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
 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                   addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 462                 }
 463               }
 464             }
 465           }
 466           if (id != null)
 467           {
 468             // create Bare ID link for this RUL
 469             String[] urls = urlLink.makeUrls(id, true);
 470             if (urls != null)
 471             {
 472               for (int u = 0; u < urls.length; u += 2)
 473               {
 474                 addshowLink(linkMenu, label, urls[u + 1]);
 475               }
 476             }
 477           }
 478           // Create urls from description but only for URL links which are regex links
 479           if (descr != null && urlLink.getRegexReplace()!=null)
 480           {
 481             // create link for this URL from description where regex matches
 482             String[] urls = urlLink.makeUrls(descr, true);
 483             if (urls != null)
 484             {
 485               for (int u = 0; u < urls.length; u += 2)
 486               {
 487                 addshowLink(linkMenu, label, urls[u + 1]);
 488               }
 489             }
 490           }
 491         }
 492         else
 493         {
 494           // Add a non-dynamic link
 495           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 496         }
 497       }
 498       if (sequence != null)
 499       {
 500         sequenceMenu.add(linkMenu);
 501       }
 502       else
 503       {
 504         add(linkMenu);
 505       }
 506     }
 507   }
 508
 509   /**
 510    * add a show URL menu item to the given linkMenu
 511    *
 512    * @param linkMenu
 513    * @param label -
 514    *                menu label string
 515    * @param url -
 516    *                url to open
 517    */
 518   private void addshowLink(JMenu linkMenu, String label, final String url)
 519   {
 520     JMenuItem item = new JMenuItem(label);
 521     item.setToolTipText("open URL: " + url);
 522     item.addActionListener(new java.awt.event.ActionListener()
 523     {
 524       public void actionPerformed(ActionEvent e)
 525       {
 526         new Thread(new Runnable()
 527         {
 528
 529           public void run()
 530           {
 531             showLink(url);
 532           }
 533
 534         }).start();
 535       }
 536     });
 537
 538     linkMenu.add(item);
 539   }
 540
 541   /**
 542    * DOCUMENT ME!
 543    *
 544    * @throws Exception
 545    *                 DOCUMENT ME!
 546    */
 547   private void jbInit() throws Exception
 548   {
 549     groupMenu.setText("Group");
 550     groupMenu.setText("Selection");
 551     groupName.setText("Name");
 552     groupName.addActionListener(new java.awt.event.ActionListener()
 553     {
 554       public void actionPerformed(ActionEvent e)
 555       {
 556         groupName_actionPerformed();
 557       }
 558     });
 559     sequenceMenu.setText("Sequence");
 560     sequenceName.setText("Edit Name/Description");
 561     sequenceName.addActionListener(new java.awt.event.ActionListener()
 562     {
 563       public void actionPerformed(ActionEvent e)
 564       {
 565         sequenceName_actionPerformed();
 566       }
 567     });
 568     PIDColour.setFocusPainted(false);
 569     unGroupMenuItem.setText("Remove Group");
 570     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 571     {
 572       public void actionPerformed(ActionEvent e)
 573       {
 574         unGroupMenuItem_actionPerformed();
 575       }
 576     });
 577
 578     outline.setText("Border colour");
 579     outline.addActionListener(new java.awt.event.ActionListener()
 580     {
 581       public void actionPerformed(ActionEvent e)
 582       {
 583         outline_actionPerformed();
 584       }
 585     });
 586     nucleotideMenuItem.setText("Nucleotide");
 587     nucleotideMenuItem.addActionListener(new ActionListener()
 588     {
 589       public void actionPerformed(ActionEvent e)
 590       {
 591         nucleotideMenuItem_actionPerformed();
 592       }
 593     });
 594     colourMenu.setText("Group Colour");
 595     showBoxes.setText("Boxes");
 596     showBoxes.setState(true);
