marked
 844    * as visible (to avoid duplication of the display). For such groups we add a
 845    * composite type name, e.g.
 846    * <p>
 847    * IUPredWS (Long), IUPredWS (Short)
 848    *
 849    * @param seq
 850    */
 851   protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
 852           List<SequenceI> forSequences)
 853   {
 854     showMenu.removeAll();
 855     hideMenu.removeAll();
 856
 857     final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
 858     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
 859     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
 860             false);
 861     showMenu.addSeparator();
 862     hideMenu.addSeparator();
 863
 864     final AlignmentAnnotation[] annotations = ap.getAlignment()
 865             .getAlignmentAnnotation();
 866
 867     /*
 868      * Find shown/hidden annotations types, distinguished by source (calcId),
 869      * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
 870      * the insertion order, which is the order of the annotations on the
 871      * alignment.
 872      */
 873     Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
 874     Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
 875     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
 876             hiddenTypes,
 877             AlignmentAnnotationUtils.asList(annotations),
 878             forSequences);
 879
 880     for (String calcId : hiddenTypes.keySet())
 881     {
 882       for (List<String> type : hiddenTypes.get(calcId))
 883       {
 884         addAnnotationTypeToShowHide(showMenu, forSequences,
 885                 calcId, type, false, true);
 886       }
 887     }
 888     // grey out 'show annotations' if none are hidden
 889     showMenu.setEnabled(!hiddenTypes.isEmpty());
 890
 891     for (String calcId : shownTypes.keySet())
 892     {
 893       for (List<String> type : shownTypes.get(calcId))
 894       {
 895         addAnnotationTypeToShowHide(hideMenu, forSequences,
 896                 calcId, type, false, false);
 897       }
 898     }
 899     // grey out 'hide annotations' if none are shown
 900     hideMenu.setEnabled(!shownTypes.isEmpty());
 901   }
 902
 903   /**
 904    * Returns a list of sequences - either the current selection group (if there
 905    * is one), else the specified single sequence.
 906    *
 907    * @param seq
 908    * @return
 909    */
 910   protected List<SequenceI> getSequenceScope(SequenceI seq)
 911   {
 912     List<SequenceI> forSequences = null;
 913     final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
 914     if (selectionGroup != null && selectionGroup.getSize() > 0)
 915     {
 916       forSequences = selectionGroup.getSequences();
 917     }
 918     else
 919     {
 920       forSequences = seq == null ? Collections.<SequenceI> emptyList()
 921               : Arrays.asList(seq);
 922     }
 923     return forSequences;
 924   }
 925
 926   /**
 927    * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
 928    * menus.
 929    *
 930    * @param showOrHideMenu
 931    *          the menu to add to
 932    * @param forSequences
 933    *          the sequences whose annotations may be shown or hidden
 934    * @param calcId
 935    * @param types
 936    *          the label to add
 937    * @param allTypes
 938    *          if true this is a special label meaning 'All'
 939    * @param actionIsShow
 940    *          if true, the select menu item action is to show the annotation
 941    *          type, else hide
 942    */
 943   protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
 944           final List<SequenceI> forSequences, String calcId,
 945           final List<String> types, final boolean allTypes,
 946           final boolean actionIsShow)
 947   {
 948     String label = types.toString(); // [a, b, c]
 949     label = label.substring(1, label.length() - 1);
 950     final JMenuItem item = new JMenuItem(label);
 951     item.setToolTipText(calcId);
 952     item.addActionListener(new java.awt.event.ActionListener()
 953     {
 954       @Override
 955       public void actionPerformed(ActionEvent e)
 956       {
 957         showHideAnnotation_actionPerformed(types, forSequences, allTypes,
 958                 actionIsShow);
 959       }
 960     });
 961     showOrHideMenu.add(item);
 962   }
 963
 964   /**
 965    * Action on selecting a list of annotation type (or the 'all types' values)
 966    * to show or hide for the specified sequences.
 967    *
 968    * @param types
 969    * @param forSequences
 970    * @param anyType
 971    * @param doShow
 972    */
 973   protected void showHideAnnotation_actionPerformed(
 974           Collection<String> types, List<SequenceI> forSequences,
 975           boolean anyType, boolean doShow)
 976   {
 977     for (AlignmentAnnotation aa : ap.getAlignment()
 978             .getAlignmentAnnotation())
 979     {
 980       if (anyType || types.contains(aa.label))
 981       {
 982         if ((aa.sequenceRef != null)
 983                 && forSequences.contains(aa.sequenceRef))
 984         {
 985           aa.visible = doShow;
 986         }
 987       }
 988     }
 989     refresh();
 990   }
 991
 992   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 993   {
 994
 995     // TODO: usability: thread off the generation of group url content so root
 996     // menu appears asap
 997     // sequence only URLs
 998     // ID/regex match URLs
 999     groupLinksMenu = new JMenu(
1000             MessageManager.getString("action.group_link"));
1001     JMenu[] linkMenus = new JMenu[]
1002     { null, new JMenu(MessageManager.getString("action.ids")),
1003         new JMenu(MessageManager.getString("action.sequences")),
1004         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
1005                                                                        // types
1006                                                                        // of url
1007                                                                        // that
1008                                                                        // might
1009                                                                        // be
1010     // created.
1011     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1012     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1013     Hashtable commonDbrefs = new Hashtable();
1014     for (int sq = 0; sq < seqs.length; sq++)
1015     {
1016
1017       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
1018               .findPosition(sg.getEndRes());
1019       // just collect ids from dataset sequence
1020       // TODO: check if IDs collected from selecton group intersects with the
1021       // current selection, too
1022       SequenceI sqi = seqs[sq];
1023       while (sqi.getDatasetSequence() != null)
1024       {
1025         sqi = sqi.getDatasetSequence();
1026       }
1027       DBRefEntry[] dbr = sqi.getDBRef();
1028       if (dbr != null && dbr.length > 0)
1029       {
1030         for (int d = 0; d < dbr.length; d++)
1031         {
1032           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
1033           Object[] sarray = (Object[]) commonDbrefs.get(src);
1034           if (sarray == null)
1035           {
1036             sarray = new Object[2];
1037             sarray[0] = new int[]
1038             { 0 };
1039             sarray[1] = new String[seqs.length];
1040
1041             commonDbrefs.put(src, sarray);
1042           }
1043
1044           if (((String[]) sarray[1])[sq] == null)
1045           {
1046             if (!dbr[d].hasMap()
1047                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
1048             {
1049               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
1050               ((int[]) sarray[0])[0]++;
1051             }
1052           }
1053         }
1054       }
1055     }
1056     // now create group links for all distinct ID/sequence sets.
1057     boolean addMenu = false; // indicates if there are any group links to give
1058                              // to user
1059     for (int i = 0; i < groupLinks.size(); i++)
1060     {
1061       String link = groupLinks.elementAt(i).toString();
1062       GroupUrlLink urlLink = null;
1063       try
1064       {
1065         urlLink = new GroupUrlLink(link);
1066       } catch (Exception foo)
1067       {
1068         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
1069                 + "'", foo);
1070         continue;
1071       }
1072       ;
1073       if (!urlLink.isValid())
1074       {
1075         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
1076         continue;
1077       }
1078       final String label = urlLink.getLabel();
1079       boolean usingNames = false;
1080       // Now see which parts of the group apply for this URL
1081       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1082       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
1083       String[] seqstr, ids; // input to makeUrl
1084       if (idset != null)
1085       {
1086         int numinput = ((int[]) idset[0])[0];
1087         String[] allids = ((String[]) idset[1]);
1088         seqstr = new String[numinput];
1089         ids = new String[numinput];
1090         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1091         {
1092           if (allids[sq] != null)
1093           {
1094             ids[idcount] = allids[sq];
1095             seqstr[idcount++] = idandseqs[1][sq];
1096           }
1097         }
1098       }
1099       else
1100       {
1101         // just use the id/seq set
1102         seqstr = idandseqs[1];
1103         ids = idandseqs[0];
1104         usingNames = true;
1105       }
1106       // and try and make the groupURL!
