src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 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.paintAlignment(true);
 944
 945     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 946   }
 947
 948   /**
 949    * DOCUMENT ME!
 950    *
 951    * @param e
 952    *                DOCUMENT ME!
 953    */
 954   protected void clustalColour_actionPerformed()
 955   {
 956     SequenceGroup sg = getGroup();
 957     sg.cs = new ClustalxColourScheme(sg
 958             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 959             .getWidth());
 960     refresh();
 961   }
 962
 963   /**
 964    * DOCUMENT ME!
 965    *
 966    * @param e
 967    *                DOCUMENT ME!
 968    */
 969   protected void zappoColour_actionPerformed()
 970   {
 971     getGroup().cs = new ZappoColourScheme();
 972     refresh();
 973   }
 974
 975   /**
 976    * DOCUMENT ME!
 977    *
 978    * @param e
 979    *                DOCUMENT ME!
 980    */
 981   protected void taylorColour_actionPerformed()
 982   {
 983     getGroup().cs = new TaylorColourScheme();
 984     refresh();
 985   }
 986
 987   /**
 988    * DOCUMENT ME!
 989    *
 990    * @param e
 991    *                DOCUMENT ME!
 992    */
 993   protected void hydrophobicityColour_actionPerformed()
 994   {
 995     getGroup().cs = new HydrophobicColourScheme();
 996     refresh();
 997   }
 998
 999   /**
1000    * DOCUMENT ME!
1001    *
1002    * @param e
1003    *                DOCUMENT ME!
1004    */
1005   protected void helixColour_actionPerformed()
1006   {
1007     getGroup().cs = new HelixColourScheme();
1008     refresh();
1009   }
1010
1011   /**
1012    * DOCUMENT ME!
1013    *
1014    * @param e
1015    *                DOCUMENT ME!
1016    */
1017   protected void strandColour_actionPerformed()
1018   {
1019     getGroup().cs = new StrandColourScheme();
1020     refresh();
1021   }
1022
1023   /**
1024    * DOCUMENT ME!
1025    *
1026    * @param e
1027    *                DOCUMENT ME!
1028    */
1029   protected void turnColour_actionPerformed()
1030   {
1031     getGroup().cs = new TurnColourScheme();
1032     refresh();
1033   }
1034
1035   /**
1036    * DOCUMENT ME!
1037    *
1038    * @param e
1039    *                DOCUMENT ME!
1040    */
1041   protected void buriedColour_actionPerformed()
1042   {
1043     getGroup().cs = new BuriedColourScheme();
1044     refresh();
1045   }
1046
1047   /**
1048    * DOCUMENT ME!
1049    *
1050    * @param e
1051    *                DOCUMENT ME!
1052    */
1053   public void nucleotideMenuItem_actionPerformed()
1054   {
1055     getGroup().cs = new NucleotideColourScheme();
1056     refresh();
1057   }
1058
1059   /**
1060    * DOCUMENT ME!
1061    *
1062    * @param e
1063    *                DOCUMENT ME!
1064    */
1065   protected void abovePIDColour_actionPerformed()
1066   {
1067     SequenceGroup sg = getGroup();
1068     if (sg.cs == null)
1069     {
1070       return;
1071     }
1072
1073     if (abovePIDColour.isSelected())
1074     {
1075       sg.cs.setConsensus(AAFrequency.calculate(sg
1076               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1077               .getEndRes() + 1));
1078
1079       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1080               .getName());
1081
1082       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1083
1084       SliderPanel.showPIDSlider();
1085     }
1086     else
1087     // remove PIDColouring
1088     {
1089       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1090     }
1091
1092     refresh();
1093   }
1094
1095   /**
1096    * DOCUMENT ME!
1097    *
1098    * @param e
1099    *                DOCUMENT ME!
1100    */
1101   protected void userDefinedColour_actionPerformed(ActionEvent e)
1102   {
1103     SequenceGroup sg = getGroup();
1104
1105     if (e.getActionCommand().equals("User Defined..."))
1106     {
1107       new UserDefinedColours(ap, sg);
1108     }
1109     else
1110     {
1111       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1112               .getUserColourSchemes().get(e.getActionCommand());
1113
1114       sg.cs = udc;
1115     }
1116     refresh();
1117   }
1118
1119   /**
1120    * DOCUMENT ME!
1121    *
1122    * @param e
1123    *                DOCUMENT ME!
1124    */
1125   protected void PIDColour_actionPerformed()
1126   {
1127     SequenceGroup sg = getGroup();
1128     sg.cs = new PIDColourScheme();
1129     sg.cs.setConsensus(AAFrequency.calculate(sg
1130             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1131             .getEndRes() + 1));
1132     refresh();
1133   }
1134
1135   /**
1136    * DOCUMENT ME!
