src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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 java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27
  28 import javax.swing.*;
  29
  30 import jalview.analysis.*;
  31 import jalview.commands.*;
  32 import jalview.datamodel.*;
  33 import jalview.io.*;
  34 import jalview.schemes.*;
  35 import jalview.util.GroupUrlLink;
  36 import jalview.util.GroupUrlLink.UrlStringTooLongException;
  37 import jalview.util.MessageManager;
  38 import jalview.util.UrlLink;
  39
  40 /**
  41  * DOCUMENT ME!
  42  *
  43  * @author $author$
  44  * @version $Revision: 1.118 $
  45  */
  46 public class PopupMenu extends JPopupMenu
  47 {
  48   JMenu groupMenu = new JMenu();
  49
  50   JMenuItem groupName = new JMenuItem();
  51
  52   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  63
  64   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  65
  66   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  67
  68   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  69
  70   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  71
  72   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  73
  74   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  75
  76   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
  77
  78   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
  79
  80   // protected JRadioButtonMenuItem covariationColour = new
  81   // JRadioButtonMenuItem();
  82
  83   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  84
  85   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  86
  87   AlignmentPanel ap;
  88
  89   JMenu sequenceMenu = new JMenu();
  90
  91   JMenuItem sequenceName = new JMenuItem();
  92
  93   JMenuItem sequenceDetails = new JMenuItem();
  94
  95   JMenuItem sequenceSelDetails = new JMenuItem();
  96
  97   SequenceI sequence;
  98
  99   JMenuItem createGroupMenuItem = new JMenuItem();
 100
 101   JMenuItem unGroupMenuItem = new JMenuItem();
 102
 103   JMenuItem outline = new JMenuItem();
 104
 105   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
 106
 107   JMenu colourMenu = new JMenu();
 108
 109   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
 110
 111   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
 112
 113   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
 114
 115   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
 116
 117   JMenu editMenu = new JMenu();
 118
 119   JMenuItem cut = new JMenuItem();
 120
 121   JMenuItem copy = new JMenuItem();
 122
 123   JMenuItem upperCase = new JMenuItem();
 124
 125   JMenuItem lowerCase = new JMenuItem();
 126
 127   JMenuItem toggle = new JMenuItem();
 128
 129   JMenu pdbMenu = new JMenu();
 130
 131   JMenuItem pdbFromFile = new JMenuItem();
 132
 133   // JBPNote: Commented these out - Should add these services via the web
 134   // services menu system.
 135   // JMenuItem ContraFold = new JMenuItem();
 136
 137   // JMenuItem RNAFold = new JMenuItem();
 138
 139   JMenuItem enterPDB = new JMenuItem();
 140
 141   JMenuItem discoverPDB = new JMenuItem();
 142
 143   JMenu outputMenu = new JMenu();
 144
 145   JMenuItem sequenceFeature = new JMenuItem();
 146
 147   JMenuItem textColour = new JMenuItem();
 148
 149   JMenu jMenu1 = new JMenu();
 150
 151   JMenu structureMenu = new JMenu();
 152
 153   JMenu viewStructureMenu = new JMenu();
 154
 155   // JMenu colStructureMenu = new JMenu();
 156   JMenuItem editSequence = new JMenuItem();
 157
 158   // JMenuItem annotationMenuItem = new JMenuItem();
 159
 160   JMenu groupLinksMenu;
 161
 162   /**
 163    * Creates a new PopupMenu object.
 164    *
 165    * @param ap
 166    *          DOCUMENT ME!
 167    * @param seq
 168    *          DOCUMENT ME!
 169    */
 170   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 171   {
 172     this(ap, seq, links, null);
 173   }
 174
 175   /**
 176    *
 177    * @param ap
 178    * @param seq
 179    * @param links
 180    * @param groupLinks
 181    */
 182   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
 183           Vector links, Vector groupLinks)
 184   {
 185     // /////////////////////////////////////////////////////////
 186     // If this is activated from the sequence panel, the user may want to
 187     // edit or annotate a particular residue. Therefore display the residue menu
 188     //
 189     // If from the IDPanel, we must display the sequence menu
 190     // ////////////////////////////////////////////////////////
 191     this.ap = ap;
 192     sequence = seq;
 193
 194     ButtonGroup colours = new ButtonGroup();
 195     colours.add(noColourmenuItem);
 196     colours.add(clustalColour);
 197     colours.add(zappoColour);
 198     colours.add(taylorColour);
 199     colours.add(hydrophobicityColour);
 200     colours.add(helixColour);
 201     colours.add(strandColour);
 202     colours.add(turnColour);
 203     colours.add(buriedColour);
 204     colours.add(abovePIDColour);
 205     colours.add(userDefinedColour);
 206     colours.add(PIDColour);
 207     colours.add(BLOSUM62Colour);
 208     colours.add(purinePyrimidineColour);
 209     colours.add(RNAInteractionColour);
 210     // colours.add(covariationColour);
 211
 212     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 213     {
 214       JMenuItem item = new JMenuItem(
 215               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 216
 217       item.addActionListener(new java.awt.event.ActionListener()
 218       {
 219         public void actionPerformed(ActionEvent e)
 220         {
 221           outputText_actionPerformed(e);
 222         }
 223       });
 224
 225       outputMenu.add(item);
 226     }
 227
 228     try
 229     {
 230       jbInit();
 231     } catch (Exception e)
 232     {
 233       e.printStackTrace();
 234     }
 235
 236     JMenuItem menuItem;
 237     if (seq != null)
 238     {
 239       sequenceMenu.setText(sequence.getName());
 240
 241       if (seq.getDatasetSequence().getPDBId() != null
 242               && seq.getDatasetSequence().getPDBId().size() > 0)
 243       {
 244         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 245                 .elements();
 246
 247         while (e.hasMoreElements())
 248         {
 249           final PDBEntry pdb = (PDBEntry) e.nextElement();
 250
 251           menuItem = new JMenuItem();
 252           menuItem.setText(pdb.getId());
 253           menuItem.addActionListener(new java.awt.event.ActionListener()
 254           {
 255             public void actionPerformed(ActionEvent e)
 256             {
 257               // TODO re JAL-860: optionally open dialog or provide a menu entry
 258               // allowing user to open just one structure per sequence
 259               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 260               { pdb })[0], null, ap);
 261               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 262             }
 263
 264           });
 265           viewStructureMenu.add(menuItem);
 266
 267           /*
 268            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 269            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 270            * public void actionPerformed(ActionEvent e) {
 271            * colourByStructure(pdb.getId()); } });
 272            * colStructureMenu.add(menuItem);
 273            */
 274         }
 275       }
 276       else
 277       {
 278         if (ap.av.getAlignment().isNucleotide() == false)
 279         {
 280           structureMenu.remove(viewStructureMenu);
 281         }
 282         // structureMenu.remove(colStructureMenu);
 283       }
 284
 285       if (ap.av.getAlignment().isNucleotide() == true)
 286       {
 287         AlignmentAnnotation[] aa = ap.av.getAlignment()
 288                 .getAlignmentAnnotation();
 289         for (int i = 0; i < aa.length; i++)
 290         {
 291           if (aa[i].getRNAStruc() != null)
 292           {
 293             final String rnastruc = aa[i].getRNAStruc();
 294             final String structureLine = aa[i].label;
 295             menuItem = new JMenuItem();
 296             menuItem.setText(MessageManager.formatMessage(
 297                     "label.2d_rna_structure_line", new String[]
 298                     { structureLine }));
 299             menuItem.addActionListener(new java.awt.event.ActionListener()
 300
 301             {
 302               public void actionPerformed(ActionEvent e)
 303               {
 304                 // System.out.println("1:"+structureLine);
 305                 System.out.println("1:sname" + seq.getName());
 306                 System.out.println("2:seq" + seq);
 307
 308                 // System.out.println("3:"+seq.getSequenceAsString());
 309                 System.out.println("3:strucseq" + rnastruc);
 310                 // System.out.println("4:struc"+seq.getRNA());
 311                 System.out.println("5:name" + seq.getName());
 312                 System.out.println("6:ap" + ap);
 313                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
 314                         rnastruc, seq.getName(), ap);
 315                 // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
 316                 // seq.getName(), ap);
 317                 System.out.println("end");
 318               }
 319             });
 320             viewStructureMenu.add(menuItem);
 321           }
 322         }
 323
 324         // SequenceFeatures[] test = seq.getSequenceFeatures();
 325