 597     showBoxes.addActionListener(new ActionListener()
 598     {
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         showBoxes_actionPerformed();
 602       }
 603     });
 604     showText.setText("Text");
 605     showText.setState(true);
 606     showText.addActionListener(new ActionListener()
 607     {
 608       public void actionPerformed(ActionEvent e)
 609       {
 610         showText_actionPerformed();
 611       }
 612     });
 613     showColourText.setText("Colour Text");
 614     showColourText.addActionListener(new ActionListener()
 615     {
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         showColourText_actionPerformed();
 619       }
 620     });
 621     displayNonconserved.setText("Show Nonconserved");
 622     displayNonconserved.setState(true);
 623     displayNonconserved.addActionListener(new ActionListener()
 624     {
 625       public void actionPerformed(ActionEvent e)
 626       {
 627         showNonconserved_actionPerformed();
 628       }
 629     });
 630     editMenu.setText("Edit");
 631     cut.setText("Cut");
 632     cut.addActionListener(new ActionListener()
 633     {
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         cut_actionPerformed();
 637       }
 638     });
 639     upperCase.setText("To Upper Case");
 640     upperCase.addActionListener(new ActionListener()
 641     {
 642       public void actionPerformed(ActionEvent e)
 643       {
 644         changeCase(e);
 645       }
 646     });
 647     copy.setText("Copy");
 648     copy.addActionListener(new ActionListener()
 649     {
 650       public void actionPerformed(ActionEvent e)
 651       {
 652         copy_actionPerformed();
 653       }
 654     });
 655     lowerCase.setText("To Lower Case");
 656     lowerCase.addActionListener(new ActionListener()
 657     {
 658       public void actionPerformed(ActionEvent e)
 659       {
 660         changeCase(e);
 661       }
 662     });
 663     toggle.setText("Toggle Case");
 664     toggle.addActionListener(new ActionListener()
 665     {
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         changeCase(e);
 669       }
 670     });
 671     pdbMenu.setText("Associate Structure with Sequence");
 672     pdbFromFile.setText("From File");
 673     pdbFromFile.addActionListener(new ActionListener()
 674     {
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         pdbFromFile_actionPerformed();
 678       }
 679     });
 680     enterPDB.setText("Enter PDB Id");
 681     enterPDB.addActionListener(new ActionListener()
 682     {
 683       public void actionPerformed(ActionEvent e)
 684       {
 685         enterPDB_actionPerformed();
 686       }
 687     });
 688     discoverPDB.setText("Discover PDB ids");
 689     discoverPDB.addActionListener(new ActionListener()
 690     {
 691       public void actionPerformed(ActionEvent e)
 692       {
 693         discoverPDB_actionPerformed();
 694       }
 695     });
 696     outputMenu.setText("Output to Textbox...");
 697     sequenceFeature.setText("Create Sequence Feature");
 698     sequenceFeature.addActionListener(new ActionListener()
 699     {
 700       public void actionPerformed(ActionEvent e)
 701       {
 702         sequenceFeature_actionPerformed();
 703       }
 704     });
 705     textColour.setText("Text Colour");
 706     textColour.addActionListener(new ActionListener()
 707     {
 708       public void actionPerformed(ActionEvent e)
 709       {
 710         textColour_actionPerformed();
 711       }
 712     });
 713     jMenu1.setText("Group");
 714     structureMenu.setText("Structure");
 715     viewStructureMenu.setText("View Structure");
 716     // colStructureMenu.setText("Colour By Structure");
 717     editSequence.setText("Edit Sequence...");
 718     editSequence.addActionListener(new ActionListener()
 719     {
 720       public void actionPerformed(ActionEvent actionEvent)
 721       {
 722         editSequence_actionPerformed(actionEvent);
 723       }
 724     });
 725     /*
 726      * annotationMenuItem.setText("By Annotation");
 727      * annotationMenuItem.addActionListener(new ActionListener() { public void
 728      * actionPerformed(ActionEvent actionEvent) {
 729      * annotationMenuItem_actionPerformed(actionEvent); } });
