src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.UrlLink;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class PopupMenu extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44
  45   JMenuItem groupName = new JMenuItem();
  46
  47   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  48
  49   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  62
  63   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  64
  65   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  66
  67   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  70
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  72
  73   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  74
  75   AlignmentPanel ap;
  76
  77   JMenu sequenceMenu = new JMenu();
  78
  79   JMenuItem sequenceName = new JMenuItem();
  80
  81   Sequence sequence;
  82
  83   JMenuItem unGroupMenuItem = new JMenuItem();
  84
  85   JMenuItem outline = new JMenuItem();
  86
  87   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  88
  89   JMenu colourMenu = new JMenu();
  90
  91   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  92
  93   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  94
  95   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  96
  97   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
  98
  99   JMenu editMenu = new JMenu();
 100
 101   JMenuItem cut = new JMenuItem();
 102
 103   JMenuItem copy = new JMenuItem();
 104
 105   JMenuItem upperCase = new JMenuItem();
 106
 107   JMenuItem lowerCase = new JMenuItem();
 108
 109   JMenuItem toggle = new JMenuItem();
 110
 111   JMenu pdbMenu = new JMenu();
 112
 113   JMenuItem pdbFromFile = new JMenuItem();
 114
 115   JMenuItem enterPDB = new JMenuItem();
 116
 117   JMenuItem discoverPDB = new JMenuItem();
 118
 119   JMenu outputMenu = new JMenu();
 120
 121   JMenuItem sequenceFeature = new JMenuItem();
 122
 123   JMenuItem textColour = new JMenuItem();
 124
 125   JMenu jMenu1 = new JMenu();
 126
 127   JMenu structureMenu = new JMenu();
 128
 129   JMenu viewStructureMenu = new JMenu();
 130
 131   // JMenu colStructureMenu = new JMenu();
 132   JMenuItem editSequence = new JMenuItem();
 133
 134   // JMenuItem annotationMenuItem = new JMenuItem();
 135
 136   /**
 137    * Creates a new PopupMenu object.
 138    *
 139    * @param ap
 140    *                DOCUMENT ME!
 141    * @param seq
 142    *                DOCUMENT ME!
 143    */
 144   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 145   {
 146     // /////////////////////////////////////////////////////////
 147     // If this is activated from the sequence panel, the user may want to
 148     // edit or annotate a particular residue. Therefore display the residue menu
 149     //
 150     // If from the IDPanel, we must display the sequence menu
 151     // ////////////////////////////////////////////////////////
 152     this.ap = ap;
 153     sequence = seq;
 154
 155     ButtonGroup colours = new ButtonGroup();
 156     colours.add(noColourmenuItem);
 157     colours.add(clustalColour);
 158     colours.add(zappoColour);
 159     colours.add(taylorColour);
 160     colours.add(hydrophobicityColour);
 161     colours.add(helixColour);
 162     colours.add(strandColour);
 163     colours.add(turnColour);
 164     colours.add(buriedColour);
 165     colours.add(abovePIDColour);
 166     colours.add(userDefinedColour);
 167     colours.add(PIDColour);
 168     colours.add(BLOSUM62Colour);
 169
 170     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 171     {
 172       JMenuItem item = new JMenuItem(
 173               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 174
 175       item.addActionListener(new java.awt.event.ActionListener()
 176       {
 177         public void actionPerformed(ActionEvent e)
 178         {
 179           outputText_actionPerformed(e);
 180         }
 181       });
 182
 183       outputMenu.add(item);
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception e)
 190     {
 191       e.printStackTrace();
 192     }
 193
 194     if (seq != null)
 195     {
 196       sequenceMenu.setText(sequence.getName());
 197
 198       JMenuItem menuItem;
 199       if (seq.getDatasetSequence().getPDBId() != null
 200               && seq.getDatasetSequence().getPDBId().size() > 0)
 201       {
 202         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 203                 .elements();
 204
 205         while (e.hasMoreElements())
 206         {
 207           final PDBEntry pdb = (PDBEntry) e.nextElement();
 208
 209           menuItem = new JMenuItem();
 210           menuItem.setText(pdb.getId());
 211           menuItem.addActionListener(new java.awt.event.ActionListener()
 212           {
 213             public void actionPerformed(ActionEvent e)
 214             {
 215               Vector seqs = new Vector();
 216               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 217               {
 218                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 219                         .getDatasetSequence().getPDBId();
 220                 if (pdbs == null)
 221                   continue;
 222
 223                 for (int p = 0; p < pdbs.size(); p++)
 224                 {
 225                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 226                   if (p1.getId().equals(pdb.getId()))
 227                   {
 228                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 229                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 230
 231                     continue;
 232                   }
 233                 }
 234               }
 235
 236               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 237               seqs.toArray(seqs2);
 238
 239               new AppJmol(pdb, seqs2, null, ap);
 240               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 241             }
 242           });
 243           viewStructureMenu.add(menuItem);
 244
 245           /*