1107
1108       Object[] urlset = null;
1109       try
1110       {
1111         urlset = urlLink.makeUrlStubs(ids, seqstr,
1112                 "FromJalview" + System.currentTimeMillis(), false);
1113       } catch (UrlStringTooLongException e)
1114       {
1115       }
1116       if (urlset != null)
1117       {
1118         int type = urlLink.getGroupURLType() & 3;
1119         // System.out.println(urlLink.getGroupURLType()
1120         // +" "+((String[])urlset[3])[0]);
1121         // first two bits ofurlLink type bitfield are sequenceids and sequences
1122         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1123         addshowLink(linkMenus[type], label
1124                 + (((type & 1) == 1) ? ("("
1125                         + (usingNames ? "Names" : ltarget) + ")") : ""),
1126                 urlLink, urlset);
1127         addMenu = true;
1128       }
1129     }
1130     if (addMenu)
1131     {
1132       groupLinksMenu = new JMenu(
1133               MessageManager.getString("action.group_link"));
1134       for (int m = 0; m < linkMenus.length; m++)
1135       {
1136         if (linkMenus[m] != null
1137                 && linkMenus[m].getMenuComponentCount() > 0)
1138         {
1139           groupLinksMenu.add(linkMenus[m]);
1140         }
1141       }
1142
1143       groupMenu.add(groupLinksMenu);
1144     }
1145   }
1146
1147   /**
1148    * add a show URL menu item to the given linkMenu
1149    *
1150    * @param linkMenu
1151    * @param label
1152    *          - menu label string
1153    * @param url
1154    *          - url to open
1155    */
1156   private void addshowLink(JMenu linkMenu, String label, final String url)
1157   {
1158     JMenuItem item = new JMenuItem(label);
1159     item.setToolTipText(MessageManager.formatMessage(
1160             "label.open_url_param", new String[]
1161             { url }));
1162     item.addActionListener(new java.awt.event.ActionListener()
1163     {
1164       @Override
1165       public void actionPerformed(ActionEvent e)
1166       {
1167         new Thread(new Runnable()
1168         {
1169
1170           @Override
1171           public void run()
1172           {
1173             showLink(url);
1174           }
1175
1176         }).start();
1177       }
1178     });
1179
1180     linkMenu.add(item);
1181   }
1182
1183   /**
1184    * add a late bound groupURL item to the given linkMenu
1185    *
1186    * @param linkMenu
1187    * @param label
1188    *          - menu label string
1189    * @param urlgenerator
1190    *          GroupURLLink used to generate URL
1191    * @param urlstub
1192    *          Object array returned from the makeUrlStubs function.
1193    */
1194   private void addshowLink(JMenu linkMenu, String label,
1195           final GroupUrlLink urlgenerator, final Object[] urlstub)
1196   {
1197     JMenuItem item = new JMenuItem(label);
1198     item.setToolTipText(MessageManager.formatMessage(
1199             "label.open_url_seqs_param",
1200             new Object[]
1201             { urlgenerator.getUrl_prefix(),
1202                 urlgenerator.getNumberInvolved(urlstub) }));
1203     // TODO: put in info about what is being sent.
1204     item.addActionListener(new java.awt.event.ActionListener()
1205     {
1206       @Override
1207       public void actionPerformed(ActionEvent e)
1208       {
1209         new Thread(new Runnable()
1210         {
1211
1212           @Override
1213           public void run()
1214           {
1215             try
1216             {
1217               showLink(urlgenerator.constructFrom(urlstub));
1218             } catch (UrlStringTooLongException e)
1219             {
1220             }
1221           }
1222
1223         }).start();
1224       }
1225     });
1226
1227     linkMenu.add(item);
1228   }
1229
1230   /**
1231    * DOCUMENT ME!
1232    *
1233    * @throws Exception
1234    *           DOCUMENT ME!
1235    */
1236   private void jbInit() throws Exception
1237   {
1238     groupMenu.setText(MessageManager.getString("label.group"));
1239     groupMenu.setText(MessageManager.getString("label.selection"));
1240     groupName.setText(MessageManager.getString("label.name"));
1241     groupName.addActionListener(new java.awt.event.ActionListener()
1242     {
1243       @Override
1244       public void actionPerformed(ActionEvent e)
1245       {
1246         groupName_actionPerformed();
1247       }
1248     });
1249     sequenceMenu.setText(MessageManager.getString("label.sequence"));
1250     sequenceName.setText(MessageManager
1251             .getString("label.edit_name_description"));
1252     sequenceName.addActionListener(new java.awt.event.ActionListener()
1253     {
1254       @Override
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         sequenceName_actionPerformed();
1258       }
1259     });
1260     chooseAnnotations.setText(MessageManager
1261             .getString("label.choose_annotations") + "...");
1262     chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1263     {
1264       @Override
1265       public void actionPerformed(ActionEvent e)
1266       {
1267         chooseAnnotations_actionPerformed(e);
1268       }
1269     });
1270     sequenceDetails.setText(MessageManager
1271             .getString("label.sequence_details") + "...");
1272     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1273     {
1274       @Override
1275       public void actionPerformed(ActionEvent e)
1276       {
1277         sequenceDetails_actionPerformed();
1278       }
1279     });
1280     sequenceSelDetails.setText(MessageManager
1281             .getString("label.sequence_details") + "...");
1282     sequenceSelDetails
1283             .addActionListener(new java.awt.event.ActionListener()
1284             {
1285               @Override
1286               public void actionPerformed(ActionEvent e)
1287               {
1288                 sequenceSelectionDetails_actionPerformed();
1289               }
1290             });
1291     PIDColour.setFocusPainted(false);
1292     unGroupMenuItem
1293             .setText(MessageManager.getString("action.remove_group"));
1294     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1295     {
1296       @Override
1297       public void actionPerformed(ActionEvent e)
1298       {
1299         unGroupMenuItem_actionPerformed();
1300       }
1301     });
1302     createGroupMenuItem.setText(MessageManager
1303             .getString("action.create_group"));
1304     createGroupMenuItem
1305             .addActionListener(new java.awt.event.ActionListener()
1306             {
1307               @Override
1308               public void actionPerformed(ActionEvent e)
1309               {
1310                 createGroupMenuItem_actionPerformed();
1311               }
1312             });
1313
1314     outline.setText(MessageManager.getString("action.border_colour"));
1315     outline.addActionListener(new java.awt.event.ActionListener()
1316     {
1317       @Override
1318       public void actionPerformed(ActionEvent e)
1319       {
1320         outline_actionPerformed();
1321       }
1322     });
1323     nucleotideMenuItem
1324             .setText(MessageManager.getString("label.nucleotide"));
1325     nucleotideMenuItem.addActionListener(new ActionListener()
1326     {
1327       @Override
1328       public void actionPerformed(ActionEvent e)
1329       {
1330         nucleotideMenuItem_actionPerformed();
1331       }
1332     });
1333     colourMenu.setText(MessageManager.getString("label.group_colour"));
1334     showBoxes.setText(MessageManager.getString("action.boxes"));
1335     showBoxes.setState(true);
1336     showBoxes.addActionListener(new ActionListener()
1337     {
1338       @Override