1137    *
1138    * @param e
1139    *                DOCUMENT ME!
1140    */
1141   protected void BLOSUM62Colour_actionPerformed()
1142   {
1143     SequenceGroup sg = getGroup();
1144
1145     sg.cs = new Blosum62ColourScheme();
1146
1147     sg.cs.setConsensus(AAFrequency.calculate(sg
1148             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1149             .getEndRes() + 1));
1150
1151     refresh();
1152   }
1153
1154   /**
1155    * DOCUMENT ME!
1156    *
1157    * @param e
1158    *                DOCUMENT ME!
1159    */
1160   protected void noColourmenuItem_actionPerformed()
1161   {
1162     getGroup().cs = null;
1163     refresh();
1164   }
1165
1166   /**
1167    * DOCUMENT ME!
1168    *
1169    * @param e
1170    *                DOCUMENT ME!
1171    */
1172   protected void conservationMenuItem_actionPerformed()
1173   {
1174     SequenceGroup sg = getGroup();
1175     if (sg.cs == null)
1176     {
1177       return;
1178     }
1179
1180     if (conservationMenuItem.isSelected())
1181     {
1182       Conservation c = new Conservation("Group",
1183               ResidueProperties.propHash, 3, sg
1184                       .getSequences(ap.av.hiddenRepSequences), sg
1185                       .getStartRes(), sg.getEndRes() + 1);
1186
1187       c.calculate();
1188       c.verdict(false, ap.av.ConsPercGaps);
1189
1190       sg.cs.setConservation(c);
1191
1192       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1193       SliderPanel.showConservationSlider();
1194     }
1195     else
1196     // remove ConservationColouring
1197     {
1198       sg.cs.setConservation(null);
1199     }
1200
1201     refresh();
1202   }
1203
1204   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1205   {
1206     SequenceGroup sg = getGroup();
1207     if (sg == null)
1208     {
1209       return;
1210     }
1211
1212     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1213             .getAnnotation()[0], null,
1214             AnnotationColourGradient.NO_THRESHOLD);
1215
1216     acg.predefinedColours = true;
1217     sg.cs = acg;
1218
1219     refresh();
1220   }
1221
1222   /**
1223    * DOCUMENT ME!
1224    *
1225    * @param e
1226    *                DOCUMENT ME!
1227    */
1228   protected void groupName_actionPerformed()
1229   {
1230
1231     SequenceGroup sg = getGroup();
1232     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1233             .getDescription(), "       Group Name ", "Group Description ",
1234             "Edit Group Name/Description");
1235
1236     if (!dialog.accept)
1237     {
1238       return;
1239     }
1240
1241     sg.setName(dialog.getName());
1242     sg.setDescription(dialog.getDescription());
1243   }
1244
1245   /**
1246    * DOCUMENT ME!
1247    *
1248    * @return DOCUMENT ME!
1249    */
1250   SequenceGroup getGroup()
1251   {
1252     SequenceGroup sg = ap.av.getSelectionGroup();
1253     // this method won't add a new group if it already exists
1254     if (sg != null)
1255     {
1256       ap.av.alignment.addGroup(sg);
1257     }
1258
1259     return sg;
1260   }
1261
1262   /**
1263    * DOCUMENT ME!
1264    *
1265    * @param e
1266    *                DOCUMENT ME!
1267    */
1268   void sequenceName_actionPerformed()
1269   {
1270     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1271             .getDescription(), "       Sequence Name ",
1272             "Sequence Description ", "Edit Sequence Name/Description");
1273
1274     if (!dialog.accept)
1275     {
1276       return;
1277     }
1278
1279     if (dialog.getName() != null)
1280     {
1281       if (dialog.getName().indexOf(" ") > -1)
1282       {
1283         JOptionPane.showMessageDialog(ap,
1284                 "Spaces have been converted to \"_\"",
1285                 "No spaces allowed in Sequence Name",
1286                 JOptionPane.WARNING_MESSAGE);
1287       }
1288
1289       sequence.setName(dialog.getName().replace(' ', '_'));
1290       ap.paintAlignment(false);
1291     }
1292
1293     sequence.setDescription(dialog.getDescription());
1294
1295     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1296             .getSequences());
1297
1298   }
1299
1300   /**
1301    * DOCUMENT ME!
1302    *
1303    * @param e
1304    *                DOCUMENT ME!
1305    */
1306   void unGroupMenuItem_actionPerformed()
1307   {
1308     SequenceGroup sg = ap.av.getSelectionGroup();
1309     ap.av.alignment.deleteGroup(sg);
1310     ap.av.setSelectionGroup(null);
1311     refresh();
1312   }
1313
1314   /**
1315    * DOCUMENT ME!