 246            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 247            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 248            * public void actionPerformed(ActionEvent e) {
 249            * colourByStructure(pdb.getId()); } });
 250            * colStructureMenu.add(menuItem);
 251            */
 252         }
 253       }
 254       else
 255       {
 256         structureMenu.remove(viewStructureMenu);
 257         // structureMenu.remove(colStructureMenu);
 258       }
 259
 260       menuItem = new JMenuItem("Hide Sequences");
 261       menuItem.addActionListener(new java.awt.event.ActionListener()
 262       {
 263         public void actionPerformed(ActionEvent e)
 264         {
 265           hideSequences(false);
 266         }
 267       });
 268       add(menuItem);
 269
 270       if (ap.av.getSelectionGroup() != null
 271               && ap.av.getSelectionGroup().getSize() > 1)
 272       {
 273         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 274         menuItem.addActionListener(new java.awt.event.ActionListener()
 275         {
 276           public void actionPerformed(ActionEvent e)
 277           {
 278             hideSequences(true);
 279           }
 280         });
 281         sequenceMenu.add(menuItem);
 282       }
 283
 284       if (ap.av.hasHiddenRows)
 285       {
 286         final int index = ap.av.alignment.findIndex(seq);
 287
 288         if (ap.av.adjustForHiddenSeqs(index)
 289                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 290         {
 291           menuItem = new JMenuItem("Reveal Sequences");
 292           menuItem.addActionListener(new ActionListener()
 293           {
 294             public void actionPerformed(ActionEvent e)
 295             {
 296               ap.av.showSequence(index);
 297               if (ap.overviewPanel != null)
 298               {
 299                 ap.overviewPanel.updateOverviewImage();
 300               }
 301             }
 302           });
 303           add(menuItem);
 304         }
 305
 306         menuItem = new JMenuItem("Reveal All");
 307         menuItem.addActionListener(new ActionListener()
 308         {
 309           public void actionPerformed(ActionEvent e)
 310           {
 311             ap.av.showAllHiddenSeqs();
 312             if (ap.overviewPanel != null)
 313             {
 314               ap.overviewPanel.updateOverviewImage();
 315             }
 316           }
 317         });
 318
 319         add(menuItem);
 320       }
 321
 322     }
 323
 324     SequenceGroup sg = ap.av.getSelectionGroup();
 325
 326     if (sg != null)
 327     {
 328       groupName.setText(sg.getName());
 329
 330       if (sg.cs instanceof ZappoColourScheme)
 331       {
 332         zappoColour.setSelected(true);
 333       }
 334       else if (sg.cs instanceof TaylorColourScheme)
 335       {
 336         taylorColour.setSelected(true);
 337       }
 338       else if (sg.cs instanceof PIDColourScheme)
 339       {
 340         PIDColour.setSelected(true);
 341       }
 342       else if (sg.cs instanceof Blosum62ColourScheme)
 343       {
 344         BLOSUM62Colour.setSelected(true);
 345       }
 346       else if (sg.cs instanceof UserColourScheme)
 347       {
 348         userDefinedColour.setSelected(true);
 349       }
 350       else if (sg.cs instanceof HydrophobicColourScheme)
 351       {
 352         hydrophobicityColour.setSelected(true);
 353       }
 354       else if (sg.cs instanceof HelixColourScheme)
 355       {
 356         helixColour.setSelected(true);
 357       }
 358       else if (sg.cs instanceof StrandColourScheme)
 359       {
 360         strandColour.setSelected(true);
 361       }
 362       else if (sg.cs instanceof TurnColourScheme)
 363       {
 364         turnColour.setSelected(true);
 365       }
 366       else if (sg.cs instanceof BuriedColourScheme)
 367       {
 368         buriedColour.setSelected(true);
 369       }
 370       else if (sg.cs instanceof ClustalxColourScheme)
 371       {
 372         clustalColour.setSelected(true);
 373       }
 374       else
 375       {
 376         noColourmenuItem.setSelected(true);
 377       }
 378
 379       if (sg.cs != null && sg.cs.conservationApplied())
 380       {
 381         conservationMenuItem.setSelected(true);
 382       }
 383       displayNonconserved.setSelected(sg.getShowunconserved());
 384       showText.setSelected(sg.getDisplayText());
 385       showColourText.setSelected(sg.getColourText());
 386       showBoxes.setSelected(sg.getDisplayBoxes());
 387     }
 388     else
 389     {
 390       groupMenu.setVisible(false);
 391       editMenu.setVisible(false);
 392     }
 393
 394     if (!ap.av.alignment.getGroups().contains(sg))
 395     {
 396       unGroupMenuItem.setVisible(false);
 397     }
 398
 399     if (seq == null)
 400     {
 401       sequenceMenu.setVisible(false);
 402       structureMenu.setVisible(false);
 403     }
 404
 405     if (links != null && links.size() > 0)
 406     {
 407       JMenu linkMenu = new JMenu("Link");
 408       Vector linkset = new Vector();
 409       for (int i = 0; i < links.size(); i++)
 410       {
 411         String link = links.elementAt(i).toString();
 412         UrlLink urlLink = null;
 413         try
 414         {
 415           urlLink = new UrlLink(link);
 416         } catch (Exception foo)
 417         {
 418           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 419                   + "'", foo);
 420           continue;
 421         }
 422         ;
 423         if (!urlLink.isValid())
 424         {
 425           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 426           continue;
 427         }
 428         final String label = urlLink.getLabel();
 429         if (urlLink.isDynamic())
 430         {
 431
 432           // collect matching db-refs
 433           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 434                   .getDBRef(), new String[]
 435           { urlLink.getTarget() });
 436           // collect id string too
 437           String id = seq.getName();
 438           String descr = seq.getDescription();