1339       public void actionPerformed(ActionEvent e)
1340       {
1341         showBoxes_actionPerformed();
1342       }
1343     });
1344     showText.setText(MessageManager.getString("action.text"));
1345     showText.setState(true);
1346     showText.addActionListener(new ActionListener()
1347     {
1348       @Override
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         showText_actionPerformed();
1352       }
1353     });
1354     showColourText.setText(MessageManager.getString("label.colour_text"));
1355     showColourText.addActionListener(new ActionListener()
1356     {
1357       @Override
1358       public void actionPerformed(ActionEvent e)
1359       {
1360         showColourText_actionPerformed();
1361       }
1362     });
1363     displayNonconserved.setText(MessageManager
1364             .getString("label.show_non_conversed"));
1365     displayNonconserved.setState(true);
1366     displayNonconserved.addActionListener(new ActionListener()
1367     {
1368       @Override
1369       public void actionPerformed(ActionEvent e)
1370       {
1371         showNonconserved_actionPerformed();
1372       }
1373     });
1374     editMenu.setText(MessageManager.getString("action.edit"));
1375     cut.setText(MessageManager.getString("action.cut"));
1376     cut.addActionListener(new ActionListener()
1377     {
1378       @Override
1379       public void actionPerformed(ActionEvent e)
1380       {
1381         cut_actionPerformed();
1382       }
1383     });
1384     upperCase.setText(MessageManager.getString("label.to_upper_case"));
1385     upperCase.addActionListener(new ActionListener()
1386     {
1387       @Override
1388       public void actionPerformed(ActionEvent e)
1389       {
1390         changeCase(e);
1391       }
1392     });
1393     copy.setText(MessageManager.getString("action.copy"));
1394     copy.addActionListener(new ActionListener()
1395     {
1396       @Override
1397       public void actionPerformed(ActionEvent e)
1398       {
1399         copy_actionPerformed();
1400       }
1401     });
1402     lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1403     lowerCase.addActionListener(new ActionListener()
1404     {
1405       @Override
1406       public void actionPerformed(ActionEvent e)
1407       {
1408         changeCase(e);
1409       }
1410     });
1411     toggle.setText(MessageManager.getString("label.toggle_case"));
1412     toggle.addActionListener(new ActionListener()
1413     {
1414       @Override
1415       public void actionPerformed(ActionEvent e)
1416       {
1417         changeCase(e);
1418       }
1419     });
1420     pdbMenu.setText(MessageManager
1421             .getString("label.associate_structure_with_sequence"));
1422     pdbFromFile.setText(MessageManager.getString("label.from_file"));
1423     pdbFromFile.addActionListener(new ActionListener()
1424     {
1425       @Override
1426       public void actionPerformed(ActionEvent e)
1427       {
1428         pdbFromFile_actionPerformed();
1429       }
1430     });
1431     // RNAFold.setText("From RNA Fold with predict2D");
1432     // RNAFold.addActionListener(new ActionListener()
1433     // {
1434     // public void actionPerformed(ActionEvent e)
1435     // {
1436     // try {
1437     // RNAFold_actionPerformed();
1438     // } catch (Exception e1) {
1439     // // TODO Auto-generated catch block
1440     // e1.printStackTrace();
1441     // }
1442     // }
1443     // });
1444     // ContraFold.setText("From Contra Fold with predict2D");
1445     // ContraFold.addActionListener(new ActionListener()
1446     // {
1447     // public void actionPerformed(ActionEvent e)
1448     // {
1449     // try {
1450     // ContraFold_actionPerformed();
1451     // } catch (Exception e1) {
1452     // // TODO Auto-generated catch block
1453     // e1.printStackTrace();
1454     // }
1455     // }
1456     // });
1457     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1458     enterPDB.addActionListener(new ActionListener()
1459     {
1460       @Override
1461       public void actionPerformed(ActionEvent e)
1462       {
1463         enterPDB_actionPerformed();
1464       }
1465     });
1466     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1467     discoverPDB.addActionListener(new ActionListener()
1468     {
1469       @Override
1470       public void actionPerformed(ActionEvent e)
1471       {
1472         discoverPDB_actionPerformed();
1473       }
1474     });
1475     outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1476             + "...");
1477     seqShowAnnotationsMenu.setText(MessageManager
1478             .getString("label.show_annotations"));
1479     seqHideAnnotationsMenu.setText(MessageManager
1480             .getString("label.hide_annotations"));
1481     groupShowAnnotationsMenu.setText(MessageManager
1482             .getString("label.show_annotations"));
1483     groupHideAnnotationsMenu.setText(MessageManager
1484             .getString("label.hide_annotations"));
1485     sequenceFeature.setText(MessageManager
1486             .getString("label.create_sequence_feature"));
1487     sequenceFeature.addActionListener(new ActionListener()
1488     {
1489       @Override
1490       public void actionPerformed(ActionEvent e)
1491       {
1492         sequenceFeature_actionPerformed();
1493       }
1494     });
1495     textColour.setText(MessageManager.getString("label.text_colour"));
1496     textColour.addActionListener(new ActionListener()
1497     {
1498       @Override
1499       public void actionPerformed(ActionEvent e)
1500       {
1501         textColour_actionPerformed();
1502       }
1503     });
1504     jMenu1.setText(MessageManager.getString("label.group"));
1505     structureMenu.setText(MessageManager.getString("label.structure"));
1506     viewStructureMenu.setText(MessageManager
1507             .getString("label.view_structure"));
1508     // colStructureMenu.setText("Colour By Structure");
1509     editSequence.setText(MessageManager.getString("label.edit_sequence")
1510             + "...");
1511     editSequence.addActionListener(new ActionListener()
1512     {
1513       @Override
1514       public void actionPerformed(ActionEvent actionEvent)
1515       {
1516         editSequence_actionPerformed(actionEvent);
1517       }
1518     });
1519     makeReferenceSeq.setText(MessageManager
1520             .getString("label.mark_as_representative"));
1521     makeReferenceSeq.addActionListener(new ActionListener()
1522     {
1523
1524       @Override
1525       public void actionPerformed(ActionEvent actionEvent)
1526       {
1527         makeReferenceSeq_actionPerformed(actionEvent);
1528
1529       }
1530     });
1531     hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
1532     hideInsertions.addActionListener(new ActionListener()
1533     {
1534
1535       @Override
1536       public void actionPerformed(ActionEvent e)
1537       {
1538         hideInsertions_actionPerformed(e);
1539       }
1540     });
1541     /*
1542      * annotationMenuItem.setText("By Annotation");
1543      * annotationMenuItem.addActionListener(new ActionListener() { public void
1544      * actionPerformed(ActionEvent actionEvent) {
1545      * annotationMenuItem_actionPerformed(actionEvent); } });
1546      */
1547     groupMenu.add(sequenceSelDetails);
1548     add(groupMenu);
1549     add(sequenceMenu);
1550     add(structureMenu);
1551     if (sequence!=null)
1552     {
1553       add(hideInsertions);
1554     }
1555     // annotations configuration panel suppressed for now
1556     // groupMenu.add(chooseAnnotations);
1557
1558     /*
1559      * Add show/hide annotations to the Sequence menu, and to the Selection menu
1560      * (if a selection group is in force).