 730      */
 731
 732     add(groupMenu);
 733
 734     add(sequenceMenu);
 735     this.add(structureMenu);
 736     groupMenu.add(editMenu);
 737     groupMenu.add(outputMenu);
 738     groupMenu.add(sequenceFeature);
 739     groupMenu.add(jMenu1);
 740     sequenceMenu.add(sequenceName);
 741     colourMenu.add(textColour);
 742     colourMenu.add(noColourmenuItem);
 743     colourMenu.add(clustalColour);
 744     colourMenu.add(BLOSUM62Colour);
 745     colourMenu.add(PIDColour);
 746     colourMenu.add(zappoColour);
 747     colourMenu.add(taylorColour);
 748     colourMenu.add(hydrophobicityColour);
 749     colourMenu.add(helixColour);
 750     colourMenu.add(strandColour);
 751     colourMenu.add(turnColour);
 752     colourMenu.add(buriedColour);
 753     colourMenu.add(nucleotideMenuItem);
 754     colourMenu.add(userDefinedColour);
 755
 756     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 757     {
 758       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 759               .getUserColourSchemes().keys();
 760
 761       while (userColours.hasMoreElements())
 762       {
 763         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 764         item.addActionListener(new ActionListener()
 765         {
 766           public void actionPerformed(ActionEvent evt)
 767           {
 768             userDefinedColour_actionPerformed(evt);
 769           }
 770         });
 771         colourMenu.add(item);
 772       }
 773     }
 774
 775     colourMenu.addSeparator();
 776     colourMenu.add(abovePIDColour);
 777     colourMenu.add(conservationMenuItem);
 778     // colourMenu.add(annotationMenuItem);
 779     editMenu.add(copy);
 780     editMenu.add(cut);
 781     editMenu.add(editSequence);
 782     editMenu.add(upperCase);
 783     editMenu.add(lowerCase);
 784     editMenu.add(toggle);
 785     pdbMenu.add(pdbFromFile);
 786     pdbMenu.add(enterPDB);
 787     pdbMenu.add(discoverPDB);
 788     jMenu1.add(groupName);
 789     jMenu1.add(unGroupMenuItem);
 790     jMenu1.add(colourMenu);
 791     jMenu1.add(showBoxes);
 792     jMenu1.add(showText);
 793     jMenu1.add(showColourText);
 794     jMenu1.add(outline);
 795     jMenu1.add(displayNonconserved);
 796     structureMenu.add(pdbMenu);
 797     structureMenu.add(viewStructureMenu);
 798     // structureMenu.add(colStructureMenu);
 799     noColourmenuItem.setText("None");
 800     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 801     {
 802       public void actionPerformed(ActionEvent e)
 803       {
 804         noColourmenuItem_actionPerformed();
 805       }
 806     });
 807
 808     clustalColour.setText("Clustalx colours");
 809     clustalColour.addActionListener(new java.awt.event.ActionListener()
 810     {
 811       public void actionPerformed(ActionEvent e)
 812       {
 813         clustalColour_actionPerformed();
 814       }
 815     });
 816     zappoColour.setText("Zappo");
 817     zappoColour.addActionListener(new java.awt.event.ActionListener()
 818     {
 819       public void actionPerformed(ActionEvent e)
 820       {
 821         zappoColour_actionPerformed();
 822       }
 823     });
 824     taylorColour.setText("Taylor");
 825     taylorColour.addActionListener(new java.awt.event.ActionListener()
 826     {
 827       public void actionPerformed(ActionEvent e)
 828       {
 829         taylorColour_actionPerformed();
 830       }
 831     });
 832     hydrophobicityColour.setText("Hydrophobicity");
 833     hydrophobicityColour
 834             .addActionListener(new java.awt.event.ActionListener()
 835             {
 836               public void actionPerformed(ActionEvent e)
 837               {
 838                 hydrophobicityColour_actionPerformed();
 839               }
 840             });
 841     helixColour.setText("Helix propensity");
 842     helixColour.addActionListener(new java.awt.event.ActionListener()
 843     {
 844       public void actionPerformed(ActionEvent e)
 845       {
 846         helixColour_actionPerformed();
 847       }
 848     });
 849     strandColour.setText("Strand propensity");
 850     strandColour.addActionListener(new java.awt.event.ActionListener()
 851     {
 852       public void actionPerformed(ActionEvent e)