 439           if (descr!=null && descr.length()<1)
 440           {
 441             descr = null;
 442           }
 443
 444           if (dbr != null)
 445           {
 446             for (int r = 0; r < dbr.length; r++)
 447             {
 448               if (id != null && dbr[r].getAccessionId().equals(id))
 449               {
 450                 // suppress duplicate link creation for the bare sequence ID
 451                 // string with this link
 452                 id = null;
 453               }
 454               // create Bare ID link for this RUL
 455               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 456                       true);
 457               if (urls != null)
 458               {
 459                 for (int u = 0; u < urls.length; u += 2)
 460                 {
 461                   if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 462                   {
 463                     linkset.addElement(urls[u]+"|"+urls[u+1]);
 464                     addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 465                   }
 466                 }
 467               }
 468             }
 469           }
 470           if (id != null)
 471           {
 472             // create Bare ID link for this RUL
 473             String[] urls = urlLink.makeUrls(id, true);
 474             if (urls != null)
 475             {
 476               for (int u = 0; u < urls.length; u += 2)
 477               {
 478                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 479                 {
 480                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 481                   addshowLink(linkMenu, label, urls[u + 1]);
 482                 }
 483               }
 484             }
 485           }
 486           // Create urls from description but only for URL links which are regex links
 487           if (descr != null && urlLink.getRegexReplace()!=null)
 488           {
 489             // create link for this URL from description where regex matches
 490             String[] urls = urlLink.makeUrls(descr, true);
 491             if (urls != null)
 492             {
 493               for (int u = 0; u < urls.length; u += 2)
 494               {
 495                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 496                 {
 497                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 498                   addshowLink(linkMenu, label, urls[u + 1]);
 499                 }
 500               }
 501             }
 502           }
 503         }
 504         else
 505         {
 506           if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
 507           {
 508             linkset.addElement(label+"|"+urlLink.getUrl_prefix());
 509             // Add a non-dynamic link
 510             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 511           }
 512         }
 513       }
 514       if (sequence != null)
 515       {
 516         sequenceMenu.add(linkMenu);
 517       }
 518       else
 519       {
 520         add(linkMenu);
 521       }
 522     }
 523   }
 524
 525   /**
 526    * add a show URL menu item to the given linkMenu
 527    *
 528    * @param linkMenu
 529    * @param label -
 530    *                menu label string
 531    * @param url -
 532    *                url to open
 533    */
 534   private void addshowLink(JMenu linkMenu, String label, final String url)
 535   {
 536     JMenuItem item = new JMenuItem(label);
 537     item.setToolTipText("open URL: " + url);
 538     item.addActionListener(new java.awt.event.ActionListener()
 539     {
 540       public void actionPerformed(ActionEvent e)
 541       {
 542         new Thread(new Runnable()
 543         {
 544
 545           public void run()
 546           {
 547             showLink(url);
 548           }
 549
 550         }).start();
 551       }
 552     });
 553
 554     linkMenu.add(item);
 555   }
 556
 557   /**
 558    * DOCUMENT ME!
 559    *
 560    * @throws Exception
 561    *                 DOCUMENT ME!
 562    */
 563   private void jbInit() throws Exception
 564   {
 565     groupMenu.setText("Group");
 566     groupMenu.setText("Selection");
 567     groupName.setText("Name");
 568     groupName.addActionListener(new java.awt.event.ActionListener()
 569     {
 570       public void actionPerformed(ActionEvent e)
 571       {
 572         groupName_actionPerformed();
 573       }
 574     });
 575     sequenceMenu.setText("Sequence");
 576     sequenceName.setText("Edit Name/Description");
 577     sequenceName.addActionListener(new java.awt.event.ActionListener()
 578     {
 579       public void actionPerformed(ActionEvent e)
 580       {
 581         sequenceName_actionPerformed();
 582       }
 583     });
 584     PIDColour.setFocusPainted(false);
 585     unGroupMenuItem.setText("Remove Group");
 586     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 587     {
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         unGroupMenuItem_actionPerformed();
 591       }
 592     });
 593
 594     outline.setText("Border colour");
 595     outline.addActionListener(new java.awt.event.ActionListener()
 596     {
 597       public void actionPerformed(ActionEvent e)
 598       {
 599         outline_actionPerformed();
 600       }
 601     });
 602     nucleotideMenuItem.setText("Nucleotide");
 603     nucleotideMenuItem.addActionListener(new ActionListener()
 604     {
 605       public void actionPerformed(ActionEvent e)
 606       {
 607         nucleotideMenuItem_actionPerformed();
 608       }
 609     });
 610     colourMenu.setText("Group Colour");
 611     showBoxes.setText("Boxes");
 612     showBoxes.setState(true);
 613     showBoxes.addActionListener(new ActionListener()
 614     {
 615       public void actionPerformed(ActionEvent e)
 616       {
 617         showBoxes_actionPerformed();
 618       }
 619     });
 620     showText.setText("Text");
 621     showText.setState(true);
 622     showText.addActionListener(new ActionListener()
 623     {
 624       public void actionPerformed(ActionEvent e)