1561      */
1562     sequenceMenu.add(seqShowAnnotationsMenu);
1563     sequenceMenu.add(seqHideAnnotationsMenu);
1564     sequenceMenu.add(seqAddReferenceAnnotations);
1565     groupMenu.add(groupShowAnnotationsMenu);
1566     groupMenu.add(groupHideAnnotationsMenu);
1567     groupMenu.add(groupAddReferenceAnnotations);
1568     groupMenu.add(editMenu);
1569     groupMenu.add(outputMenu);
1570     groupMenu.add(sequenceFeature);
1571     groupMenu.add(createGroupMenuItem);
1572     groupMenu.add(unGroupMenuItem);
1573     groupMenu.add(jMenu1);
1574     sequenceMenu.add(sequenceName);
1575     sequenceMenu.add(sequenceDetails);
1576     sequenceMenu.add(makeReferenceSeq);
1577     colourMenu.add(textColour);
1578     colourMenu.add(noColourmenuItem);
1579     colourMenu.add(clustalColour);
1580     colourMenu.add(BLOSUM62Colour);
1581     colourMenu.add(PIDColour);
1582     colourMenu.add(zappoColour);
1583     colourMenu.add(taylorColour);
1584     colourMenu.add(hydrophobicityColour);
1585     colourMenu.add(helixColour);
1586     colourMenu.add(strandColour);
1587     colourMenu.add(turnColour);
1588     colourMenu.add(buriedColour);
1589     colourMenu.add(nucleotideMenuItem);
1590     if (ap.getAlignment().isNucleotide())
1591     {
1592       // JBPNote - commented since the colourscheme isn't functional
1593       // colourMenu.add(RNAInteractionColour);
1594       colourMenu.add(purinePyrimidineColour);
1595     }
1596     // colourMenu.add(covariationColour);
1597     colourMenu.add(userDefinedColour);
1598
1599     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1600     {
1601       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1602               .getUserColourSchemes().keys();
1603
1604       while (userColours.hasMoreElements())
1605       {
1606         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1607         item.addActionListener(new ActionListener()
1608         {
1609           @Override
1610           public void actionPerformed(ActionEvent evt)
1611           {
1612             userDefinedColour_actionPerformed(evt);
1613           }
1614         });
1615         colourMenu.add(item);
1616       }
1617     }
1618
1619     colourMenu.addSeparator();
1620     colourMenu.add(abovePIDColour);
1621     colourMenu.add(conservationMenuItem);
1622     // colourMenu.add(annotationMenuItem);
1623     editMenu.add(copy);
1624     editMenu.add(cut);
1625     editMenu.add(editSequence);
1626     editMenu.add(upperCase);
1627     editMenu.add(lowerCase);
1628     editMenu.add(toggle);
1629     pdbMenu.add(pdbFromFile);
1630     // JBPNote: These shouldn't be added here - should appear in a generic
1631     // 'apply web service to this sequence menu'
1632     // pdbMenu.add(RNAFold);
1633     // pdbMenu.add(ContraFold);
1634     pdbMenu.add(enterPDB);
1635     pdbMenu.add(discoverPDB);
1636     jMenu1.add(groupName);
1637     jMenu1.add(colourMenu);
1638     jMenu1.add(showBoxes);
1639     jMenu1.add(showText);
1640     jMenu1.add(showColourText);
1641     jMenu1.add(outline);
1642     jMenu1.add(displayNonconserved);
1643     structureMenu.add(pdbMenu);
1644     structureMenu.add(viewStructureMenu);
1645     // structureMenu.add(colStructureMenu);
1646     noColourmenuItem.setText(MessageManager.getString("label.none"));
1647     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1648     {
1649       @Override
1650       public void actionPerformed(ActionEvent e)
1651       {
1652         noColourmenuItem_actionPerformed();
1653       }
1654     });
1655
1656     clustalColour.setText(MessageManager
1657             .getString("label.clustalx_colours"));
1658     clustalColour.addActionListener(new java.awt.event.ActionListener()
1659     {
1660       @Override
1661       public void actionPerformed(ActionEvent e)
1662       {
1663         clustalColour_actionPerformed();
1664       }
1665     });
1666     zappoColour.setText(MessageManager.getString("label.zappo"));
1667     zappoColour.addActionListener(new java.awt.event.ActionListener()
1668     {
1669       @Override
1670       public void actionPerformed(ActionEvent e)
1671       {
1672         zappoColour_actionPerformed();
1673       }
1674     });
1675     taylorColour.setText(MessageManager.getString("label.taylor"));
1676     taylorColour.addActionListener(new java.awt.event.ActionListener()
1677     {
1678       @Override
1679       public void actionPerformed(ActionEvent e)
1680       {
1681         taylorColour_actionPerformed();
1682       }
1683     });
1684     hydrophobicityColour.setText(MessageManager
1685             .getString("label.hydrophobicity"));
1686     hydrophobicityColour
1687             .addActionListener(new java.awt.event.ActionListener()
1688             {
1689               @Override
1690               public void actionPerformed(ActionEvent e)
1691               {
1692                 hydrophobicityColour_actionPerformed();
1693               }
1694             });
1695     helixColour.setText(MessageManager.getString("label.helix_propensity"));
1696     helixColour.addActionListener(new java.awt.event.ActionListener()
1697     {
1698       @Override
1699       public void actionPerformed(ActionEvent e)
1700       {
1701         helixColour_actionPerformed();
1702       }
1703     });
1704     strandColour.setText(MessageManager
1705             .getString("label.strand_propensity"));
1706     strandColour.addActionListener(new java.awt.event.ActionListener()
1707     {
1708       @Override
1709       public void actionPerformed(ActionEvent e)
1710       {
1711         strandColour_actionPerformed();
1712       }
1713     });
1714     turnColour.setText(MessageManager.getString("label.turn_propensity"));
1715     turnColour.addActionListener(new java.awt.event.ActionListener()
1716     {
1717       @Override
1718       public void actionPerformed(ActionEvent e)
1719       {
1720         turnColour_actionPerformed();
1721       }
1722     });
1723     buriedColour.setText(MessageManager.getString("label.buried_index"));
1724     buriedColour.addActionListener(new java.awt.event.ActionListener()
1725     {
1726       @Override
1727       public void actionPerformed(ActionEvent e)
1728       {
1729         buriedColour_actionPerformed();
1730       }
1731     });
1732     abovePIDColour.setText(MessageManager
1733             .getString("label.above_identity_percentage"));
1734     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1735     {
1736       @Override
1737       public void actionPerformed(ActionEvent e)
1738       {
1739         abovePIDColour_actionPerformed();
1740       }
1741     });
1742     userDefinedColour.setText(MessageManager
1743             .getString("action.user_defined"));
1744     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1745     {
1746       @Override
1747       public void actionPerformed(ActionEvent e)
1748       {
1749         userDefinedColour_actionPerformed(e);
1750       }
1751     });
1752     PIDColour
1753             .setText(MessageManager.getString("label.percentage_identity"));
1754     PIDColour.addActionListener(new java.awt.event.ActionListener()
1755     {
1756       @Override
1757       public void actionPerformed(ActionEvent e)
1758       {
1759         PIDColour_actionPerformed();
1760       }
1761     });
1762     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1763     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1764     {
1765       @Override
1766       public void actionPerformed(ActionEvent e)
1767       {
1768         BLOSUM62Colour_actionPerformed();
1769       }
1770     });
1771     purinePyrimidineColour.setText(MessageManager
1772             .getString("label.purine_pyrimidine"));
1773     purinePyrimidineColour
1774             .addActionListener(new java.awt.event.ActionListener()
1775             {
1776               @Override
1777               public void actionPerformed(ActionEvent e)
1778               {
1779                 purinePyrimidineColour_actionPerformed();
1780               }
1781             });
1782
1783     /*
1784      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1785      * public void actionPerformed(ActionEvent e) {
1786      * covariationColour_actionPerformed(); } });
1787      */
1788
1789     conservationMenuItem.setText(MessageManager
1790             .getString("label.conservation"));
1791     conservationMenuItem
1792             .addActionListener(new java.awt.event.ActionListener()
1793             {
1794               @Override
1795               public void actionPerformed(ActionEvent e)
1796               {
1797                 conservationMenuItem_actionPerformed();
1798               }
1799             });
1800   }
1801
1802   /**
1803    * Check for any annotations on the underlying dataset sequences (for the
1804    * current selection group) which are not 'on the alignment'.If any are found,
1805    * enable the option to add them to the alignment. The criteria for 'on the
1806    * alignment' is finding an alignment annotation on the alignment, matched on
1807    * calcId, label and sequenceRef.