 326         if (seq.getAnnotation() != null)
 327         {
 328           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
 329           for (int i = 0; i < seqAnno.length; i++)
 330           {
 331             if (seqAnno[i].getRNAStruc() != null)
 332             {
 333               final String rnastruc = seqAnno[i].getRNAStruc();
 334
 335               // TODO: make rnastrucF a bit more nice
 336               menuItem = new JMenuItem();
 337               menuItem.setText(MessageManager.formatMessage(
 338                       "label.2d_rna_sequence_name", new String[]
 339                       { seq.getName() }));
 340               menuItem.addActionListener(new java.awt.event.ActionListener()
 341               {
 342                 public void actionPerformed(ActionEvent e)
 343                 {
 344                   // TODO: VARNA does'nt print gaps in the sequence
 345
 346                   new AppVarna(seq.getName() + " structure", seq, seq
 347                           .getSequenceAsString(), rnastruc, seq.getName(),
 348                           ap);
 349                 }
 350               });
 351               viewStructureMenu.add(menuItem);
 352             }
 353           }
 354         }
 355
 356       }
 357
 358       menuItem = new JMenuItem(
 359               MessageManager.getString("action.hide_sequences"));
 360       menuItem.addActionListener(new java.awt.event.ActionListener()
 361       {
 362         public void actionPerformed(ActionEvent e)
 363         {
 364           hideSequences(false);
 365         }
 366       });
 367       add(menuItem);
 368
 369       if (ap.av.getSelectionGroup() != null
 370               && ap.av.getSelectionGroup().getSize() > 1)
 371       {
 372         menuItem = new JMenuItem(MessageManager.formatMessage(
 373                 "label.represent_group_with", new String[]
 374                 { seq.getName() }));
 375         menuItem.addActionListener(new java.awt.event.ActionListener()
 376         {
 377           public void actionPerformed(ActionEvent e)
 378           {
 379             hideSequences(true);
 380           }
 381         });
 382         sequenceMenu.add(menuItem);
 383       }
 384
 385       if (ap.av.hasHiddenRows())
 386       {
 387         final int index = ap.av.getAlignment().findIndex(seq);
 388
 389         if (ap.av.adjustForHiddenSeqs(index)
 390                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 391         {
 392           menuItem = new JMenuItem(
 393                   MessageManager.getString("action.reveal_sequences"));
 394           menuItem.addActionListener(new ActionListener()
 395           {
 396             public void actionPerformed(ActionEvent e)
 397             {
 398               ap.av.showSequence(index);
 399               if (ap.overviewPanel != null)
 400               {
 401                 ap.overviewPanel.updateOverviewImage();
 402               }
 403             }
 404           });
 405           add(menuItem);
 406         }
 407       }
 408     }
 409     // for the case when no sequences are even visible
 410     if (ap.av.hasHiddenRows())
 411     {
 412       {
 413         menuItem = new JMenuItem(
 414                 MessageManager.getString("action.reveal_all"));
 415         menuItem.addActionListener(new ActionListener()
 416         {
 417           public void actionPerformed(ActionEvent e)
 418           {
 419             ap.av.showAllHiddenSeqs();
 420             if (ap.overviewPanel != null)
 421             {
 422               ap.overviewPanel.updateOverviewImage();
 423             }
 424           }
 425         });
 426
 427         add(menuItem);
 428       }
 429
 430     }
 431
 432     SequenceGroup sg = ap.av.getSelectionGroup();
 433     boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
 434             .getGroups().contains(sg) : false;
 435
 436     if (sg != null && sg.getSize() > 0)
 437     {
 438       groupName.setText(MessageManager.formatMessage("label.name_param",
 439               new String[]
 440               { sg.getName() }));
 441       groupName.setText(MessageManager
 442               .getString("label.edit_name_and_description_current_group"));
 443
 444       if (sg.cs instanceof ZappoColourScheme)
 445       {
 446         zappoColour.setSelected(true);
 447       }
 448       else if (sg.cs instanceof TaylorColourScheme)
 449       {
 450         taylorColour.setSelected(true);
 451       }
 452       else if (sg.cs instanceof PIDColourScheme)
 453       {
 454         PIDColour.setSelected(true);
 455       }
 456       else if (sg.cs instanceof Blosum62ColourScheme)
 457       {
 458         BLOSUM62Colour.setSelected(true);
 459       }
 460       else if (sg.cs instanceof UserColourScheme)
 461       {
 462         userDefinedColour.setSelected(true);
 463       }
 464       else if (sg.cs instanceof HydrophobicColourScheme)
 465       {
 466         hydrophobicityColour.setSelected(true);
 467       }
 468       else if (sg.cs instanceof HelixColourScheme)
 469       {
 470         helixColour.setSelected(true);
 471       }
 472       else if (sg.cs instanceof StrandColourScheme)
 473       {
 474         strandColour.setSelected(true);
 475       }
 476       else if (sg.cs instanceof TurnColourScheme)
 477       {
 478         turnColour.setSelected(true);
 479       }
 480       else if (sg.cs instanceof BuriedColourScheme)
 481       {
 482         buriedColour.setSelected(true);
 483       }
 484       else if (sg.cs instanceof ClustalxColourScheme)
 485       {
 486         clustalColour.setSelected(true);
 487       }
 488       else if (sg.cs instanceof PurinePyrimidineColourScheme)
 489       {
 490         purinePyrimidineColour.setSelected(true);
 491       }
 492
 493       /*
 494        * else if (sg.cs instanceof CovariationColourScheme) {
 495        * covariationColour.setSelected(true); }
 496        */
 497       else
 498       {
 499         noColourmenuItem.setSelected(true);
 500       }
 501
 502       if (sg.cs != null && sg.cs.conservationApplied())
 503       {
 504         conservationMenuItem.setSelected(true);
 505       }
 506       displayNonconserved.setSelected(sg.getShowNonconserved());
 507       showText.setSelected(sg.getDisplayText());
 508       showColourText.setSelected(sg.getColourText());
 509       showBoxes.setSelected(sg.getDisplayBoxes());
 510       // add any groupURLs to the groupURL submenu and make it visible
 511       if (groupLinks != null && groupLinks.size() > 0)
 512       {
 513         buildGroupURLMenu(sg, groupLinks);
 514       }
 515       // Add a 'show all structures' for the current selection
 516       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
 517       SequenceI sqass = null;
 518       for (SequenceI sq : ap.av.getSequenceSelection())
 519       {
 520         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
 521                 .getPDBId();
 522         if (pes != null)
 523         {
 524           reppdb.put(pes.get(0).getId(), pes.get(0));
 525           for (PDBEntry pe : pes)
 526           {
 527             pdbe.put(pe.getId(), pe);
 528             if (sqass == null)
 529             {
 530               sqass = sq;
 531             }
 532           }
 533         }
 534       }
 535       if (pdbe.size() > 0)
 536       {
 537         final PDBEntry[] pe = pdbe.values().toArray(
 538                 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
 539                 new PDBEntry[reppdb.size()]);
 540         final JMenuItem gpdbview, rpdbview;
 541         if (pdbe.size() == 1)
 542         {
 543           structureMenu.add(gpdbview = new JMenuItem(MessageManager
 544                   .formatMessage("label.view_structure_for", new String[]
 545                   { sqass.getDisplayId(false) })));
 546         }
 547         else
 548         {
 549           structureMenu.add(gpdbview = new JMenuItem(MessageManager
 550                   .formatMessage("label.view_all_structures", new String[]
 551                   { new Integer(pdbe.size()).toString() })));
 552         }
 553         gpdbview.setToolTipText(MessageManager
 554                 .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
 555         gpdbview.addActionListener(new ActionListener()
 556         {
 557
 558           @Override
 559           public void actionPerformed(ActionEvent e)
 560           {
 561             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 562           }
 563         });
 564         if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
 565         {
 566           structureMenu.add(rpdbview = new JMenuItem(MessageManager
 567                   .formatMessage(
 568                           "label.view_all_representative_structures",
 569                           new String[]
 570                           { new Integer(reppdb.size()).toString() })));
 571           rpdbview.setToolTipText(MessageManager
 572                   .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
 573           rpdbview.addActionListener(new ActionListener()
 574           {
 575
 576             @Override
 577             public void actionPerformed(ActionEvent e)
 578             {
 579               new AppJmol(ap, pr, ap.av.collateForPDB(pr));
 580             }
 581           });
 582         }
 583       }
 584     }
 585     else
 586     {
 587       groupMenu.setVisible(false);
 588       editMenu.setVisible(false);
 589     }
 590
 591     if (!isDefinedGroup)