 625       {
 626         showText_actionPerformed();
 627       }
 628     });
 629     showColourText.setText("Colour Text");
 630     showColourText.addActionListener(new ActionListener()
 631     {
 632       public void actionPerformed(ActionEvent e)
 633       {
 634         showColourText_actionPerformed();
 635       }
 636     });
 637     displayNonconserved.setText("Show Nonconserved");
 638     displayNonconserved.setState(true);
 639     displayNonconserved.addActionListener(new ActionListener()
 640     {
 641       public void actionPerformed(ActionEvent e)
 642       {
 643         showNonconserved_actionPerformed();
 644       }
 645     });
 646     editMenu.setText("Edit");
 647     cut.setText("Cut");
 648     cut.addActionListener(new ActionListener()
 649     {
 650       public void actionPerformed(ActionEvent e)
 651       {
 652         cut_actionPerformed();
 653       }
 654     });
 655     upperCase.setText("To Upper Case");
 656     upperCase.addActionListener(new ActionListener()
 657     {
 658       public void actionPerformed(ActionEvent e)
 659       {
 660         changeCase(e);
 661       }
 662     });
 663     copy.setText("Copy");
 664     copy.addActionListener(new ActionListener()
 665     {
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         copy_actionPerformed();
 669       }
 670     });
 671     lowerCase.setText("To Lower Case");
 672     lowerCase.addActionListener(new ActionListener()
 673     {
 674       public void actionPerformed(ActionEvent e)
 675       {
 676         changeCase(e);
 677       }
 678     });
 679     toggle.setText("Toggle Case");
 680     toggle.addActionListener(new ActionListener()
 681     {
 682       public void actionPerformed(ActionEvent e)
 683       {
 684         changeCase(e);
 685       }
 686     });
 687     pdbMenu.setText("Associate Structure with Sequence");
 688     pdbFromFile.setText("From File");
 689     pdbFromFile.addActionListener(new ActionListener()
 690     {
 691       public void actionPerformed(ActionEvent e)
 692       {
 693         pdbFromFile_actionPerformed();
 694       }
 695     });
 696     enterPDB.setText("Enter PDB Id");
 697     enterPDB.addActionListener(new ActionListener()
 698     {
 699       public void actionPerformed(ActionEvent e)
 700       {
 701         enterPDB_actionPerformed();
 702       }
 703     });
 704     discoverPDB.setText("Discover PDB ids");
 705     discoverPDB.addActionListener(new ActionListener()
 706     {
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         discoverPDB_actionPerformed();
 710       }
 711     });
 712     outputMenu.setText("Output to Textbox...");
 713     sequenceFeature.setText("Create Sequence Feature");
 714     sequenceFeature.addActionListener(new ActionListener()
 715     {
 716       public void actionPerformed(ActionEvent e)
 717       {
 718         sequenceFeature_actionPerformed();
 719       }
 720     });
 721     textColour.setText("Text Colour");
 722     textColour.addActionListener(new ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         textColour_actionPerformed();
 727       }
 728     });
 729     jMenu1.setText("Group");
 730     structureMenu.setText("Structure");
 731     viewStructureMenu.setText("View Structure");
 732     // colStructureMenu.setText("Colour By Structure");
 733     editSequence.setText("Edit Sequence...");
 734     editSequence.addActionListener(new ActionListener()
 735     {
 736       public void actionPerformed(ActionEvent actionEvent)
 737       {
 738         editSequence_actionPerformed(actionEvent);
 739       }
 740     });
 741     /*
 742      * annotationMenuItem.setText("By Annotation");
 743      * annotationMenuItem.addActionListener(new ActionListener() { public void
 744      * actionPerformed(ActionEvent actionEvent) {
 745      * annotationMenuItem_actionPerformed(actionEvent); } });
 746      */
 747
 748     add(groupMenu);
 749
 750     add(sequenceMenu);
 751     this.add(structureMenu);
 752     groupMenu.add(editMenu);
 753     groupMenu.add(outputMenu);
 754     groupMenu.add(sequenceFeature);
 755     groupMenu.add(jMenu1);
 756     sequenceMenu.add(sequenceName);
 757     colourMenu.add(textColour);
 758     colourMenu.add(noColourmenuItem);
 759     colourMenu.add(clustalColour);
 760     colourMenu.add(BLOSUM62Colour);
 761     colourMenu.add(PIDColour);
 762     colourMenu.add(zappoColour);
 763     colourMenu.add(taylorColour);
 764     colourMenu.add(hydrophobicityColour);
 765     colourMenu.add(helixColour);
 766     colourMenu.add(strandColour);
 767     colourMenu.add(turnColour);
 768     colourMenu.add(buriedColour);
 769     colourMenu.add(nucleotideMenuItem);
 770     colourMenu.add(userDefinedColour);
 771
 772     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 773     {
 774       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 775               .getUserColourSchemes().keys();
 776
 777       while (userColours.hasMoreElements())
 778       {
 779         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 780         item.addActionListener(new ActionListener()
 781         {
 782           public void actionPerformed(ActionEvent evt)
 783           {
 784             userDefinedColour_actionPerformed(evt);
 785           }
 786         });
 787         colourMenu.add(item);
 788       }
 789     }
 790
 791     colourMenu.addSeparator();
 792     colourMenu.add(abovePIDColour);
 793     colourMenu.add(conservationMenuItem);
 794     // colourMenu.add(annotationMenuItem);
 795     editMenu.add(copy);
 796     editMenu.add(cut);
 797     editMenu.add(editSequence);
 798     editMenu.add(upperCase);
 799     editMenu.add(lowerCase);
 800     editMenu.add(toggle);
 801     pdbMenu.add(pdbFromFile);
 802     pdbMenu.add(enterPDB);
 803     pdbMenu.add(discoverPDB);
 804     jMenu1.add(groupName);
 805     jMenu1.add(unGroupMenuItem);
 806     jMenu1.add(colourMenu);
 807     jMenu1.add(showBoxes);
 808     jMenu1.add(showText);
 809     jMenu1.add(showColourText);
 810     jMenu1.add(outline);
 811     jMenu1.add(displayNonconserved);