1316    *
1317    * @param e
1318    *                DOCUMENT ME!
1319    */
1320   protected void outline_actionPerformed()
1321   {
1322     SequenceGroup sg = getGroup();
1323     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1324             Color.BLUE);
1325
1326     if (col != null)
1327     {
1328       sg.setOutlineColour(col);
1329     }
1330
1331     refresh();
1332   }
1333
1334   /**
1335    * DOCUMENT ME!
1336    *
1337    * @param e
1338    *                DOCUMENT ME!
1339    */
1340   public void showBoxes_actionPerformed()
1341   {
1342     getGroup().setDisplayBoxes(showBoxes.isSelected());
1343     refresh();
1344   }
1345
1346   /**
1347    * DOCUMENT ME!
1348    *
1349    * @param e
1350    *                DOCUMENT ME!
1351    */
1352   public void showText_actionPerformed()
1353   {
1354     getGroup().setDisplayText(showText.isSelected());
1355     refresh();
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *                DOCUMENT ME!
1363    */
1364   public void showColourText_actionPerformed()
1365   {
1366     getGroup().setColourText(showColourText.isSelected());
1367     refresh();
1368   }
1369
1370   public void showLink(String url)
1371   {
1372     try
1373     {
1374       jalview.util.BrowserLauncher.openURL(url);
1375     } catch (Exception ex)
1376     {
1377       JOptionPane
1378               .showInternalMessageDialog(
1379                       Desktop.desktop,
1380                       "Unixers: Couldn't find default web browser."
1381                               + "\nAdd the full path to your browser in Preferences.",
1382                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1383
1384       ex.printStackTrace();
1385     }
1386   }
1387
1388   void hideSequences(boolean representGroup)
1389   {
1390     SequenceGroup sg = ap.av.getSelectionGroup();
1391     if (sg == null || sg.getSize() < 1)
1392     {
1393       ap.av.hideSequence(new SequenceI[]
1394       { sequence });
1395       return;
1396     }
1397
1398     ap.av.setSelectionGroup(null);
1399
1400     if (representGroup)
1401     {
1402       ap.av.hideRepSequences(sequence, sg);
1403
1404       return;
1405     }
1406
1407     int gsize = sg.getSize();
1408     SequenceI[] hseqs;
1409
1410     hseqs = new SequenceI[gsize];
1411
1412     int index = 0;
1413     for (int i = 0; i < gsize; i++)
1414     {
1415       hseqs[index++] = sg.getSequenceAt(i);
1416     }
1417
1418     ap.av.hideSequence(hseqs);
1419     ap.av.sendSelection();
1420   }
1421
1422   public void copy_actionPerformed()
1423   {
1424     ap.alignFrame.copy_actionPerformed(null);
1425   }
1426
1427   public void cut_actionPerformed()
1428   {
1429     ap.alignFrame.cut_actionPerformed(null);
1430   }
1431
1432   void changeCase(ActionEvent e)
1433   {
1434     Object source = e.getSource();
1435     SequenceGroup sg = ap.av.getSelectionGroup();
1436
1437     if (sg != null)
1438     {
1439       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1440               sg.getEndRes() + 1);
1441
1442       String description;
1443       int caseChange;
1444
1445       if (source == toggle)
1446       {
1447         description = "Toggle Case";
1448         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1449       }
1450       else if (source == upperCase)
1451       {
1452         description = "To Upper Case";
1453         caseChange = ChangeCaseCommand.TO_UPPER;
1454       }
1455       else
1456       {
1457         description = "To Lower Case";
1458         caseChange = ChangeCaseCommand.TO_LOWER;
1459       }
1460
1461       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1462               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1463               caseChange);
1464
1465       ap.alignFrame.addHistoryItem(caseCommand);
1466
1467       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1468               .getSequences());
1469
1470     }
1471   }
1472
1473   public void outputText_actionPerformed(ActionEvent e)
1474   {
1475     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1476     cap.setForInput(null);
1477     Desktop.addInternalFrame(cap, "Alignment output - "
1478             + e.getActionCommand(), 600, 500);
1479
1480     String[] omitHidden = null;
1481
1482     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1483                                             // or we simply trust the user wants
1484                                             // wysiwig behaviour
1485     SequenceGroup sg = ap.av.getSelectionGroup();
1486     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1487     omitHidden = ap.av.getViewAsString(true);
1488     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1489     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1490     for (int i = 0; i < nala.length; i++)
1491     {
1492       AlignmentAnnotation na = nala[i];
1493       oal.addAnnotation(na);
1494     }
1495     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1496             oal, omitHidden, csel, sg));
1497     oal = null;
1498   }
1499
1500   public void pdbFromFile_actionPerformed()
1501   {
1502     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1503             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1504     chooser.setFileView(new jalview.io.JalviewFileView());
1505     chooser.setDialogTitle("Select a PDB file");
1506     chooser.setToolTipText("Load a PDB file");
1507
1508     int value = chooser.showOpenDialog(null);
1509
1510     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1511     {
1512       PDBEntry entry = new PDBEntry();
1513       String choice = chooser.getSelectedFile().getPath();
1514       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1515       try
1516       {
1517         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1518                 jalview.io.AppletFormatAdapter.FILE);
1519
1520         if (pdbfile.id == null)
1521         {
1522           String reply = JOptionPane
1523                   .showInternalInputDialog(
1524                           Desktop.desktop,
1525                           "Couldn't find a PDB id in the file supplied."