 592     {
 593       createGroupMenuItem.setVisible(true);
 594       unGroupMenuItem.setVisible(false);
 595       jMenu1.setText(MessageManager.getString("action.edit_new_group"));
 596     }
 597     else
 598     {
 599       createGroupMenuItem.setVisible(false);
 600       unGroupMenuItem.setVisible(true);
 601       jMenu1.setText(MessageManager.getString("action.edit_group"));
 602     }
 603
 604     if (seq == null)
 605     {
 606       sequenceMenu.setVisible(false);
 607       structureMenu.setVisible(false);
 608     }
 609
 610     if (links != null && links.size() > 0)
 611     {
 612
 613       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
 614       Vector linkset = new Vector();
 615       for (int i = 0; i < links.size(); i++)
 616       {
 617         String link = links.elementAt(i).toString();
 618         UrlLink urlLink = null;
 619         try
 620         {
 621           urlLink = new UrlLink(link);
 622         } catch (Exception foo)
 623         {
 624           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 625                   + "'", foo);
 626           continue;
 627         }
 628         ;
 629         if (!urlLink.isValid())
 630         {
 631           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 632           continue;
 633         }
 634         final String label = urlLink.getLabel();
 635         if (seq != null && urlLink.isDynamic())
 636         {
 637
 638           // collect matching db-refs
 639           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
 640                   seq.getDBRef(), new String[]
 641                   { urlLink.getTarget() });
 642           // collect id string too
 643           String id = seq.getName();
 644           String descr = seq.getDescription();
 645           if (descr != null && descr.length() < 1)
 646           {
 647             descr = null;
 648           }
 649
 650           if (dbr != null)
 651           {
 652             for (int r = 0; r < dbr.length; r++)
 653             {
 654               if (id != null && dbr[r].getAccessionId().equals(id))
 655               {
 656                 // suppress duplicate link creation for the bare sequence ID
 657                 // string with this link
 658                 id = null;
 659               }
 660               // create Bare ID link for this RUL
 661               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 662                       true);
 663               if (urls != null)
 664               {
 665                 for (int u = 0; u < urls.length; u += 2)
 666                 {
 667                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 668                   {
 669                     linkset.addElement(urls[u] + "|" + urls[u + 1]);
 670                     addshowLink(linkMenu, label + "|" + urls[u],
 671                             urls[u + 1]);
 672                   }
 673                 }
 674               }
 675             }
 676           }
 677           if (id != null)
 678           {
 679             // create Bare ID link for this RUL
 680             String[] urls = urlLink.makeUrls(id, true);
 681             if (urls != null)
 682             {
 683               for (int u = 0; u < urls.length; u += 2)
 684               {
 685                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 686                 {
 687                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 688                   addshowLink(linkMenu, label, urls[u + 1]);
 689                 }
 690               }
 691             }
 692           }
 693           // Create urls from description but only for URL links which are regex
 694           // links
 695           if (descr != null && urlLink.getRegexReplace() != null)
 696           {
 697             // create link for this URL from description where regex matches
 698             String[] urls = urlLink.makeUrls(descr, true);
 699             if (urls != null)
 700             {
 701               for (int u = 0; u < urls.length; u += 2)
 702               {
 703                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
 704                 {
 705                   linkset.addElement(urls[u] + "|" + urls[u + 1]);
 706                   addshowLink(linkMenu, label, urls[u + 1]);
 707                 }
 708               }
 709             }
 710           }
 711         }
 712         else
 713         {
 714           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
 715           {
 716             linkset.addElement(label + "|" + urlLink.getUrl_prefix());
 717             // Add a non-dynamic link
 718             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 719           }
 720         }
 721       }
 722       if (sequence != null)
 723       {
 724         sequenceMenu.add(linkMenu);
 725       }
 726       else
 727       {
 728         add(linkMenu);
 729       }
 730     }
 731   }
 732
 733   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 734   {
 735
 736     // TODO: usability: thread off the generation of group url content so root
 737     // menu appears asap
 738     // sequence only URLs
 739     // ID/regex match URLs
 740     groupLinksMenu = new JMenu(
 741             MessageManager.getString("action.group_link"));
 742     JMenu[] linkMenus = new JMenu[]
 743     { null, new JMenu(MessageManager.getString("action.ids")),
 744         new JMenu(MessageManager.getString("action.sequences")),
 745         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
 746                                                                        // types
 747                                                                        // of url
 748                                                                        // that
 749                                                                        // might
 750                                                                        // be
 751     // created.
 752     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 753     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 754     Hashtable commonDbrefs = new Hashtable();
 755     for (int sq = 0; sq < seqs.length; sq++)
 756     {
 757
 758       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
 759               .findPosition(sg.getEndRes());
 760       // just collect ids from dataset sequence
 761       // TODO: check if IDs collected from selecton group intersects with the
 762       // current selection, too
 763       SequenceI sqi = seqs[sq];
 764       while (sqi.getDatasetSequence() != null)
 765       {
 766         sqi = sqi.getDatasetSequence();
 767       }
 768       DBRefEntry[] dbr = sqi.getDBRef();
 769       if (dbr != null && dbr.length > 0)
 770       {
 771         for (int d = 0; d < dbr.length; d++)
 772         {
 773           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 774           Object[] sarray = (Object[]) commonDbrefs.get(src);
 775           if (sarray == null)
 776           {
 777             sarray = new Object[2];
 778             sarray[0] = new int[]
 779             { 0 };
 780             sarray[1] = new String[seqs.length];
 781
 782             commonDbrefs.put(src, sarray);
 783           }
 784
 785           if (((String[]) sarray[1])[sq] == null)
 786           {
 787             if (!dbr[d].hasMap()
 788                     || (dbr[d].getMap().locateMappedRange(start, end) != null))
 789             {
 790               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
 791               ((int[]) sarray[0])[0]++;
 792             }
 793           }
 794         }
 795       }
 796     }
 797     // now create group links for all distinct ID/sequence sets.
 798     boolean addMenu = false; // indicates if there are any group links to give
 799                              // to user
 800     for (int i = 0; i < groupLinks.size(); i++)
 801     {
 802       String link = groupLinks.elementAt(i).toString();
 803       GroupUrlLink urlLink = null;
 804       try
 805       {
 806         urlLink = new GroupUrlLink(link);
 807       } catch (Exception foo)
 808       {
 809         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 810                 + "'", foo);
 811         continue;
 812       }
 813       ;
 814       if (!urlLink.isValid())
 815       {
 816         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 817         continue;
 818       }
 819       final String label = urlLink.getLabel();
 820       boolean usingNames = false;
 821       // Now see which parts of the group apply for this URL
 822       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 823       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 824       String[] seqstr, ids; // input to makeUrl
 825       if (idset != null)
 826       {
 827         int numinput = ((int[]) idset[0])[0];
 828         String[] allids = ((String[]) idset[1]);
 829         seqstr = new String[numinput];
 830         ids = new String[numinput];
 831         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
 832         {
 833           if (allids[sq] != null)
 834           {
 835             ids[idcount] = allids[sq];
 836             seqstr[idcount++] = idandseqs[1][sq];
 837           }
 838         }
 839       }
 840       else
 841       {
 842         // just use the id/seq set
 843         seqstr = idandseqs[1];
 844         ids = idandseqs[0];
 845         usingNames = true;
 846       }
 847       // and try and make the groupURL!