 812     structureMenu.add(pdbMenu);
 813     structureMenu.add(viewStructureMenu);
 814     // structureMenu.add(colStructureMenu);
 815     noColourmenuItem.setText("None");
 816     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 817     {
 818       public void actionPerformed(ActionEvent e)
 819       {
 820         noColourmenuItem_actionPerformed();
 821       }
 822     });
 823
 824     clustalColour.setText("Clustalx colours");
 825     clustalColour.addActionListener(new java.awt.event.ActionListener()
 826     {
 827       public void actionPerformed(ActionEvent e)
 828       {
 829         clustalColour_actionPerformed();
 830       }
 831     });
 832     zappoColour.setText("Zappo");
 833     zappoColour.addActionListener(new java.awt.event.ActionListener()
 834     {
 835       public void actionPerformed(ActionEvent e)
 836       {
 837         zappoColour_actionPerformed();
 838       }
 839     });
 840     taylorColour.setText("Taylor");
 841     taylorColour.addActionListener(new java.awt.event.ActionListener()
 842     {
 843       public void actionPerformed(ActionEvent e)
 844       {
 845         taylorColour_actionPerformed();
 846       }
 847     });
 848     hydrophobicityColour.setText("Hydrophobicity");
 849     hydrophobicityColour
 850             .addActionListener(new java.awt.event.ActionListener()
 851             {
 852               public void actionPerformed(ActionEvent e)
 853               {
 854                 hydrophobicityColour_actionPerformed();
 855               }
 856             });
 857     helixColour.setText("Helix propensity");
 858     helixColour.addActionListener(new java.awt.event.ActionListener()
 859     {
 860       public void actionPerformed(ActionEvent e)
 861       {
 862         helixColour_actionPerformed();
 863       }
 864     });
 865     strandColour.setText("Strand propensity");
 866     strandColour.addActionListener(new java.awt.event.ActionListener()
 867     {
 868       public void actionPerformed(ActionEvent e)
 869       {
 870         strandColour_actionPerformed();
 871       }
 872     });
 873     turnColour.setText("Turn propensity");
 874     turnColour.addActionListener(new java.awt.event.ActionListener()
 875     {
 876       public void actionPerformed(ActionEvent e)
 877       {
 878         turnColour_actionPerformed();
 879       }
 880     });
 881     buriedColour.setText("Buried Index");
 882     buriedColour.addActionListener(new java.awt.event.ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         buriedColour_actionPerformed();
 887       }
 888     });
 889     abovePIDColour.setText("Above % Identity");
 890     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         abovePIDColour_actionPerformed();
 895       }
 896     });
 897     userDefinedColour.setText("User Defined...");
 898     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         userDefinedColour_actionPerformed(e);
 903       }
 904     });
 905     PIDColour.setText("Percentage Identity");
 906     PIDColour.addActionListener(new java.awt.event.ActionListener()
 907     {
 908       public void actionPerformed(ActionEvent e)
 909       {
 910         PIDColour_actionPerformed();
 911       }
 912     });
 913     BLOSUM62Colour.setText("BLOSUM62");
 914     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 915     {
 916       public void actionPerformed(ActionEvent e)
 917       {
 918         BLOSUM62Colour_actionPerformed();
 919       }
 920     });
 921     conservationMenuItem.setText("Conservation");
 922     conservationMenuItem
 923             .addActionListener(new java.awt.event.ActionListener()
 924             {
 925               public void actionPerformed(ActionEvent e)
 926               {
 927                 conservationMenuItem_actionPerformed();
 928               }
 929             });
 930   }
 931
 932   protected void showNonconserved_actionPerformed()
 933   {
 934     getGroup().setShowunconserved(displayNonconserved.isSelected());
 935     refresh();
 936   }
 937
 938   /**
 939    * call to refresh view after settings change
 940    */
 941   void refresh()
 942   {
 943     ap.updateAnnotation();
 944     ap.paintAlignment(true);
 945
 946     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 947   }
 948
 949   /**
 950    * DOCUMENT ME!
 951    *
 952    * @param e
 953    *                DOCUMENT ME!
 954    */
 955   protected void clustalColour_actionPerformed()
 956   {
 957     SequenceGroup sg = getGroup();
 958     sg.cs = new ClustalxColourScheme(sg
 959             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 960             .getWidth());
 961     refresh();
 962   }
 963
 964   /**
 965    * DOCUMENT ME!
 966    *
 967    * @param e
 968    *                DOCUMENT ME!
 969    */
 970   protected void zappoColour_actionPerformed()
 971   {
 972     getGroup().cs = new ZappoColourScheme();
 973     refresh();
 974   }
 975
 976   /**
 977    * DOCUMENT ME!
 978    *
 979    * @param e
 980    *                DOCUMENT ME!
 981    */
 982   protected void taylorColour_actionPerformed()
 983   {
 984     getGroup().cs = new TaylorColourScheme();
 985     refresh();
 986   }
 987
 988   /**
 989    * DOCUMENT ME!
 990    *
 991    * @param e
 992    *                DOCUMENT ME!
 993    */
 994   protected void hydrophobicityColour_actionPerformed()
 995   {
 996     getGroup().cs = new HydrophobicColourScheme();
 997     refresh();
 998   }
 999
1000   /**
1001    * DOCUMENT ME!
1002    *
1003    * @param e
1004    *                DOCUMENT ME!
1005    */
1006   protected void helixColour_actionPerformed()
1007   {
1008     getGroup().cs = new HelixColourScheme();
1009     refresh();
1010   }
1011
1012   /**
1013    * DOCUMENT ME!
1014    *
1015    * @param e
1016    *                DOCUMENT ME!
1017    */
1018   protected void strandColour_actionPerformed()
1019   {
1020     getGroup().cs = new StrandColourScheme();
1021     refresh();
1022   }
1023
1024   /**
1025    * DOCUMENT ME!
1026    *
1027    * @param e
1028    *                DOCUMENT ME!