1808    *
1809    * A tooltip is also constructed that displays the source (calcId) and type
1810    * (label) of the annotations that can be added.
1811    *
1812    * @param menuItem
1813    * @param forSequences
1814    */
1815   protected void configureReferenceAnnotationsMenu(
1816           JMenuItem menuItem, List<SequenceI> forSequences)
1817   {
1818     menuItem.setText(MessageManager
1819             .getString("label.add_reference_annotations"));
1820     menuItem.setEnabled(false);
1821     if (forSequences == null)
1822     {
1823       return;
1824     }
1825
1826     /*
1827      * Temporary store to hold distinct calcId / type pairs for the tooltip.
1828      * Using TreeMap means calcIds are shown in alphabetical order.
1829      */
1830     Map<String, String> tipEntries = new TreeMap<String, String>();
1831     StringBuilder tooltip = new StringBuilder(64);
1832     tooltip.append(MessageManager.getString("label.add_annotations_for"));
1833
1834     /*
1835      * For each sequence selected in the alignment, make a list of any
1836      * annotations on the underlying dataset sequence which are not already on
1837      * the alignment.
1838      *
1839      * Build a map of { alignmentSequence, <List of annotations to add> }
1840      */
1841     AlignmentI al = this.ap.av.getAlignment();
1842     final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1843     for (SequenceI seq : forSequences)
1844     {
1845       SequenceI dataset = seq.getDatasetSequence();
1846       if (dataset == null)
1847       {
1848         continue;
1849       }
1850       AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
1851       if (datasetAnnotations == null)
1852       {
1853         continue;
1854       }
1855       final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
1856       for (AlignmentAnnotation dsann : datasetAnnotations)
1857       {
1858         /*
1859          * Find matching annotations on the alignment.
1860          */
1861         final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
1862                 .findAnnotations(seq, dsann.getCalcId(),
1863                         dsann.label);
1864         if (!matchedAlignmentAnnotations.iterator().hasNext())
1865         {
1866           result.add(dsann);
1867           tipEntries.put(dsann.getCalcId(), dsann.label);
1868         }
1869       }
1870       /*
1871        * Save any addable annotations for this sequence
1872        */
1873       if (!result.isEmpty())
1874       {
1875         candidates.put(seq, result);
1876       }
1877     }
1878     if (!candidates.isEmpty())
1879     {
1880       /*
1881        * Found annotations that could be added. Enable the menu item, and
1882        * configure its tooltip and action.
1883        */
1884       menuItem.setEnabled(true);
1885       for (String calcId : tipEntries.keySet())
1886       {
1887         tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1888       }
1889       String tooltipText = JvSwingUtils.wrapTooltip(true,
1890               tooltip.toString());
1891       menuItem.setToolTipText(tooltipText);
1892
1893       menuItem.addActionListener(new ActionListener()
1894       {
1895         @Override
1896         public void actionPerformed(ActionEvent e)
1897         {
1898           addReferenceAnnotations_actionPerformed(candidates);
1899         }
1900       });
1901     }
1902   }
1903
1904   /**
1905    * Add annotations to the sequences and to the alignment.
1906    *
1907    * @param candidates
1908    *          a map whose keys are sequences on the alignment, and values a list
1909    *          of annotations to add to each sequence
1910    */
1911   protected void addReferenceAnnotations_actionPerformed(
1912           Map<SequenceI, List<AlignmentAnnotation>> candidates)
1913   {
1914     /*
1915      * Add annotations at the top of the annotation, in the same order as their
1916      * related sequences.
1917      */
1918     for (SequenceI seq : candidates.keySet())
1919     {
1920       for (AlignmentAnnotation ann : candidates.get(seq))
1921       {
1922         AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
1923         int startRes = 0;
1924         int endRes = ann.annotations.length;
1925         final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1926         if (selectionGroup != null)
1927         {
1928           startRes = selectionGroup.getStartRes();
1929           endRes = selectionGroup.getEndRes();
1930         }
1931         copyAnn.restrict(startRes, endRes);
1932
1933         /*
1934          * Add to the sequence (sets copyAnn.datasetSequence), unless the
1935          * original annotation is already on the sequence.
1936          */
1937         if (!seq.hasAnnotation(ann))
1938         {
1939           seq.addAlignmentAnnotation(copyAnn);
1940         }
1941         // adjust for gaps
1942         copyAnn.adjustForAlignment();
1943         // add to the alignment and set visible
1944         this.ap.getAlignment().addAnnotation(copyAnn);
1945         copyAnn.visible = true;
1946       }
1947     }
1948     refresh();
1949   }
1950
1951   protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1952   {
1953     if (!ap.av.getAlignment().hasSeqrep())
1954     {
1955       // initialise the display flags so the user sees something happen
1956       ap.av.setDisplayReferenceSeq(true);
1957       ap.av.setColourByReferenceSeq(true);
1958       ap.av.getAlignment().setSeqrep(sequence);
1959     }
1960     else
1961     {
1962       if (ap.av.getAlignment().getSeqrep() == sequence)
1963       {
1964         ap.av.getAlignment().setSeqrep(null);
1965       }
1966       else
1967       {
1968         ap.av.getAlignment().setSeqrep(sequence);
1969       }
1970     }
1971     refresh();
1972   }
1973
1974   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1975   {
1976     if (sequence != null)
1977     {
1978       ColumnSelection cs = ap.av.getColumnSelection();
1979       if (cs == null)
1980       {
1981         cs = new ColumnSelection();
1982       }
1983       cs.hideInsertionsFor(sequence);
1984       ap.av.setColumnSelection(cs);
1985     }
1986     refresh();
1987   }
1988   protected void sequenceSelectionDetails_actionPerformed()
1989   {
1990     createSequenceDetailsReport(ap.av.getSequenceSelection());
1991   }
1992
1993   protected void sequenceDetails_actionPerformed()
1994   {
1995     createSequenceDetailsReport(new SequenceI[]
1996     { sequence });
1997   }
1998
1999   public void createSequenceDetailsReport(SequenceI[] sequences)
2000   {
2001     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
2002     StringBuffer contents = new StringBuffer();
2003     for (SequenceI seq : sequences)
2004     {
2005       contents.append("<p><h2>"
2006               + MessageManager
2007                       .formatMessage(
2008                               "label.create_sequence_details_report_annotation_for",
2009                               new String[]
2010                               { seq.getDisplayId(true) }) + "</h2></p><p>");
2011       new SequenceAnnotationReport(null)
2012               .createSequenceAnnotationReport(
2013                       contents,
2014                       seq,
2015                       true,
2016                       true,
2017                       false,
2018                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
2019                               .getSeqPanel().seqCanvas.fr
2020                               .getMinMax()
2021                               : null);
2022       contents.append("</p>");
2023     }
2024     cap.setText("<html>" + contents.toString() + "</html>");
2025
2026     Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
2027             "label.sequece_details_for",
2028             (sequences.length == 1 ? new String[]
2029             { sequences[0].getDisplayId(true) } : new String[]
2030             { MessageManager.getString("label.selection") })), 500, 400);
2031
2032   }
2033
2034   protected void showNonconserved_actionPerformed()
2035   {
2036     getGroup().setShowNonconserved(displayNonconserved.isSelected());
2037     refresh();
2038   }
2039
2040   /**
2041    * call to refresh view after settings change
2042    */
2043   void refresh()
2044   {
2045     ap.updateAnnotation();
2046     ap.paintAlignment(true);
2047
2048     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
2049   }
2050
2051   /**
2052    * DOCUMENT ME!