 848
 849       Object[] urlset = null;
 850       try
 851       {
 852         urlset = urlLink.makeUrlStubs(ids, seqstr,
 853                 "FromJalview" + System.currentTimeMillis(), false);
 854       } catch (UrlStringTooLongException e)
 855       {
 856       }
 857       if (urlset != null)
 858       {
 859         int type = urlLink.getGroupURLType() & 3;
 860         // System.out.println(urlLink.getGroupURLType()
 861         // +" "+((String[])urlset[3])[0]);
 862         // first two bits ofurlLink type bitfield are sequenceids and sequences
 863         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 864         addshowLink(linkMenus[type], label
 865                 + (((type & 1) == 1) ? ("("
 866                         + (usingNames ? "Names" : ltarget) + ")") : ""),
 867                 urlLink, urlset);
 868         addMenu = true;
 869       }
 870     }
 871     if (addMenu)
 872     {
 873       groupLinksMenu = new JMenu(
 874               MessageManager.getString("action.group_link"));
 875       for (int m = 0; m < linkMenus.length; m++)
 876       {
 877         if (linkMenus[m] != null
 878                 && linkMenus[m].getMenuComponentCount() > 0)
 879         {
 880           groupLinksMenu.add(linkMenus[m]);
 881         }
 882       }
 883
 884       groupMenu.add(groupLinksMenu);
 885     }
 886   }
 887
 888   /**
 889    * add a show URL menu item to the given linkMenu
 890    *
 891    * @param linkMenu
 892    * @param label
 893    *          - menu label string
 894    * @param url
 895    *          - url to open
 896    */
 897   private void addshowLink(JMenu linkMenu, String label, final String url)
 898   {
 899     JMenuItem item = new JMenuItem(label);
 900     item.setToolTipText(MessageManager.formatMessage(
 901             "label.open_url_param", new String[]
 902             { url }));
 903     item.addActionListener(new java.awt.event.ActionListener()
 904     {
 905       public void actionPerformed(ActionEvent e)
 906       {
 907         new Thread(new Runnable()
 908         {
 909
 910           public void run()
 911           {
 912             showLink(url);
 913           }
 914
 915         }).start();
 916       }
 917     });
 918
 919     linkMenu.add(item);
 920   }
 921
 922   /**
 923    * add a late bound groupURL item to the given linkMenu
 924    *
 925    * @param linkMenu
 926    * @param label
 927    *          - menu label string
 928    * @param urlgenerator
 929    *          GroupURLLink used to generate URL
 930    * @param urlstub
 931    *          Object array returned from the makeUrlStubs function.
 932    */
 933   private void addshowLink(JMenu linkMenu, String label,
 934           final GroupUrlLink urlgenerator, final Object[] urlstub)
 935   {
 936     JMenuItem item = new JMenuItem(label);
 937     item.setToolTipText(MessageManager.formatMessage(
 938             "label.open_url_seqs_param",
 939             new Object[]
 940             { urlgenerator.getUrl_prefix(),
 941                 urlgenerator.getNumberInvolved(urlstub) }));
 942     // TODO: put in info about what is being sent.
 943     item.addActionListener(new java.awt.event.ActionListener()
 944     {
 945       public void actionPerformed(ActionEvent e)
 946       {
 947         new Thread(new Runnable()
 948         {
 949
 950           public void run()
 951           {
 952             try
 953             {
 954               showLink(urlgenerator.constructFrom(urlstub));
 955             } catch (UrlStringTooLongException e)
 956             {
 957             }
 958           }
 959
 960         }).start();
 961       }
 962     });
 963
 964     linkMenu.add(item);
 965   }
 966
 967   /**
 968    * DOCUMENT ME!
 969    *
 970    * @throws Exception
 971    *           DOCUMENT ME!
 972    */
 973   private void jbInit() throws Exception
 974   {
 975     groupMenu.setText(MessageManager.getString("label.group"));
 976     groupMenu.setText(MessageManager.getString("label.selection"));
 977     groupName.setText(MessageManager.getString("label.name"));
 978     groupName.addActionListener(new java.awt.event.ActionListener()
 979     {
 980       public void actionPerformed(ActionEvent e)
 981       {
 982         groupName_actionPerformed();
 983       }
 984     });
 985     sequenceMenu.setText(MessageManager.getString("label.sequence"));
 986     sequenceName.setText(MessageManager
 987             .getString("label.edit_name_description"));
 988     sequenceName.addActionListener(new java.awt.event.ActionListener()
 989     {
 990       public void actionPerformed(ActionEvent e)
 991       {
 992         sequenceName_actionPerformed();
 993       }
 994     });
 995     sequenceDetails.setText(MessageManager
 996             .getString("label.sequence_details") + "...");
 997     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
 998     {
 999       public void actionPerformed(ActionEvent e)
1000       {
1001         sequenceDetails_actionPerformed();
1002       }
1003     });
1004     sequenceSelDetails.setText(MessageManager
1005             .getString("label.sequence_details") + "...");
1006     sequenceSelDetails
1007             .addActionListener(new java.awt.event.ActionListener()
1008             {
1009               public void actionPerformed(ActionEvent e)
1010               {
1011                 sequenceSelectionDetails_actionPerformed();
1012               }
1013             });
1014     PIDColour.setFocusPainted(false);
1015     unGroupMenuItem
1016             .setText(MessageManager.getString("action.remove_group"));
1017     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1018     {
1019       public void actionPerformed(ActionEvent e)
1020       {
1021         unGroupMenuItem_actionPerformed();
1022       }
1023     });
1024     createGroupMenuItem.setText(MessageManager
1025             .getString("action.create_group"));
1026     createGroupMenuItem
1027             .addActionListener(new java.awt.event.ActionListener()
1028             {
1029               public void actionPerformed(ActionEvent e)
1030               {
1031                 createGroupMenuItem_actionPerformed();
1032               }
1033             });
1034
1035     outline.setText(MessageManager.getString("action.border_colour"));
1036     outline.addActionListener(new java.awt.event.ActionListener()
1037     {
1038       public void actionPerformed(ActionEvent e)
1039       {
1040         outline_actionPerformed();
1041       }
1042     });
1043     nucleotideMenuItem
1044             .setText(MessageManager.getString("label.nucleotide"));
1045     nucleotideMenuItem.addActionListener(new ActionListener()
1046     {
1047       public void actionPerformed(ActionEvent e)
1048       {
1049         nucleotideMenuItem_actionPerformed();
1050       }
1051     });
1052     colourMenu.setText(MessageManager.getString("label.group_colour"));
1053     showBoxes.setText(MessageManager.getString("action.boxes"));
1054     showBoxes.setState(true);
1055     showBoxes.addActionListener(new ActionListener()
1056     {
1057       public void actionPerformed(ActionEvent e)
1058       {
1059         showBoxes_actionPerformed();
1060       }
1061     });
1062     showText.setText(MessageManager.getString("action.text"));
1063     showText.setState(true);
1064     showText.addActionListener(new ActionListener()
1065     {
1066       public void actionPerformed(ActionEvent e)
1067       {
1068         showText_actionPerformed();
1069       }
1070     });
1071     showColourText.setText(MessageManager.getString("label.colour_text"));
1072     showColourText.addActionListener(new ActionListener()
1073     {
1074       public void actionPerformed(ActionEvent e)
1075       {
1076         showColourText_actionPerformed();
1077       }
1078     });
1079     displayNonconserved.setText(MessageManager
1080             .getString("label.show_non_conversed"));
1081     displayNonconserved.setState(true);
1082     displayNonconserved.addActionListener(new ActionListener()
1083     {
1084       public void actionPerformed(ActionEvent e)
1085       {
1086         showNonconserved_actionPerformed();
1087       }
1088     });
1089     editMenu.setText(MessageManager.getString("action.edit"));
1090     cut.setText(MessageManager.getString("action.cut"));
1091     cut.addActionListener(new ActionListener()
1092     {
1093       public void actionPerformed(ActionEvent e)
1094       {
1095         cut_actionPerformed();
1096       }
1097     });
1098     upperCase.setText(MessageManager.getString("label.to_upper_case"));
1099     upperCase.addActionListener(new ActionListener()
1100     {
1101       public void actionPerformed(ActionEvent e)
1102       {
1103         changeCase(e);
1104       }
1105     });
1106     copy.setText(MessageManager.getString("action.copy"));
1107     copy.addActionListener(new ActionListener()
1108     {
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         copy_actionPerformed();
1112       }
1113     });
1114     lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1115     lowerCase.addActionListener(new ActionListener()