1029    */
1030   protected void turnColour_actionPerformed()
1031   {
1032     getGroup().cs = new TurnColourScheme();
1033     refresh();
1034   }
1035
1036   /**
1037    * DOCUMENT ME!
1038    *
1039    * @param e
1040    *                DOCUMENT ME!
1041    */
1042   protected void buriedColour_actionPerformed()
1043   {
1044     getGroup().cs = new BuriedColourScheme();
1045     refresh();
1046   }
1047
1048   /**
1049    * DOCUMENT ME!
1050    *
1051    * @param e
1052    *                DOCUMENT ME!
1053    */
1054   public void nucleotideMenuItem_actionPerformed()
1055   {
1056     getGroup().cs = new NucleotideColourScheme();
1057     refresh();
1058   }
1059
1060   /**
1061    * DOCUMENT ME!
1062    *
1063    * @param e
1064    *                DOCUMENT ME!
1065    */
1066   protected void abovePIDColour_actionPerformed()
1067   {
1068     SequenceGroup sg = getGroup();
1069     if (sg.cs == null)
1070     {
1071       return;
1072     }
1073
1074     if (abovePIDColour.isSelected())
1075     {
1076       sg.cs.setConsensus(AAFrequency.calculate(sg
1077               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1078               .getEndRes() + 1));
1079
1080       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1081               .getName());
1082
1083       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1084
1085       SliderPanel.showPIDSlider();
1086     }
1087     else
1088     // remove PIDColouring
1089     {
1090       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1091     }
1092
1093     refresh();
1094   }
1095
1096   /**
1097    * DOCUMENT ME!
1098    *
1099    * @param e
1100    *                DOCUMENT ME!
1101    */
1102   protected void userDefinedColour_actionPerformed(ActionEvent e)
1103   {
1104     SequenceGroup sg = getGroup();
1105
1106     if (e.getActionCommand().equals("User Defined..."))
1107     {
1108       new UserDefinedColours(ap, sg);
1109     }
1110     else
1111     {
1112       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1113               .getUserColourSchemes().get(e.getActionCommand());
1114
1115       sg.cs = udc;
1116     }
1117     refresh();
1118   }
1119
1120   /**
1121    * DOCUMENT ME!
1122    *
1123    * @param e
1124    *                DOCUMENT ME!
1125    */
1126   protected void PIDColour_actionPerformed()
1127   {
1128     SequenceGroup sg = getGroup();
1129     sg.cs = new PIDColourScheme();
1130     sg.cs.setConsensus(AAFrequency.calculate(sg
1131             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1132             .getEndRes() + 1));
1133     refresh();
1134   }
1135
1136   /**
1137    * DOCUMENT ME!
1138    *
1139    * @param e
1140    *                DOCUMENT ME!
1141    */
1142   protected void BLOSUM62Colour_actionPerformed()
1143   {
1144     SequenceGroup sg = getGroup();
1145
1146     sg.cs = new Blosum62ColourScheme();
1147
1148     sg.cs.setConsensus(AAFrequency.calculate(sg
1149             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1150             .getEndRes() + 1));
1151
1152     refresh();
1153   }
1154
1155   /**
1156    * DOCUMENT ME!
1157    *
1158    * @param e
1159    *                DOCUMENT ME!
1160    */
1161   protected void noColourmenuItem_actionPerformed()
1162   {
1163     getGroup().cs = null;
1164     refresh();
1165   }
1166
1167   /**
1168    * DOCUMENT ME!
1169    *
1170    * @param e
1171    *                DOCUMENT ME!
1172    */
1173   protected void conservationMenuItem_actionPerformed()
1174   {
1175     SequenceGroup sg = getGroup();
1176     if (sg.cs == null)
1177     {
1178       return;
1179     }
1180
1181     if (conservationMenuItem.isSelected())
1182     {
1183       Conservation c = new Conservation("Group",
1184               ResidueProperties.propHash, 3, sg
1185                       .getSequences(ap.av.hiddenRepSequences), sg
1186                       .getStartRes(), sg.getEndRes() + 1);
1187
1188       c.calculate();
1189       c.verdict(false, ap.av.ConsPercGaps);
1190
1191       sg.cs.setConservation(c);
1192
1193       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1194       SliderPanel.showConservationSlider();
1195     }
1196     else
1197     // remove ConservationColouring
1198     {
1199       sg.cs.setConservation(null);
1200     }
1201
1202     refresh();
1203   }
1204
1205   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1206   {
1207     SequenceGroup sg = getGroup();
1208     if (sg == null)
1209     {
1210       return;
1211     }
1212
1213     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1214             .getAnnotation()[0], null,
1215             AnnotationColourGradient.NO_THRESHOLD);
1216
1217     acg.predefinedColours = true;
1218     sg.cs = acg;
1219
1220     refresh();
1221   }
1222
1223   /**
1224    * DOCUMENT ME!
1225    *
1226    * @param e
1227    *                DOCUMENT ME!
1228    */
1229   protected void groupName_actionPerformed()
1230   {
1231
1232     SequenceGroup sg = getGroup();
1233     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1234             .getDescription(), "       Group Name ", "Group Description ",
1235             "Edit Group Name/Description");
1236
1237     if (!dialog.accept)
1238     {
1239       return;
1240     }
1241
1242     sg.setName(dialog.getName());
1243     sg.setDescription(dialog.getDescription());
1244   }
1245
1246   /**
1247    * DOCUMENT ME!
1248    *
1249    * @return DOCUMENT ME!