2053    *
2054    * @param e
2055    *          DOCUMENT ME!
2056    */
2057   protected void clustalColour_actionPerformed()
2058   {
2059     SequenceGroup sg = getGroup();
2060     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
2061     refresh();
2062   }
2063
2064   /**
2065    * DOCUMENT ME!
2066    *
2067    * @param e
2068    *          DOCUMENT ME!
2069    */
2070   protected void zappoColour_actionPerformed()
2071   {
2072     getGroup().cs = new ZappoColourScheme();
2073     refresh();
2074   }
2075
2076   /**
2077    * DOCUMENT ME!
2078    *
2079    * @param e
2080    *          DOCUMENT ME!
2081    */
2082   protected void taylorColour_actionPerformed()
2083   {
2084     getGroup().cs = new TaylorColourScheme();
2085     refresh();
2086   }
2087
2088   /**
2089    * DOCUMENT ME!
2090    *
2091    * @param e
2092    *          DOCUMENT ME!
2093    */
2094   protected void hydrophobicityColour_actionPerformed()
2095   {
2096     getGroup().cs = new HydrophobicColourScheme();
2097     refresh();
2098   }
2099
2100   /**
2101    * DOCUMENT ME!
2102    *
2103    * @param e
2104    *          DOCUMENT ME!
2105    */
2106   protected void helixColour_actionPerformed()
2107   {
2108     getGroup().cs = new HelixColourScheme();
2109     refresh();
2110   }
2111
2112   /**
2113    * DOCUMENT ME!
2114    *
2115    * @param e
2116    *          DOCUMENT ME!
2117    */
2118   protected void strandColour_actionPerformed()
2119   {
2120     getGroup().cs = new StrandColourScheme();
2121     refresh();
2122   }
2123
2124   /**
2125    * DOCUMENT ME!
2126    *
2127    * @param e
2128    *          DOCUMENT ME!
2129    */
2130   protected void turnColour_actionPerformed()
2131   {
2132     getGroup().cs = new TurnColourScheme();
2133     refresh();
2134   }
2135
2136   /**
2137    * DOCUMENT ME!
2138    *
2139    * @param e
2140    *          DOCUMENT ME!
2141    */
2142   protected void buriedColour_actionPerformed()
2143   {
2144     getGroup().cs = new BuriedColourScheme();
2145     refresh();
2146   }
2147
2148   /**
2149    * DOCUMENT ME!
2150    *
2151    * @param e
2152    *          DOCUMENT ME!
2153    */
2154   public void nucleotideMenuItem_actionPerformed()
2155   {
2156     getGroup().cs = new NucleotideColourScheme();
2157     refresh();
2158   }
2159
2160   protected void purinePyrimidineColour_actionPerformed()
2161   {
2162     getGroup().cs = new PurinePyrimidineColourScheme();
2163     refresh();
2164   }
2165
2166   /*
2167    * protected void covariationColour_actionPerformed() { getGroup().cs = new
2168    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
2169    */
2170   /**
2171    * DOCUMENT ME!
2172    *
2173    * @param e
2174    *          DOCUMENT ME!
2175    */
2176   protected void abovePIDColour_actionPerformed()
2177   {
2178     SequenceGroup sg = getGroup();
2179     if (sg.cs == null)
2180     {
2181       return;
2182     }
2183
2184     if (abovePIDColour.isSelected())
2185     {
2186       sg.cs.setConsensus(AAFrequency.calculate(
2187               sg.getSequences(ap.av.getHiddenRepSequences()),
2188               sg.getStartRes(), sg.getEndRes() + 1));
2189
2190       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
2191               .getName());
2192
2193       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
2194
2195       SliderPanel.showPIDSlider();
2196     }
2197     else
2198     // remove PIDColouring
2199     {
2200       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
2201     }
2202
2203     refresh();
2204   }
2205
2206   /**
2207    * DOCUMENT ME!
2208    *
2209    * @param e
2210    *          DOCUMENT ME!
2211    */
2212   protected void userDefinedColour_actionPerformed(ActionEvent e)
2213   {
2214     SequenceGroup sg = getGroup();
2215
2216     if (e.getSource().equals(userDefinedColour))
2217     {
2218       new UserDefinedColours(ap, sg);
2219     }
2220     else
2221     {
2222       UserColourScheme udc = (UserColourScheme) UserDefinedColours
2223               .getUserColourSchemes().get(e.getActionCommand());
2224
2225       sg.cs = udc;
2226     }
2227     refresh();
2228   }
2229
2230   /**
2231    * Open a panel where the user can choose which types of sequence annotation
2232    * to show or hide.
2233    *
2234    * @param e
2235    */
2236   protected void chooseAnnotations_actionPerformed(ActionEvent e)
2237   {
2238     // todo correct way to guard against opening a duplicate panel?
2239     new AnnotationChooser(ap);
2240   }
2241
2242   /**
2243    * DOCUMENT ME!
2244    *
2245    * @param e
2246    *          DOCUMENT ME!
2247    */
2248   protected void PIDColour_actionPerformed()
2249   {
2250     SequenceGroup sg = getGroup();
2251     sg.cs = new PIDColourScheme();
2252     sg.cs.setConsensus(AAFrequency.calculate(
2253             sg.getSequences(ap.av.getHiddenRepSequences()),
2254             sg.getStartRes(), sg.getEndRes() + 1));
2255     refresh();
2256   }
2257
2258   /**
2259    * DOCUMENT ME!
2260    *
2261    * @param e
2262    *          DOCUMENT ME!
2263    */
2264   protected void BLOSUM62Colour_actionPerformed()
2265   {
2266     SequenceGroup sg = getGroup();
2267
2268     sg.cs = new Blosum62ColourScheme();
2269
2270     sg.cs.setConsensus(AAFrequency.calculate(
2271             sg.getSequences(ap.av.getHiddenRepSequences()),
2272             sg.getStartRes(), sg.getEndRes() + 1));
2273
2274     refresh();
2275   }
2276
2277   /**
2278    * DOCUMENT ME!
2279    *
2280    * @param e
2281    *          DOCUMENT ME!