1116     {
1117       public void actionPerformed(ActionEvent e)
1118       {
1119         changeCase(e);
1120       }
1121     });
1122     toggle.setText(MessageManager.getString("label.toggle_case"));
1123     toggle.addActionListener(new ActionListener()
1124     {
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         changeCase(e);
1128       }
1129     });
1130     pdbMenu.setText(MessageManager
1131             .getString("label.associate_structure_with_sequence"));
1132     pdbFromFile.setText(MessageManager.getString("label.from_file"));
1133     pdbFromFile.addActionListener(new ActionListener()
1134     {
1135       public void actionPerformed(ActionEvent e)
1136       {
1137         pdbFromFile_actionPerformed();
1138       }
1139     });
1140     // RNAFold.setText("From RNA Fold with predict2D");
1141     // RNAFold.addActionListener(new ActionListener()
1142     // {
1143     // public void actionPerformed(ActionEvent e)
1144     // {
1145     // try {
1146     // RNAFold_actionPerformed();
1147     // } catch (Exception e1) {
1148     // // TODO Auto-generated catch block
1149     // e1.printStackTrace();
1150     // }
1151     // }
1152     // });
1153     // ContraFold.setText("From Contra Fold with predict2D");
1154     // ContraFold.addActionListener(new ActionListener()
1155     // {
1156     // public void actionPerformed(ActionEvent e)
1157     // {
1158     // try {
1159     // ContraFold_actionPerformed();
1160     // } catch (Exception e1) {
1161     // // TODO Auto-generated catch block
1162     // e1.printStackTrace();
1163     // }
1164     // }
1165     // });
1166     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1167     enterPDB.addActionListener(new ActionListener()
1168     {
1169       public void actionPerformed(ActionEvent e)
1170       {
1171         enterPDB_actionPerformed();
1172       }
1173     });
1174     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1175     discoverPDB.addActionListener(new ActionListener()
1176     {
1177       public void actionPerformed(ActionEvent e)
1178       {
1179         discoverPDB_actionPerformed();
1180       }
1181     });
1182     outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1183             + "...");
1184     sequenceFeature.setText(MessageManager
1185             .getString("label.create_sequence_feature"));
1186     sequenceFeature.addActionListener(new ActionListener()
1187     {
1188       public void actionPerformed(ActionEvent e)
1189       {
1190         sequenceFeature_actionPerformed();
1191       }
1192     });
1193     textColour.setText(MessageManager.getString("label.text_colour"));
1194     textColour.addActionListener(new ActionListener()
1195     {
1196       public void actionPerformed(ActionEvent e)
1197       {
1198         textColour_actionPerformed();
1199       }
1200     });
1201     jMenu1.setText(MessageManager.getString("label.group"));
1202     structureMenu.setText(MessageManager.getString("label.structure"));
1203     viewStructureMenu.setText(MessageManager
1204             .getString("label.view_structure"));
1205     // colStructureMenu.setText("Colour By Structure");
1206     editSequence.setText(MessageManager.getString("label.edit_sequence")
1207             + "...");
1208     editSequence.addActionListener(new ActionListener()
1209     {
1210       public void actionPerformed(ActionEvent actionEvent)
1211       {
1212         editSequence_actionPerformed(actionEvent);
1213       }
1214     });
1215
1216     /*
1217      * annotationMenuItem.setText("By Annotation");
1218      * annotationMenuItem.addActionListener(new ActionListener() { public void
1219      * actionPerformed(ActionEvent actionEvent) {
1220      * annotationMenuItem_actionPerformed(actionEvent); } });
1221      */
1222     groupMenu.add(sequenceSelDetails);
1223     add(groupMenu);
1224     add(sequenceMenu);
1225     this.add(structureMenu);
1226     groupMenu.add(editMenu);
1227     groupMenu.add(outputMenu);
1228     groupMenu.add(sequenceFeature);
1229     groupMenu.add(createGroupMenuItem);
1230     groupMenu.add(unGroupMenuItem);
1231     groupMenu.add(jMenu1);
1232     sequenceMenu.add(sequenceName);
1233     sequenceMenu.add(sequenceDetails);
1234     colourMenu.add(textColour);
1235     colourMenu.add(noColourmenuItem);
1236     colourMenu.add(clustalColour);
1237     colourMenu.add(BLOSUM62Colour);
1238     colourMenu.add(PIDColour);
1239     colourMenu.add(zappoColour);
1240     colourMenu.add(taylorColour);
1241     colourMenu.add(hydrophobicityColour);
1242     colourMenu.add(helixColour);
1243     colourMenu.add(strandColour);
1244     colourMenu.add(turnColour);
1245     colourMenu.add(buriedColour);
1246     colourMenu.add(nucleotideMenuItem);
1247     if (ap.getAlignment().isNucleotide())
1248     {
1249       // JBPNote - commented since the colourscheme isn't functional
1250       // colourMenu.add(RNAInteractionColour);
1251       colourMenu.add(purinePyrimidineColour);
1252     }
1253     // colourMenu.add(covariationColour);
1254     colourMenu.add(userDefinedColour);
1255
1256     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1257     {
1258       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1259               .getUserColourSchemes().keys();
1260
1261       while (userColours.hasMoreElements())
1262       {
1263         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1264         item.addActionListener(new ActionListener()
1265         {
1266           public void actionPerformed(ActionEvent evt)
1267           {
1268             userDefinedColour_actionPerformed(evt);
1269           }
1270         });
1271         colourMenu.add(item);
1272       }
1273     }
1274
1275     colourMenu.addSeparator();
1276     colourMenu.add(abovePIDColour);
1277     colourMenu.add(conservationMenuItem);
1278     // colourMenu.add(annotationMenuItem);
1279     editMenu.add(copy);
1280     editMenu.add(cut);
1281     editMenu.add(editSequence);
1282     editMenu.add(upperCase);
1283     editMenu.add(lowerCase);
1284     editMenu.add(toggle);
1285     pdbMenu.add(pdbFromFile);
1286     // JBPNote: These shouldn't be added here - should appear in a generic
1287     // 'apply web service to this sequence menu'
1288     // pdbMenu.add(RNAFold);
1289     // pdbMenu.add(ContraFold);
1290     pdbMenu.add(enterPDB);
1291     pdbMenu.add(discoverPDB);
1292     jMenu1.add(groupName);
1293     jMenu1.add(colourMenu);
1294     jMenu1.add(showBoxes);
1295     jMenu1.add(showText);
1296     jMenu1.add(showColourText);
1297     jMenu1.add(outline);
1298     jMenu1.add(displayNonconserved);
1299     structureMenu.add(pdbMenu);
1300     structureMenu.add(viewStructureMenu);
1301     // structureMenu.add(colStructureMenu);
1302     noColourmenuItem.setText(MessageManager.getString("label.none"));
1303     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1304     {
1305       public void actionPerformed(ActionEvent e)
1306       {
1307         noColourmenuItem_actionPerformed();
1308       }
1309     });
1310
1311     clustalColour.setText(MessageManager
1312             .getString("label.clustalx_colours"));
1313     clustalColour.addActionListener(new java.awt.event.ActionListener()
1314     {
1315       public void actionPerformed(ActionEvent e)
1316       {
1317         clustalColour_actionPerformed();
1318       }
1319     });
1320     zappoColour.setText(MessageManager.getString("label.zappo"));
1321     zappoColour.addActionListener(new java.awt.event.ActionListener()
1322     {
1323       public void actionPerformed(ActionEvent e)
1324       {
1325         zappoColour_actionPerformed();
1326       }
1327     });
1328     taylorColour.setText(MessageManager.getString("label.taylor"));
1329     taylorColour.addActionListener(new java.awt.event.ActionListener()
1330     {
1331       public void actionPerformed(ActionEvent e)
1332       {
1333         taylorColour_actionPerformed();
1334       }
1335     });
1336     hydrophobicityColour.setText(MessageManager
1337             .getString("label.hydrophobicity"));
1338     hydrophobicityColour
1339             .addActionListener(new java.awt.event.ActionListener()
1340             {
1341               public void actionPerformed(ActionEvent e)
1342               {
1343                 hydrophobicityColour_actionPerformed();
1344               }
1345             });
1346     helixColour.setText(MessageManager.getString("label.helix_propensity"));
1347     helixColour.addActionListener(new java.awt.event.ActionListener()
1348     {
1349       public void actionPerformed(ActionEvent e)
1350       {
1351         helixColour_actionPerformed();
1352       }
1353     });
1354     strandColour.setText(MessageManager
1355             .getString("label.strand_propensity"));
1356     strandColour.addActionListener(new java.awt.event.ActionListener()
1357     {
1358       public void actionPerformed(ActionEvent e)
1359       {
1360         strandColour_actionPerformed();
1361       }
1362     });
1363     turnColour.setText(MessageManager.getString("label.turn_propensity"));