1250    */
1251   SequenceGroup getGroup()
1252   {
1253     SequenceGroup sg = ap.av.getSelectionGroup();
1254     // this method won't add a new group if it already exists
1255     if (sg != null)
1256     {
1257       ap.av.alignment.addGroup(sg);
1258     }
1259
1260     return sg;
1261   }
1262
1263   /**
1264    * DOCUMENT ME!
1265    *
1266    * @param e
1267    *                DOCUMENT ME!
1268    */
1269   void sequenceName_actionPerformed()
1270   {
1271     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1272             .getDescription(), "       Sequence Name ",
1273             "Sequence Description ", "Edit Sequence Name/Description");
1274
1275     if (!dialog.accept)
1276     {
1277       return;
1278     }
1279
1280     if (dialog.getName() != null)
1281     {
1282       if (dialog.getName().indexOf(" ") > -1)
1283       {
1284         JOptionPane.showMessageDialog(ap,
1285                 "Spaces have been converted to \"_\"",
1286                 "No spaces allowed in Sequence Name",
1287                 JOptionPane.WARNING_MESSAGE);
1288       }
1289
1290       sequence.setName(dialog.getName().replace(' ', '_'));
1291       ap.paintAlignment(false);
1292     }
1293
1294     sequence.setDescription(dialog.getDescription());
1295
1296     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1297             .getSequences());
1298
1299   }
1300
1301   /**
1302    * DOCUMENT ME!
1303    *
1304    * @param e
1305    *                DOCUMENT ME!
1306    */
1307   void unGroupMenuItem_actionPerformed()
1308   {
1309     SequenceGroup sg = ap.av.getSelectionGroup();
1310     ap.av.alignment.deleteGroup(sg);
1311     ap.av.setSelectionGroup(null);
1312     refresh();
1313   }
1314
1315   /**
1316    * DOCUMENT ME!
1317    *
1318    * @param e
1319    *                DOCUMENT ME!
1320    */
1321   protected void outline_actionPerformed()
1322   {
1323     SequenceGroup sg = getGroup();
1324     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1325             Color.BLUE);
1326
1327     if (col != null)
1328     {
1329       sg.setOutlineColour(col);
1330     }
1331
1332     refresh();
1333   }
1334
1335   /**
1336    * DOCUMENT ME!
1337    *
1338    * @param e
1339    *                DOCUMENT ME!
1340    */
1341   public void showBoxes_actionPerformed()
1342   {
1343     getGroup().setDisplayBoxes(showBoxes.isSelected());
1344     refresh();
1345   }
1346
1347   /**
1348    * DOCUMENT ME!
1349    *
1350    * @param e
1351    *                DOCUMENT ME!
1352    */
1353   public void showText_actionPerformed()
1354   {
1355     getGroup().setDisplayText(showText.isSelected());
1356     refresh();
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *                DOCUMENT ME!
1364    */
1365   public void showColourText_actionPerformed()
1366   {
1367     getGroup().setColourText(showColourText.isSelected());
1368     refresh();
1369   }
1370
1371   public void showLink(String url)
1372   {
1373     try
1374     {
1375       jalview.util.BrowserLauncher.openURL(url);
1376     } catch (Exception ex)
1377     {
1378       JOptionPane
1379               .showInternalMessageDialog(
1380                       Desktop.desktop,
1381                       "Unixers: Couldn't find default web browser."
1382                               + "\nAdd the full path to your browser in Preferences.",
1383                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1384
1385       ex.printStackTrace();
1386     }
1387   }
1388
1389   void hideSequences(boolean representGroup)
1390   {
1391     SequenceGroup sg = ap.av.getSelectionGroup();
1392     if (sg == null || sg.getSize() < 1)
1393     {
1394       ap.av.hideSequence(new SequenceI[]
1395       { sequence });
1396       return;
1397     }
1398
1399     ap.av.setSelectionGroup(null);
1400
1401     if (representGroup)
1402     {
1403       ap.av.hideRepSequences(sequence, sg);
1404
1405       return;
1406     }
1407
1408     int gsize = sg.getSize();
1409     SequenceI[] hseqs;
1410
1411     hseqs = new SequenceI[gsize];
1412
1413     int index = 0;
1414     for (int i = 0; i < gsize; i++)
1415     {
1416       hseqs[index++] = sg.getSequenceAt(i);
1417     }
1418
1419     ap.av.hideSequence(hseqs);
1420     ap.av.sendSelection();
1421   }
1422
1423   public void copy_actionPerformed()
1424   {
1425     ap.alignFrame.copy_actionPerformed(null);
1426   }
1427
1428   public void cut_actionPerformed()
1429   {
1430     ap.alignFrame.cut_actionPerformed(null);
1431   }
1432
1433   void changeCase(ActionEvent e)
1434   {
1435     Object source = e.getSource();
1436     SequenceGroup sg = ap.av.getSelectionGroup();
1437
1438     if (sg != null)
1439     {
1440       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1441               sg.getEndRes() + 1);
1442
1443       String description;
1444       int caseChange;
1445
1446       if (source == toggle)
1447       {
1448         description = "Toggle Case";
1449         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1450       }
1451       else if (source == upperCase)
1452       {
1453         description = "To Upper Case";
1454         caseChange = ChangeCaseCommand.TO_UPPER;
1455       }
1456       else
1457       {
1458         description = "To Lower Case";
1459         caseChange = ChangeCaseCommand.TO_LOWER;
1460       }
1461
1462       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1463               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1464               caseChange);
1465
1466       ap.alignFrame.addHistoryItem(caseCommand);
1467
1468       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1469               .getSequences());
1470
1471     }
1472   }
1473
1474   public void outputText_actionPerformed(ActionEvent e)
1475   {
1476     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1477     cap.setForInput(null);
1478     Desktop.addInternalFrame(cap, "Alignment output - "
1479             + e.getActionCommand(), 600, 500);
1480
1481     String[] omitHidden = null;
1482
1483     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1484                                             // or we simply trust the user wants
1485                                             // wysiwig behaviour
1486     SequenceGroup sg = ap.av.getSelectionGroup();
1487     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1488     omitHidden = ap.av.getViewAsString(true);
1489     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1490     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1491     for (int i = 0; i < nala.length; i++)
1492     {
1493       AlignmentAnnotation na = nala[i];
1494       oal.addAnnotation(na);
1495     }
1496     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1497             oal, omitHidden, csel, sg));
1498     oal = null;
1499   }
1500
1501   public void pdbFromFile_actionPerformed()
1502   {
1503     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1504             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1505     chooser.setFileView(new jalview.io.JalviewFileView());
1506     chooser.setDialogTitle("Select a PDB file");
1507     chooser.setToolTipText("Load a PDB file");
1508
1509     int value = chooser.showOpenDialog(null);
1510
1511     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1512     {
1513       PDBEntry entry = new PDBEntry();
1514       String choice = chooser.getSelectedFile().getPath();
1515       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1516       try
1517       {
1518         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1519                 jalview.io.AppletFormatAdapter.FILE);
1520
1521         if (pdbfile.id == null)
1522         {
1523           String reply = JOptionPane
1524                   .showInternalInputDialog(
1525                           Desktop.desktop,
1526                           "Couldn't find a PDB id in the file supplied."