 853       {
 854         strandColour_actionPerformed();
 855       }
 856     });
 857     turnColour.setText("Turn propensity");
 858     turnColour.addActionListener(new java.awt.event.ActionListener()
 859     {
 860       public void actionPerformed(ActionEvent e)
 861       {
 862         turnColour_actionPerformed();
 863       }
 864     });
 865     buriedColour.setText("Buried Index");
 866     buriedColour.addActionListener(new java.awt.event.ActionListener()
 867     {
 868       public void actionPerformed(ActionEvent e)
 869       {
 870         buriedColour_actionPerformed();
 871       }
 872     });
 873     abovePIDColour.setText("Above % Identity");
 874     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 875     {
 876       public void actionPerformed(ActionEvent e)
 877       {
 878         abovePIDColour_actionPerformed();
 879       }
 880     });
 881     userDefinedColour.setText("User Defined...");
 882     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 883     {
 884       public void actionPerformed(ActionEvent e)
 885       {
 886         userDefinedColour_actionPerformed(e);
 887       }
 888     });
 889     PIDColour.setText("Percentage Identity");
 890     PIDColour.addActionListener(new java.awt.event.ActionListener()
 891     {
 892       public void actionPerformed(ActionEvent e)
 893       {
 894         PIDColour_actionPerformed();
 895       }
 896     });
 897     BLOSUM62Colour.setText("BLOSUM62");
 898     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 899     {
 900       public void actionPerformed(ActionEvent e)
 901       {
 902         BLOSUM62Colour_actionPerformed();
 903       }
 904     });
 905     conservationMenuItem.setText("Conservation");
 906     conservationMenuItem
 907             .addActionListener(new java.awt.event.ActionListener()
 908             {
 909               public void actionPerformed(ActionEvent e)
 910               {
 911                 conservationMenuItem_actionPerformed();
 912               }
 913             });
 914   }
 915
 916   protected void showNonconserved_actionPerformed()
 917   {
 918     getGroup().setShowunconserved(displayNonconserved.isSelected());
 919     refresh();
 920   }
 921
 922   /**
 923    * call to refresh view after settings change
 924    */
 925   void refresh()
 926   {
 927     ap.paintAlignment(true);
 928
 929     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 930   }
 931
 932   /**
 933    * DOCUMENT ME!
 934    *
 935    * @param e
 936    *                DOCUMENT ME!
 937    */
 938   protected void clustalColour_actionPerformed()
 939   {
 940     SequenceGroup sg = getGroup();
 941     sg.cs = new ClustalxColourScheme(sg
 942             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 943             .getWidth());
 944     refresh();
 945   }
 946
 947   /**
 948    * DOCUMENT ME!
 949    *
 950    * @param e
 951    *                DOCUMENT ME!
 952    */
 953   protected void zappoColour_actionPerformed()
 954   {
 955     getGroup().cs = new ZappoColourScheme();
 956     refresh();
 957   }
 958
 959   /**
 960    * DOCUMENT ME!
 961    *
 962    * @param e
 963    *                DOCUMENT ME!
 964    */
 965   protected void taylorColour_actionPerformed()
 966   {
 967     getGroup().cs = new TaylorColourScheme();
 968     refresh();
 969   }
 970
 971   /**
 972    * DOCUMENT ME!
 973    *
 974    * @param e
 975    *                DOCUMENT ME!
 976    */
 977   protected void hydrophobicityColour_actionPerformed()
 978   {
 979     getGroup().cs = new HydrophobicColourScheme();
 980     refresh();
 981   }
 982
 983   /**
 984    * DOCUMENT ME!
 985    *
 986    * @param e
 987    *                DOCUMENT ME!
 988    */
 989   protected void helixColour_actionPerformed()
 990   {
 991     getGroup().cs = new HelixColourScheme();
 992     refresh();
 993   }
 994
 995   /**
 996    * DOCUMENT ME!
 997    *
 998    * @param e
 999    *                DOCUMENT ME!
1000    */
1001   protected void strandColour_actionPerformed()
1002   {
1003     getGroup().cs = new StrandColourScheme();
1004     refresh();
1005   }
1006
1007   /**
1008    * DOCUMENT ME!
1009    *
1010    * @param e
1011    *                DOCUMENT ME!