2282    */
2283   protected void noColourmenuItem_actionPerformed()
2284   {
2285     getGroup().cs = null;
2286     refresh();
2287   }
2288
2289   /**
2290    * DOCUMENT ME!
2291    *
2292    * @param e
2293    *          DOCUMENT ME!
2294    */
2295   protected void conservationMenuItem_actionPerformed()
2296   {
2297     SequenceGroup sg = getGroup();
2298     if (sg.cs == null)
2299     {
2300       return;
2301     }
2302
2303     if (conservationMenuItem.isSelected())
2304     {
2305       // JBPNote: Conservation name shouldn't be i18n translated
2306       Conservation c = new Conservation("Group",
2307               ResidueProperties.propHash, 3, sg.getSequences(ap.av
2308                       .getHiddenRepSequences()), sg.getStartRes(),
2309               sg.getEndRes() + 1);
2310
2311       c.calculate();
2312       c.verdict(false, ap.av.getConsPercGaps());
2313
2314       sg.cs.setConservation(c);
2315
2316       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2317       SliderPanel.showConservationSlider();
2318     }
2319     else
2320     // remove ConservationColouring
2321     {
2322       sg.cs.setConservation(null);
2323     }
2324
2325     refresh();
2326   }
2327
2328   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2329   {
2330     SequenceGroup sg = getGroup();
2331     if (sg == null)
2332     {
2333       return;
2334     }
2335
2336     AnnotationColourGradient acg = new AnnotationColourGradient(
2337             sequence.getAnnotation()[0], null,
2338             AnnotationColourGradient.NO_THRESHOLD);
2339
2340     acg.setPredefinedColours(true);
2341     sg.cs = acg;
2342
2343     refresh();
2344   }
2345
2346   /**
2347    * DOCUMENT ME!
2348    *
2349    * @param e
2350    *          DOCUMENT ME!
2351    */
2352   protected void groupName_actionPerformed()
2353   {
2354
2355     SequenceGroup sg = getGroup();
2356     EditNameDialog dialog = new EditNameDialog(sg.getName(),
2357             sg.getDescription(), "       "
2358                     + MessageManager.getString("label.group_name") + " ",
2359             MessageManager.getString("label.group_description") + " ",
2360             MessageManager.getString("label.edit_group_name_description"),
2361             ap.alignFrame);
2362
2363     if (!dialog.accept)
2364     {
2365       return;
2366     }
2367
2368     sg.setName(dialog.getName());
2369     sg.setDescription(dialog.getDescription());
2370     refresh();
2371   }
2372
2373   /**
2374    * Get selection group - adding it to the alignment if necessary.
2375    *
2376    * @return sequence group to operate on
2377    */
2378   SequenceGroup getGroup()
2379   {
2380     SequenceGroup sg = ap.av.getSelectionGroup();
2381     // this method won't add a new group if it already exists
2382     if (sg != null)
2383     {
2384       ap.av.getAlignment().addGroup(sg);
2385     }
2386
2387     return sg;
2388   }
2389
2390   /**
2391    * DOCUMENT ME!
2392    *
2393    * @param e
2394    *          DOCUMENT ME!
2395    */
2396   void sequenceName_actionPerformed()
2397   {
2398     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2399             sequence.getDescription(),
2400             "       " + MessageManager.getString("label.sequence_name")
2401                     + " ",
2402             MessageManager.getString("label.sequence_description") + " ",
2403             MessageManager
2404                     .getString("label.edit_sequence_name_description"),
2405             ap.alignFrame);
2406
2407     if (!dialog.accept)
2408     {
2409       return;
2410     }
2411
2412     if (dialog.getName() != null)
2413     {
2414       if (dialog.getName().indexOf(" ") > -1)
2415       {
2416         JOptionPane
2417                 .showMessageDialog(
2418                         ap,
2419                         MessageManager
2420                                 .getString("label.spaces_converted_to_backslashes"),
2421                         MessageManager
2422                                 .getString("label.no_spaces_allowed_sequence_name"),
2423                         JOptionPane.WARNING_MESSAGE);
2424       }
2425
2426       sequence.setName(dialog.getName().replace(' ', '_'));
2427       ap.paintAlignment(false);
2428     }
2429
2430     sequence.setDescription(dialog.getDescription());
2431
2432     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2433             .getSequences());
2434
2435   }
2436
2437   /**
2438    * DOCUMENT ME!
2439    *
2440    * @param e
2441    *          DOCUMENT ME!
2442    */
2443   void unGroupMenuItem_actionPerformed()
2444   {
2445     SequenceGroup sg = ap.av.getSelectionGroup();
2446     ap.av.getAlignment().deleteGroup(sg);
2447     ap.av.setSelectionGroup(null);
2448     refresh();
2449   }
2450
2451   void createGroupMenuItem_actionPerformed()
2452   {
2453     getGroup(); // implicitly creates group - note - should apply defaults / use
2454                 // standard alignment window logic for this
2455     refresh();
2456   }
2457
2458   /**
2459    * DOCUMENT ME!
2460    *
2461    * @param e
2462    *          DOCUMENT ME!
2463    */
2464   protected void outline_actionPerformed()
2465   {
2466     SequenceGroup sg = getGroup();
2467     Color col = JColorChooser.showDialog(this,
2468             MessageManager.getString("label.select_outline_colour"),
2469             Color.BLUE);
2470
2471     if (col != null)
2472     {
2473       sg.setOutlineColour(col);
2474     }
2475
2476     refresh();
2477   }
2478
2479   /**
2480    * DOCUMENT ME!
2481    *
2482    * @param e
2483    *          DOCUMENT ME!
2484    */
2485   public void showBoxes_actionPerformed()
2486   {
2487     getGroup().setDisplayBoxes(showBoxes.isSelected());
2488     refresh();
2489   }
2490
2491   /**
2492    * DOCUMENT ME!
2493    *
2494    * @param e
2495    *          DOCUMENT ME!
2496    */
2497   public void showText_actionPerformed()
2498   {
2499     getGroup().setDisplayText(showText.isSelected());
2500     refresh();
2501   }
2502
2503   /**
2504    * DOCUMENT ME!
2505    *
2506    * @param e
2507    *          DOCUMENT ME!
2508    */
2509   public void showColourText_actionPerformed()
2510   {
2511     getGroup().setColourText(showColourText.isSelected());
2512     refresh();
2513   }
2514
2515   public void showLink(String url)
2516   {
2517     try
2518     {
2519       jalview.util.BrowserLauncher.openURL(url);
2520     } catch (Exception ex)
2521     {
2522       JOptionPane.showInternalMessageDialog(Desktop.desktop,
2523               MessageManager.getString("label.web_browser_not_found_unix"),
2524               MessageManager.getString("label.web_browser_not_found"),
2525               JOptionPane.WARNING_MESSAGE);
2526
2527       ex.printStackTrace();
2528     }
2529   }
2530
2531   void hideSequences(boolean representGroup)
2532   {
2533     SequenceGroup sg = ap.av.getSelectionGroup();
2534     if (sg == null || sg.getSize() < 1)
2535     {
2536       ap.av.hideSequence(new SequenceI[]
2537       { sequence });
2538       return;
2539     }
2540
2541     ap.av.setSelectionGroup(null);
2542
2543     if (representGroup)
2544     {
2545       ap.av.hideRepSequences(sequence, sg);
2546
2547       return;
2548     }
2549
2550     int gsize = sg.getSize();
2551     SequenceI[] hseqs;
2552
2553     hseqs = new SequenceI[gsize];
2554
2555     int index = 0;
2556     for (int i = 0; i < gsize; i++)
2557     {
2558       hseqs[index++] = sg.getSequenceAt(i);
2559     }
2560
2561     ap.av.hideSequence(hseqs);
2562     // refresh(); TODO: ? needed ?