1527                                   + "Please enter an Id to identify this structure.",
1528                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1529           if (reply == null)
1530           {
1531             return;
1532           }
1533
1534           entry.setId(reply);
1535         }
1536         else
1537         {
1538           entry.setId(pdbfile.id);
1539         }
1540       } catch (java.io.IOException ex)
1541       {
1542         ex.printStackTrace();
1543       }
1544
1545       entry.setFile(choice);
1546       sequence.getDatasetSequence().addPDBId(entry);
1547     }
1548
1549   }
1550
1551   public void enterPDB_actionPerformed()
1552   {
1553     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1554             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1555
1556     if (id != null && id.length() > 0)
1557     {
1558       PDBEntry entry = new PDBEntry();
1559       entry.setId(id.toUpperCase());
1560       sequence.getDatasetSequence().addPDBId(entry);
1561     }
1562   }
1563
1564   public void discoverPDB_actionPerformed()
1565   {
1566
1567     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1568     { sequence }
1569             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1570     Thread discpdb = new Thread(new Runnable()
1571     {
1572       public void run()
1573       {
1574
1575         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1576                 .fetchDBRefs(false);
1577       }
1578
1579     });
1580     discpdb.start();
1581   }
1582
1583   public void sequenceFeature_actionPerformed()
1584   {
1585     SequenceGroup sg = ap.av.getSelectionGroup();
1586     if (sg == null)
1587     {
1588       return;
1589     }
1590
1591     int gSize = sg.getSize();
1592     SequenceI[] seqs = new SequenceI[gSize];
1593     SequenceFeature[] features = new SequenceFeature[gSize];
1594
1595     for (int i = 0; i < gSize; i++)
1596     {
1597       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1598       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1599       int end = sg.findEndRes(sg.getSequenceAt(i));
1600       features[i] = new SequenceFeature(null, null, null, start, end,
1601               "Jalview");
1602     }
1603
1604     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1605             features, true, ap))
1606     {
1607       ap.alignFrame.setShowSeqFeatures(true);
1608       ap.highlightSearchResults(null);
1609     }
1610   }
1611
1612   public void textColour_actionPerformed()
1613   {
1614     SequenceGroup sg = getGroup();
1615     if (sg != null)
1616     {
1617       new TextColourChooser().chooseColour(ap, sg);
1618     }
1619   }
1620
1621   public void colourByStructure(String pdbid)
1622   {
1623     Annotation[] anots = jalview.structure.StructureSelectionManager
1624             .getStructureSelectionManager().colourSequenceFromStructure(
1625                     sequence, pdbid);
1626
1627     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1628             "Coloured by " + pdbid, anots);
1629
1630     ap.av.alignment.addAnnotation(an);
1631     an.createSequenceMapping(sequence, 0, true);
1632     // an.adjustForAlignment();
1633     ap.av.alignment.setAnnotationIndex(an, 0);
1634
1635     ap.adjustAnnotationHeight();
1636
1637     sequence.addAlignmentAnnotation(an);
1638
1639   }
1640
1641   public void editSequence_actionPerformed(ActionEvent actionEvent)
1642   {
1643     SequenceGroup sg = ap.av.getSelectionGroup();
1644
1645     if (sg != null)
1646     {
1647       if (sequence == null)
1648         sequence = (Sequence) sg.getSequenceAt(0);
1649
1650       EditNameDialog dialog = new EditNameDialog(sequence
1651               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1652               null, "Edit Sequence ", null, "Edit Sequence");
1653
1654       if (dialog.accept)
1655       {
1656         EditCommand editCommand = new EditCommand("Edit Sequences",
1657                 EditCommand.REPLACE, dialog.getName().replace(' ',
1658                         ap.av.getGapCharacter()), sg
1659                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1660                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1661
1662         ap.alignFrame.addHistoryItem(editCommand);
1663
1664         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1665                 .getSequences());
1666       }
1667     }
1668   }
1669
1670 }