1526                                   + "Please enter an Id to identify this structure.",
1527                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1528           if (reply == null)
1529           {
1530             return;
1531           }
1532
1533           entry.setId(reply);
1534         }
1535         else
1536         {
1537           entry.setId(pdbfile.id);
1538         }
1539       } catch (java.io.IOException ex)
1540       {
1541         ex.printStackTrace();
1542       }
1543
1544       entry.setFile(choice);
1545       sequence.getDatasetSequence().addPDBId(entry);
1546     }
1547
1548   }
1549
1550   public void enterPDB_actionPerformed()
1551   {
1552     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1553             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1554
1555     if (id != null && id.length() > 0)
1556     {
1557       PDBEntry entry = new PDBEntry();
1558       entry.setId(id.toUpperCase());
1559       sequence.getDatasetSequence().addPDBId(entry);
1560     }
1561   }
1562
1563   public void discoverPDB_actionPerformed()
1564   {
1565
1566     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1567     { sequence }
1568             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1569     Thread discpdb = new Thread(new Runnable()
1570     {
1571       public void run()
1572       {
1573
1574         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1575                 .fetchDBRefs(false);
1576       }
1577
1578     });
1579     discpdb.start();
1580   }
1581
1582   public void sequenceFeature_actionPerformed()
1583   {
1584     SequenceGroup sg = ap.av.getSelectionGroup();
1585     if (sg == null)
1586     {
1587       return;
1588     }
1589
1590     int gSize = sg.getSize();
1591     SequenceI[] seqs = new SequenceI[gSize];
1592     SequenceFeature[] features = new SequenceFeature[gSize];
1593
1594     for (int i = 0; i < gSize; i++)
1595     {
1596       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1597       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1598       int end = sg.findEndRes(sg.getSequenceAt(i));
1599       features[i] = new SequenceFeature(null, null, null, start, end,
1600               "Jalview");
1601     }
1602
1603     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1604             features, true, ap))
1605     {
1606       ap.alignFrame.setShowSeqFeatures(true);
1607       ap.highlightSearchResults(null);
1608     }
1609   }
1610
1611   public void textColour_actionPerformed()
1612   {
1613     SequenceGroup sg = getGroup();
1614     if (sg != null)
1615     {
1616       new TextColourChooser().chooseColour(ap, sg);
1617     }
1618   }
1619
1620   public void colourByStructure(String pdbid)
1621   {
1622     Annotation[] anots = jalview.structure.StructureSelectionManager
1623             .getStructureSelectionManager().colourSequenceFromStructure(
1624                     sequence, pdbid);
1625
1626     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1627             "Coloured by " + pdbid, anots);
1628
1629     ap.av.alignment.addAnnotation(an);
1630     an.createSequenceMapping(sequence, 0, true);
1631     // an.adjustForAlignment();
1632     ap.av.alignment.setAnnotationIndex(an, 0);
1633
1634     ap.adjustAnnotationHeight();
1635
1636     sequence.addAlignmentAnnotation(an);
1637
1638   }
1639
1640   public void editSequence_actionPerformed(ActionEvent actionEvent)
1641   {
1642     SequenceGroup sg = ap.av.getSelectionGroup();
1643
1644     if (sg != null)
1645     {
1646       if (sequence == null)
1647         sequence = (Sequence) sg.getSequenceAt(0);
1648
1649       EditNameDialog dialog = new EditNameDialog(sequence
1650               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1651               null, "Edit Sequence ", null, "Edit Sequence");
1652
1653       if (dialog.accept)
1654       {
1655         EditCommand editCommand = new EditCommand("Edit Sequences",
1656                 EditCommand.REPLACE, dialog.getName().replace(' ',
1657                         ap.av.getGapCharacter()), sg
1658                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1659                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1660
1661         ap.alignFrame.addHistoryItem(editCommand);
1662
1663         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1664                 .getSequences());
1665       }
1666     }
1667   }
1668
1669 }