1364     turnColour.addActionListener(new java.awt.event.ActionListener()
1365     {
1366       public void actionPerformed(ActionEvent e)
1367       {
1368         turnColour_actionPerformed();
1369       }
1370     });
1371     buriedColour.setText(MessageManager.getString("label.buried_index"));
1372     buriedColour.addActionListener(new java.awt.event.ActionListener()
1373     {
1374       public void actionPerformed(ActionEvent e)
1375       {
1376         buriedColour_actionPerformed();
1377       }
1378     });
1379     abovePIDColour.setText(MessageManager
1380             .getString("label.above_identity_percentage"));
1381     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1382     {
1383       public void actionPerformed(ActionEvent e)
1384       {
1385         abovePIDColour_actionPerformed();
1386       }
1387     });
1388     userDefinedColour.setText(MessageManager
1389             .getString("action.user_defined"));
1390     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1391     {
1392       public void actionPerformed(ActionEvent e)
1393       {
1394         userDefinedColour_actionPerformed(e);
1395       }
1396     });
1397     PIDColour
1398             .setText(MessageManager.getString("label.percentage_identity"));
1399     PIDColour.addActionListener(new java.awt.event.ActionListener()
1400     {
1401       public void actionPerformed(ActionEvent e)
1402       {
1403         PIDColour_actionPerformed();
1404       }
1405     });
1406     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1407     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1408     {
1409       public void actionPerformed(ActionEvent e)
1410       {
1411         BLOSUM62Colour_actionPerformed();
1412       }
1413     });
1414     purinePyrimidineColour.setText(MessageManager
1415             .getString("label.purine_pyrimidine"));
1416     purinePyrimidineColour
1417             .addActionListener(new java.awt.event.ActionListener()
1418             {
1419               public void actionPerformed(ActionEvent e)
1420               {
1421                 purinePyrimidineColour_actionPerformed();
1422               }
1423             });
1424
1425     /*
1426      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1427      * public void actionPerformed(ActionEvent e) {
1428      * covariationColour_actionPerformed(); } });
1429      */
1430
1431     conservationMenuItem.setText(MessageManager
1432             .getString("label.conservation"));
1433     conservationMenuItem
1434             .addActionListener(new java.awt.event.ActionListener()
1435             {
1436               public void actionPerformed(ActionEvent e)
1437               {
1438                 conservationMenuItem_actionPerformed();
1439               }
1440             });
1441   }
1442
1443   protected void sequenceSelectionDetails_actionPerformed()
1444   {
1445     createSequenceDetailsReport(ap.av.getSequenceSelection());
1446   }
1447
1448   protected void sequenceDetails_actionPerformed()
1449   {
1450     createSequenceDetailsReport(new SequenceI[]
1451     { sequence });
1452   }
1453
1454   public void createSequenceDetailsReport(SequenceI[] sequences)
1455   {
1456     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1457     StringBuffer contents = new StringBuffer();
1458     for (SequenceI seq : sequences)
1459     {
1460       contents.append("<p><h2>"
1461               + MessageManager
1462                       .formatMessage(
1463                               "label.create_sequence_details_report_annotation_for",
1464                               new String[]
1465                               { seq.getDisplayId(true) }) + "</h2></p><p>");
1466       new SequenceAnnotationReport(null)
1467               .createSequenceAnnotationReport(
1468                       contents,
1469                       seq,
1470                       true,
1471                       true,
1472                       false,
1473                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1474                               : null);
1475       contents.append("</p>");
1476     }
1477     cap.setText("<html>" + contents.toString() + "</html>");
1478
1479     Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
1480             "label.sequece_details_for",
1481             (sequences.length == 1 ? new String[]
1482             { sequences[0].getDisplayId(true) } : new String[]
1483             { MessageManager.getString("label.selection") })), 500, 400);
1484
1485   }
1486
1487   protected void showNonconserved_actionPerformed()
1488   {
1489     getGroup().setShowNonconserved(displayNonconserved.isSelected());
1490     refresh();
1491   }
1492
1493   /**
1494    * call to refresh view after settings change
1495    */
1496   void refresh()
1497   {
1498     ap.updateAnnotation();
1499     ap.paintAlignment(true);
1500
1501     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1502   }
1503
1504   /**
1505    * DOCUMENT ME!
1506    *
1507    * @param e
1508    *          DOCUMENT ME!
1509    */
1510   protected void clustalColour_actionPerformed()
1511   {
1512     SequenceGroup sg = getGroup();
1513     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1514     refresh();
1515   }
1516
1517   /**
1518    * DOCUMENT ME!
1519    *
1520    * @param e
1521    *          DOCUMENT ME!
1522    */
1523   protected void zappoColour_actionPerformed()
1524   {
1525     getGroup().cs = new ZappoColourScheme();
1526     refresh();
1527   }
1528
1529   /**
1530    * DOCUMENT ME!
1531    *
1532    * @param e
1533    *          DOCUMENT ME!
1534    */
1535   protected void taylorColour_actionPerformed()
1536   {
1537     getGroup().cs = new TaylorColourScheme();
1538     refresh();
1539   }
1540
1541   /**
1542    * DOCUMENT ME!
1543    *
1544    * @param e
1545    *          DOCUMENT ME!
1546    */
1547   protected void hydrophobicityColour_actionPerformed()
1548   {
1549     getGroup().cs = new HydrophobicColourScheme();
1550     refresh();
1551   }
1552
1553   /**
1554    * DOCUMENT ME!
1555    *
1556    * @param e
1557    *          DOCUMENT ME!
1558    */
1559   protected void helixColour_actionPerformed()
1560   {
1561     getGroup().cs = new HelixColourScheme();
1562     refresh();
1563   }
1564
1565   /**
1566    * DOCUMENT ME!
1567    *
1568    * @param e
1569    *          DOCUMENT ME!
1570    */
1571   protected void strandColour_actionPerformed()
1572   {
1573     getGroup().cs = new StrandColourScheme();
1574     refresh();
1575   }
1576
1577   /**
1578    * DOCUMENT ME!
1579    *
1580    * @param e
1581    *          DOCUMENT ME!
1582    */
1583   protected void turnColour_actionPerformed()
1584   {
1585     getGroup().cs = new TurnColourScheme();
1586     refresh();
1587   }
1588
1589   /**
1590    * DOCUMENT ME!
1591    *
1592    * @param e
1593    *          DOCUMENT ME!
1594    */
1595   protected void buriedColour_actionPerformed()
1596   {
1597     getGroup().cs = new BuriedColourScheme();
1598     refresh();
1599   }
1600
1601   /**
1602    * DOCUMENT ME!
1603    *
1604    * @param e
1605    *          DOCUMENT ME!
1606    */
1607   public void nucleotideMenuItem_actionPerformed()
1608   {
1609     getGroup().cs = new NucleotideColourScheme();
1610     refresh();
1611   }
1612
1613   protected void purinePyrimidineColour_actionPerformed()
1614   {
1615     getGroup().cs = new PurinePyrimidineColourScheme();
1616     refresh();
1617   }
1618
1619   /*
1620    * protected void covariationColour_actionPerformed() { getGroup().cs = new
1621    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1622    */
1623   /**
1624    * DOCUMENT ME!
1625    *
1626    * @param e
1627    *          DOCUMENT ME!
1628    */
1629   protected void abovePIDColour_actionPerformed()
1630   {
1631     SequenceGroup sg = getGroup();
1632     if (sg.cs == null)
1633     {
1634       return;
1635     }
1636
1637     if (abovePIDColour.isSelected())
1638     {
1639       sg.cs.setConsensus(AAFrequency.calculate(
1640               sg.getSequences(ap.av.getHiddenRepSequences()),
1641               sg.getStartRes(), sg.getEndRes() + 1));
1642
1643       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1644               .getName());
1645
1646       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1647
1648       SliderPanel.showPIDSlider();
1649     }
1650     else
1651     // remove PIDColouring
1652     {
1653       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1654     }
1655
1656     refresh();
1657   }
1658
1659   /**
1660    * DOCUMENT ME!
1661    *
1662    * @param e
1663    *          DOCUMENT ME!
1664    */
1665   protected void userDefinedColour_actionPerformed(ActionEvent e)
1666   {
1667     SequenceGroup sg = getGroup();
1668
1669     if (e.getSource().equals(userDefinedColour))
1670     {
1671       new UserDefinedColours(ap, sg);
1672     }
1673     else
1674     {
1675       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1676               .getUserColourSchemes().get(e.getActionCommand());
1677
1678       sg.cs = udc;
1679     }
1680     refresh();
1681   }
1682
1683   /**
1684    * DOCUMENT ME!