1012    */
1013   protected void turnColour_actionPerformed()
1014   {
1015     getGroup().cs = new TurnColourScheme();
1016     refresh();
1017   }
1018
1019   /**
1020    * DOCUMENT ME!
1021    *
1022    * @param e
1023    *                DOCUMENT ME!
1024    */
1025   protected void buriedColour_actionPerformed()
1026   {
1027     getGroup().cs = new BuriedColourScheme();
1028     refresh();
1029   }
1030
1031   /**
1032    * DOCUMENT ME!
1033    *
1034    * @param e
1035    *                DOCUMENT ME!
1036    */
1037   public void nucleotideMenuItem_actionPerformed()
1038   {
1039     getGroup().cs = new NucleotideColourScheme();
1040     refresh();
1041   }
1042
1043   /**
1044    * DOCUMENT ME!
1045    *
1046    * @param e
1047    *                DOCUMENT ME!
1048    */
1049   protected void abovePIDColour_actionPerformed()
1050   {
1051     SequenceGroup sg = getGroup();
1052     if (sg.cs == null)
1053     {
1054       return;
1055     }
1056
1057     if (abovePIDColour.isSelected())
1058     {
1059       sg.cs.setConsensus(AAFrequency.calculate(sg
1060               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1061               .getEndRes() + 1));
1062
1063       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1064               .getName());
1065
1066       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1067
1068       SliderPanel.showPIDSlider();
1069     }
1070     else
1071     // remove PIDColouring
1072     {
1073       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1074     }
1075
1076     refresh();
1077   }
1078
1079   /**
1080    * DOCUMENT ME!
1081    *
1082    * @param e
1083    *                DOCUMENT ME!
1084    */
1085   protected void userDefinedColour_actionPerformed(ActionEvent e)
1086   {
1087     SequenceGroup sg = getGroup();
1088
1089     if (e.getActionCommand().equals("User Defined..."))
1090     {
1091       new UserDefinedColours(ap, sg);
1092     }
1093     else
1094     {
1095       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1096               .getUserColourSchemes().get(e.getActionCommand());
1097
1098       sg.cs = udc;
1099     }
1100     refresh();
1101   }
1102
1103   /**
1104    * DOCUMENT ME!
1105    *
1106    * @param e
1107    *                DOCUMENT ME!
1108    */
1109   protected void PIDColour_actionPerformed()
1110   {
1111     SequenceGroup sg = getGroup();
1112     sg.cs = new PIDColourScheme();
1113     sg.cs.setConsensus(AAFrequency.calculate(sg
1114             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1115             .getEndRes() + 1));
1116     refresh();
1117   }
1118
1119   /**
1120    * DOCUMENT ME!
1121    *
1122    * @param e
1123    *                DOCUMENT ME!
1124    */
1125   protected void BLOSUM62Colour_actionPerformed()
1126   {
1127     SequenceGroup sg = getGroup();
1128
1129     sg.cs = new Blosum62ColourScheme();
1130
1131     sg.cs.setConsensus(AAFrequency.calculate(sg
1132             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1133             .getEndRes() + 1));
1134
1135     refresh();
1136   }
1137
1138   /**
1139    * DOCUMENT ME!
1140    *
1141    * @param e
1142    *                DOCUMENT ME!
1143    */
1144   protected void noColourmenuItem_actionPerformed()
1145   {
1146     getGroup().cs = null;
1147     refresh();
1148   }
1149
1150   /**
1151    * DOCUMENT ME!
1152    *
1153    * @param e
1154    *                DOCUMENT ME!