2563     ap.av.sendSelection();
2564   }
2565
2566   public void copy_actionPerformed()
2567   {
2568     ap.alignFrame.copy_actionPerformed(null);
2569   }
2570
2571   public void cut_actionPerformed()
2572   {
2573     ap.alignFrame.cut_actionPerformed(null);
2574   }
2575
2576   void changeCase(ActionEvent e)
2577   {
2578     Object source = e.getSource();
2579     SequenceGroup sg = ap.av.getSelectionGroup();
2580
2581     if (sg != null)
2582     {
2583       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
2584               sg.getEndRes() + 1);
2585
2586       String description;
2587       int caseChange;
2588
2589       if (source == toggle)
2590       {
2591         description = MessageManager.getString("label.toggle_case");
2592         caseChange = ChangeCaseCommand.TOGGLE_CASE;
2593       }
2594       else if (source == upperCase)
2595       {
2596         description = MessageManager.getString("label.to_upper_case");
2597         caseChange = ChangeCaseCommand.TO_UPPER;
2598       }
2599       else
2600       {
2601         description = MessageManager.getString("label.to_lower_case");
2602         caseChange = ChangeCaseCommand.TO_LOWER;
2603       }
2604
2605       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2606               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2607               startEnd, caseChange);
2608
2609       ap.alignFrame.addHistoryItem(caseCommand);
2610
2611       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2612               .getSequences());
2613
2614     }
2615   }
2616
2617   public void outputText_actionPerformed(ActionEvent e)
2618   {
2619     CutAndPasteTransfer cap = new CutAndPasteTransfer();
2620     cap.setForInput(null);
2621     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2622             "label.alignment_output_command", new String[]
2623             { e.getActionCommand() }), 600, 500);
2624
2625     String[] omitHidden = null;
2626
2627     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2628     // or we simply trust the user wants
2629     // wysiwig behaviour
2630
2631     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2632             ap.av, true));
2633   }
2634
2635   public void pdbFromFile_actionPerformed()
2636   {
2637     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2638             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2639     chooser.setFileView(new jalview.io.JalviewFileView());
2640     chooser.setDialogTitle(MessageManager.formatMessage(
2641             "label.select_pdb_file_for", new String[]
2642             { sequence.getDisplayId(false) }));
2643     chooser.setToolTipText(MessageManager.formatMessage(
2644             "label.load_pdb_file_associate_with_sequence", new String[]
2645             { sequence.getDisplayId(false) }));
2646
2647     int value = chooser.showOpenDialog(null);
2648
2649     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2650     {
2651       String choice = chooser.getSelectedFile().getPath();
2652       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2653       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2654               jalview.io.AppletFormatAdapter.FILE, sequence, true,
2655               Desktop.instance);
2656     }
2657
2658   }
2659
2660   // JBNote: commented out - these won't be instantiated here...!
2661   // public void RNAFold_actionPerformed() throws Exception
2662   // {
2663   // Predict2D P2D = new Predict2D();
2664   // P2D.getStructure2DFromRNAFold("toto");
2665   // }
2666   //
2667   // public void ContraFold_actionPerformed() throws Exception
2668   // {
2669   // Predict2D P2D = new Predict2D();
2670   // P2D.getStructure2DFromContraFold("toto");
2671   // }
2672   public void enterPDB_actionPerformed()
2673   {
2674     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2675             MessageManager.getString("label.enter_pdb_id"),
2676             MessageManager.getString("label.enter_pdb_id"),
2677             JOptionPane.QUESTION_MESSAGE);
2678
2679     if (id != null && id.length() > 0)
2680     {
2681       PDBEntry entry = new PDBEntry();
2682       entry.setId(id.toUpperCase());
2683       sequence.getDatasetSequence().addPDBId(entry);
2684     }
2685   }
2686
2687   public void discoverPDB_actionPerformed()
2688   {
2689
2690     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2691     { sequence }
2692             : ap.av.getSequenceSelection());
2693     Thread discpdb = new Thread(new Runnable()
2694     {
2695       @Override
2696       public void run()
2697       {
2698
2699         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2700                 .fetchDBRefs(false);
2701       }
2702
2703     });
2704     discpdb.start();
2705   }
2706
2707   public void sequenceFeature_actionPerformed()
2708   {
2709     SequenceGroup sg = ap.av.getSelectionGroup();
2710     if (sg == null)
2711     {
2712       return;
2713     }
2714
2715     int rsize = 0, gSize = sg.getSize();
2716     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2717     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2718
2719     for (int i = 0; i < gSize; i++)
2720     {
2721       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2722       int end = sg.findEndRes(sg.getSequenceAt(i));
2723       if (start <= end)
2724       {
2725         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2726         features[rsize] = new SequenceFeature(null, null, null, start, end,
2727                 "Jalview");
2728         rsize++;
2729       }
2730     }
2731     rseqs = new SequenceI[rsize];
2732     tfeatures = new SequenceFeature[rsize];
2733     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2734     System.arraycopy(features, 0, tfeatures, 0, rsize);
2735     features = tfeatures;
2736     seqs = rseqs;
2737     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2738             features, true, ap))
2739     {
2740       ap.alignFrame.setShowSeqFeatures(true);
2741       ap.highlightSearchResults(null);
2742     }
2743   }
2744
2745   public void textColour_actionPerformed()
2746   {
2747     SequenceGroup sg = getGroup();
2748     if (sg != null)
2749     {
2750       new TextColourChooser().chooseColour(ap, sg);
2751     }
2752   }
2753
2754   public void colourByStructure(String pdbid)
2755   {
2756     Annotation[] anots = ap.av.getStructureSelectionManager()
2757             .colourSequenceFromStructure(sequence, pdbid);
2758
2759     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2760             "Coloured by " + pdbid, anots);
2761
2762     ap.av.getAlignment().addAnnotation(an);
2763     an.createSequenceMapping(sequence, 0, true);
2764     // an.adjustForAlignment();
2765     ap.av.getAlignment().setAnnotationIndex(an, 0);
2766
2767     ap.adjustAnnotationHeight();
2768
2769     sequence.addAlignmentAnnotation(an);
2770
2771   }
2772
2773   public void editSequence_actionPerformed(ActionEvent actionEvent)
2774   {
2775     SequenceGroup sg = ap.av.getSelectionGroup();
2776
2777     if (sg != null)
2778     {
2779       if (sequence == null)
2780       {
2781         sequence = sg.getSequenceAt(0);
2782       }
2783
2784       EditNameDialog dialog = new EditNameDialog(
2785               sequence.getSequenceAsString(sg.getStartRes(),
2786                       sg.getEndRes() + 1), null,
2787               MessageManager.getString("label.edit_sequence"), null,
2788               MessageManager.getString("label.edit_sequence"),
2789               ap.alignFrame);
2790
2791       if (dialog.accept)
2792       {
2793         EditCommand editCommand = new EditCommand(
2794                 MessageManager.getString("label.edit_sequences"),
2795                 Action.REPLACE, dialog.getName().replace(' ',
2796                         ap.av.getGapCharacter()),
2797                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2798                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2799
2800         ap.alignFrame.addHistoryItem(editCommand);
2801
2802         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2803                 .getSequences());
2804       }
2805     }
2806   }
2807
2808 }