1685    *
1686    * @param e
1687    *          DOCUMENT ME!
1688    */
1689   protected void PIDColour_actionPerformed()
1690   {
1691     SequenceGroup sg = getGroup();
1692     sg.cs = new PIDColourScheme();
1693     sg.cs.setConsensus(AAFrequency.calculate(
1694             sg.getSequences(ap.av.getHiddenRepSequences()),
1695             sg.getStartRes(), sg.getEndRes() + 1));
1696     refresh();
1697   }
1698
1699   /**
1700    * DOCUMENT ME!
1701    *
1702    * @param e
1703    *          DOCUMENT ME!
1704    */
1705   protected void BLOSUM62Colour_actionPerformed()
1706   {
1707     SequenceGroup sg = getGroup();
1708
1709     sg.cs = new Blosum62ColourScheme();
1710
1711     sg.cs.setConsensus(AAFrequency.calculate(
1712             sg.getSequences(ap.av.getHiddenRepSequences()),
1713             sg.getStartRes(), sg.getEndRes() + 1));
1714
1715     refresh();
1716   }
1717
1718   /**
1719    * DOCUMENT ME!
1720    *
1721    * @param e
1722    *          DOCUMENT ME!
1723    */
1724   protected void noColourmenuItem_actionPerformed()
1725   {
1726     getGroup().cs = null;
1727     refresh();
1728   }
1729
1730   /**
1731    * DOCUMENT ME!
1732    *
1733    * @param e
1734    *          DOCUMENT ME!
1735    */
1736   protected void conservationMenuItem_actionPerformed()
1737   {
1738     SequenceGroup sg = getGroup();
1739     if (sg.cs == null)
1740     {
1741       return;
1742     }
1743
1744     if (conservationMenuItem.isSelected())
1745     {
1746       // JBPNote: Conservation name shouldn't be i18n translated
1747       Conservation c = new Conservation("Group",
1748               ResidueProperties.propHash, 3, sg.getSequences(ap.av
1749                       .getHiddenRepSequences()), sg.getStartRes(),
1750               sg.getEndRes() + 1);
1751
1752       c.calculate();
1753       c.verdict(false, ap.av.getConsPercGaps());
1754
1755       sg.cs.setConservation(c);
1756
1757       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1758       SliderPanel.showConservationSlider();
1759     }
1760     else
1761     // remove ConservationColouring
1762     {
1763       sg.cs.setConservation(null);
1764     }
1765
1766     refresh();
1767   }
1768
1769   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1770   {
1771     SequenceGroup sg = getGroup();
1772     if (sg == null)
1773     {
1774       return;
1775     }
1776
1777     AnnotationColourGradient acg = new AnnotationColourGradient(
1778             sequence.getAnnotation()[0], null,
1779             AnnotationColourGradient.NO_THRESHOLD);
1780
1781     acg.setPredefinedColours(true);
1782     sg.cs = acg;
1783
1784     refresh();
1785   }
1786
1787   /**
1788    * DOCUMENT ME!
1789    *
1790    * @param e
1791    *          DOCUMENT ME!
1792    */
1793   protected void groupName_actionPerformed()
1794   {
1795
1796     SequenceGroup sg = getGroup();
1797     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1798             sg.getDescription(), "       "
1799                     + MessageManager.getString("label.group_name") + " ",
1800             MessageManager.getString("label.group_description") + " ",
1801             MessageManager.getString("label.edit_group_name_description"),
1802             ap.alignFrame);
1803
1804     if (!dialog.accept)
1805     {
1806       return;
1807     }
1808
1809     sg.setName(dialog.getName());
1810     sg.setDescription(dialog.getDescription());
1811     refresh();
1812   }
1813
1814   /**
1815    * Get selection group - adding it to the alignment if necessary.
1816    *
1817    * @return sequence group to operate on
1818    */
1819   SequenceGroup getGroup()
1820   {
1821     SequenceGroup sg = ap.av.getSelectionGroup();
1822     // this method won't add a new group if it already exists
1823     if (sg != null)
1824     {
1825       ap.av.getAlignment().addGroup(sg);
1826     }
1827
1828     return sg;
1829   }
1830
1831   /**
1832    * DOCUMENT ME!
1833    *
1834    * @param e
1835    *          DOCUMENT ME!
1836    */
1837   void sequenceName_actionPerformed()
1838   {
1839     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1840             sequence.getDescription(),
1841             "       " + MessageManager.getString("label.sequence_name")
1842                     + " ",
1843             MessageManager.getString("label.sequence_description") + " ",
1844             MessageManager
1845                     .getString("label.edit_sequence_name_description"),
1846             ap.alignFrame);
1847
1848     if (!dialog.accept)
1849     {
1850       return;
1851     }
1852
1853     if (dialog.getName() != null)
1854     {
1855       if (dialog.getName().indexOf(" ") > -1)
1856       {
1857         JOptionPane
1858                 .showMessageDialog(
1859                         ap,
1860                         MessageManager
1861                                 .getString("label.spaces_converted_to_backslashes"),
1862                         MessageManager
1863                                 .getString("label.no_spaces_allowed_sequence_name"),
1864                         JOptionPane.WARNING_MESSAGE);
1865       }
1866
1867       sequence.setName(dialog.getName().replace(' ', '_'));
1868       ap.paintAlignment(false);
1869     }
1870
1871     sequence.setDescription(dialog.getDescription());
1872
1873     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1874             .getSequences());
1875
1876   }
1877
1878   /**
1879    * DOCUMENT ME!
1880    *
1881    * @param e
1882    *          DOCUMENT ME!
1883    */
1884   void unGroupMenuItem_actionPerformed()
1885   {
1886     SequenceGroup sg = ap.av.getSelectionGroup();
1887     ap.av.getAlignment().deleteGroup(sg);
1888     ap.av.setSelectionGroup(null);
1889     refresh();
1890   }
1891
1892   void createGroupMenuItem_actionPerformed()
1893   {
1894     getGroup(); // implicitly creates group - note - should apply defaults / use
1895                 // standard alignment window logic for this
1896     refresh();
1897   }
1898
1899   /**
1900    * DOCUMENT ME!
1901    *
1902    * @param e
1903    *          DOCUMENT ME!
1904    */
1905   protected void outline_actionPerformed()
1906   {
1907     SequenceGroup sg = getGroup();
1908     Color col = JColorChooser.showDialog(this,
1909             MessageManager.getString("label.select_outline_colour"),
1910             Color.BLUE);
1911
1912     if (col != null)
1913     {
1914       sg.setOutlineColour(col);
1915     }
1916
1917     refresh();
1918   }
1919
1920   /**
1921    * DOCUMENT ME!
1922    *
1923    * @param e
1924    *          DOCUMENT ME!
1925    */
1926   public void showBoxes_actionPerformed()
1927   {
1928     getGroup().setDisplayBoxes(showBoxes.isSelected());
1929     refresh();
1930   }
1931
1932   /**
1933    * DOCUMENT ME!
1934    *
1935    * @param e
1936    *          DOCUMENT ME!
1937    */
1938   public void showText_actionPerformed()
1939   {
1940     getGroup().setDisplayText(showText.isSelected());
1941     refresh();
1942   }
1943
1944   /**
1945    * DOCUMENT ME!
1946    *
1947    * @param e
1948    *          DOCUMENT ME!
1949    */
1950   public void showColourText_actionPerformed()
1951   {
1952     getGroup().setColourText(showColourText.isSelected());
1953     refresh();
1954   }
1955
1956   public void showLink(String url)
1957   {
1958     try
1959     {
1960       jalview.util.BrowserLauncher.openURL(url);
1961     } catch (Exception ex)
1962     {
1963       JOptionPane.showInternalMessageDialog(Desktop.desktop,
1964               MessageManager.getString("label.web_browser_not_found_unix"),
1965               MessageManager.getString("label.web_browser_not_found"),
1966               JOptionPane.WARNING_MESSAGE);
1967
1968       ex.printStackTrace();
1969     }
1970   }
1971
1972   void hideSequences(boolean representGroup)
1973   {
1974     SequenceGroup sg = ap.av.getSelectionGroup();
1975     if (sg == null || sg.getSize() < 1)
1976     {
1977       ap.av.hideSequence(new SequenceI[]
1978       { sequence });
1979       return;
1980     }
1981
1982     ap.av.setSelectionGroup(null);
1983
1984     if (representGroup)
1985     {
1986       ap.av.hideRepSequences(sequence, sg);
1987
1988       return;
1989     }
1990
1991     int gsize = sg.getSize();
1992     SequenceI[] hseqs;
1993
1994     hseqs = new SequenceI[gsize];
1995
1996     int index = 0;
1997     for (int i = 0; i < gsize; i++)
1998     {
1999       hseqs[index++] = sg.getSequenceAt(i);
2000     }
2001
2002     ap.av.hideSequence(hseqs);
2003     // refresh(); TODO: ? needed ?
2004     ap.av.sendSelection();
2005   }
2006
2007   public void copy_actionPerformed()
2008   {
2009     ap.alignFrame.copy_actionPerformed(null);
2010   }
2011
2012   public void cut_actionPerformed()
2013   {
2014     ap.alignFrame.cut_actionPerformed(null);
2015   }
2016
2017   void changeCase(ActionEvent e)
2018   {
2019     Object source = e.getSource();
2020     SequenceGroup sg = ap.av.getSelectionGroup();
2021
2022     if (sg != null)
2023     {
2024       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
2025               sg.getEndRes() + 1);
2026
2027       String description;
2028       int caseChange;
2029
2030       if (source == toggle)
2031       {
2032         description = MessageManager.getString("label.toggle_case");
2033         caseChange = ChangeCaseCommand.TOGGLE_CASE;
2034       }
2035       else if (source == upperCase)
2036       {
2037         description = MessageManager.getString("label.to_upper_case");
2038         caseChange = ChangeCaseCommand.TO_UPPER;
2039       }
2040       else
2041       {
2042         description = MessageManager.getString("label.to_lower_case");
2043         caseChange = ChangeCaseCommand.TO_LOWER;
2044       }
2045
2046       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2047               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2048               startEnd, caseChange);
2049
2050       ap.alignFrame.addHistoryItem(caseCommand);
2051
2052       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2053               .getSequences());
2054
2055     }
2056   }
2057
2058   public void outputText_actionPerformed(ActionEvent e)
2059   {
2060     CutAndPasteTransfer cap = new CutAndPasteTransfer();
2061     cap.setForInput(null);
2062     Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2063             "label.alignment_output_command", new String[]
2064             { e.getActionCommand() }), 600, 500);
2065
2066     String[] omitHidden = null;
2067
2068     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2069     // or we simply trust the user wants
2070     // wysiwig behaviour
2071     SequenceGroup sg = ap.av.getSelectionGroup();
2072     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
2073     omitHidden = ap.av.getViewAsString(true);
2074     Alignment oal = new Alignment(ap.av.getSequenceSelection());
2075     AlignmentAnnotation[] nala = ap.av.getAlignment()
2076             .getAlignmentAnnotation();
2077     if (nala != null)
2078     {
2079       for (int i = 0; i < nala.length; i++)
2080       {
2081         AlignmentAnnotation na = nala[i];
2082         oal.addAnnotation(na);
2083       }
2084     }
2085     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2086             oal, omitHidden, csel, sg));
2087     oal = null;
2088   }
2089
2090   public void pdbFromFile_actionPerformed()
2091   {
2092     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2093             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2094     chooser.setFileView(new jalview.io.JalviewFileView());
2095     chooser.setDialogTitle(MessageManager.formatMessage(
2096             "label.select_pdb_file_for", new String[]
2097             { sequence.getDisplayId(false) }));
2098     chooser.setToolTipText(MessageManager.formatMessage(
2099             "label.load_pdb_file_associate_with_sequence", new String[]
2100             { new Integer(sequence.getDisplayId(false)).toString() }));
2101
2102     int value = chooser.showOpenDialog(null);
2103
2104     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2105     {
2106       String choice = chooser.getSelectedFile().getPath();
2107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2108       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2109               jalview.io.AppletFormatAdapter.FILE, sequence, true);
2110     }
2111
2112   }
2113
2114   // JBNote: commented out - these won't be instantiated here...!
2115   // public void RNAFold_actionPerformed() throws Exception
2116   // {
2117   // Predict2D P2D = new Predict2D();
2118   // P2D.getStructure2DFromRNAFold("toto");
2119   // }
2120   //
2121   // public void ContraFold_actionPerformed() throws Exception
2122   // {
2123   // Predict2D P2D = new Predict2D();
2124   // P2D.getStructure2DFromContraFold("toto");
2125   // }
2126   public void enterPDB_actionPerformed()
2127   {
2128     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2129             MessageManager.getString("label.enter_pdb_id"),
2130             MessageManager.getString("label.enter_pdb_id"),
2131             JOptionPane.QUESTION_MESSAGE);
2132
2133     if (id != null && id.length() > 0)
2134     {
2135       PDBEntry entry = new PDBEntry();
2136       entry.setId(id.toUpperCase());
2137       sequence.getDatasetSequence().addPDBId(entry);
2138     }
2139   }
2140
2141   public void discoverPDB_actionPerformed()
2142   {
2143
2144     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2145     { sequence }
2146             : ap.av.getSequenceSelection());
2147     Thread discpdb = new Thread(new Runnable()
2148     {
2149       public void run()
2150       {
2151
2152         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2153                 .fetchDBRefs(false);
2154       }
2155
2156     });
2157     discpdb.start();
2158   }
2159
2160   public void sequenceFeature_actionPerformed()
2161   {
2162     SequenceGroup sg = ap.av.getSelectionGroup();
2163     if (sg == null)
2164     {
2165       return;
2166     }
2167
2168     int rsize = 0, gSize = sg.getSize();
2169     SequenceI[] rseqs, seqs = new SequenceI[gSize];
2170     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2171
2172     for (int i = 0; i < gSize; i++)
2173     {
2174       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2175       int end = sg.findEndRes(sg.getSequenceAt(i));
2176       if (start <= end)
2177       {
2178         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2179         features[rsize] = new SequenceFeature(null, null, null, start, end,
2180                 "Jalview");
2181         rsize++;
2182       }
2183     }
2184     rseqs = new SequenceI[rsize];
2185     tfeatures = new SequenceFeature[rsize];
2186     System.arraycopy(seqs, 0, rseqs, 0, rsize);
2187     System.arraycopy(features, 0, tfeatures, 0, rsize);
2188     features = tfeatures;
2189     seqs = rseqs;
2190     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2191             features, true, ap))
2192     {
2193       ap.alignFrame.setShowSeqFeatures(true);
2194       ap.highlightSearchResults(null);
2195     }
2196   }
2197
2198   public void textColour_actionPerformed()
2199   {
2200     SequenceGroup sg = getGroup();
2201     if (sg != null)
2202     {
2203       new TextColourChooser().chooseColour(ap, sg);
2204     }
2205   }
2206
2207   public void colourByStructure(String pdbid)
2208   {
2209     Annotation[] anots = ap.av.getStructureSelectionManager()
2210             .colourSequenceFromStructure(sequence, pdbid);
2211
2212     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2213             "Coloured by " + pdbid, anots);
2214
2215     ap.av.getAlignment().addAnnotation(an);
2216     an.createSequenceMapping(sequence, 0, true);
2217     // an.adjustForAlignment();
2218     ap.av.getAlignment().setAnnotationIndex(an, 0);
2219
2220     ap.adjustAnnotationHeight();
2221
2222     sequence.addAlignmentAnnotation(an);
2223
2224   }
2225
2226   public void editSequence_actionPerformed(ActionEvent actionEvent)
2227   {
2228     SequenceGroup sg = ap.av.getSelectionGroup();
2229
2230     if (sg != null)
2231     {
2232       if (sequence == null)
2233         sequence = (Sequence) sg.getSequenceAt(0);
2234
2235       EditNameDialog dialog = new EditNameDialog(
2236               sequence.getSequenceAsString(sg.getStartRes(),
2237                       sg.getEndRes() + 1), null,
2238               MessageManager.getString("label.edit_sequence"), null,
2239               MessageManager.getString("label.edit_sequence"),
2240               ap.alignFrame);
2241
2242       if (dialog.accept)
2243       {
2244         EditCommand editCommand = new EditCommand(
2245                 MessageManager.getString("label.edit_sequences"),
2246                 EditCommand.REPLACE, dialog.getName().replace(' ',
2247                         ap.av.getGapCharacter()),
2248                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2249                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2250
2251         ap.alignFrame.addHistoryItem(editCommand);
2252
2253         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2254                 .getSequences());
2255       }
2256     }
2257   }
2258
2259 }