1155    */
1156   protected void conservationMenuItem_actionPerformed()
1157   {
1158     SequenceGroup sg = getGroup();
1159     if (sg.cs == null)
1160     {
1161       return;
1162     }
1163
1164     if (conservationMenuItem.isSelected())
1165     {
1166       Conservation c = new Conservation("Group",
1167               ResidueProperties.propHash, 3, sg
1168                       .getSequences(ap.av.hiddenRepSequences), sg
1169                       .getStartRes(), sg.getEndRes() + 1);
1170
1171       c.calculate();
1172       c.verdict(false, ap.av.ConsPercGaps);
1173
1174       sg.cs.setConservation(c);
1175
1176       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1177       SliderPanel.showConservationSlider();
1178     }
1179     else
1180     // remove ConservationColouring
1181     {
1182       sg.cs.setConservation(null);
1183     }
1184
1185     refresh();
1186   }
1187
1188   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1189   {
1190     SequenceGroup sg = getGroup();
1191     if (sg == null)
1192     {
1193       return;
1194     }
1195
1196     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1197             .getAnnotation()[0], null,
1198             AnnotationColourGradient.NO_THRESHOLD);
1199
1200     acg.predefinedColours = true;
1201     sg.cs = acg;
1202
1203     refresh();
1204   }
1205
1206   /**
1207    * DOCUMENT ME!
1208    *
1209    * @param e
1210    *                DOCUMENT ME!
1211    */
1212   protected void groupName_actionPerformed()
1213   {
1214
1215     SequenceGroup sg = getGroup();
1216     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1217             .getDescription(), "       Group Name ", "Group Description ",
1218             "Edit Group Name/Description");
1219
1220     if (!dialog.accept)
1221     {
1222       return;
1223     }
1224
1225     sg.setName(dialog.getName());
1226     sg.setDescription(dialog.getDescription());
1227   }
1228
1229   /**
1230    * DOCUMENT ME!
1231    *
1232    * @return DOCUMENT ME!
1233    */
1234   SequenceGroup getGroup()
1235   {
1236     SequenceGroup sg = ap.av.getSelectionGroup();
1237     // this method won't add a new group if it already exists
1238     if (sg != null)
1239     {
1240       ap.av.alignment.addGroup(sg);
1241     }
1242
1243     return sg;
1244   }
1245
1246   /**
1247    * DOCUMENT ME!
1248    *
1249    * @param e
1250    *                DOCUMENT ME!
1251    */
1252   void sequenceName_actionPerformed()
1253   {
1254     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1255             .getDescription(), "       Sequence Name ",
1256             "Sequence Description ", "Edit Sequence Name/Description");
1257
1258     if (!dialog.accept)
1259     {
1260       return;
1261     }
1262
1263     if (dialog.getName() != null)
1264     {
1265       if (dialog.getName().indexOf(" ") > -1)
1266       {
1267         JOptionPane.showMessageDialog(ap,
1268                 "Spaces have been converted to \"_\"",
1269                 "No spaces allowed in Sequence Name",
1270                 JOptionPane.WARNING_MESSAGE);
1271       }
1272
1273       sequence.setName(dialog.getName().replace(' ', '_'));
1274       ap.paintAlignment(false);
1275     }
1276
1277     sequence.setDescription(dialog.getDescription());
1278
1279     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1280             .getSequences());
1281
1282   }
1283
1284   /**
1285    * DOCUMENT ME!
1286    *
1287    * @param e
1288    *                DOCUMENT ME!
1289    */
1290   void unGroupMenuItem_actionPerformed()
1291   {
1292     SequenceGroup sg = ap.av.getSelectionGroup();
1293     ap.av.alignment.deleteGroup(sg);
1294     ap.av.setSelectionGroup(null);
1295     refresh();
1296   }
1297
1298   /**
1299    * DOCUMENT ME!
1300    *
1301    * @param e
1302    *                DOCUMENT ME!
1303    */
1304   protected void outline_actionPerformed()
1305   {
1306     SequenceGroup sg = getGroup();
1307     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1308             Color.BLUE);
1309
1310     if (col != null)
1311     {
1312       sg.setOutlineColour(col);
1313     }
1314
1315     refresh();
1316   }
1317
1318   /**
1319    * DOCUMENT ME!
1320    *
1321    * @param e
1322    *                DOCUMENT ME!
1323    */
1324   public void showBoxes_actionPerformed()
1325   {
1326     getGroup().setDisplayBoxes(showBoxes.isSelected());
1327     refresh();
1328   }
1329
1330   /**
1331    * DOCUMENT ME!
1332    *
1333    * @param e
1334    *                DOCUMENT ME!
1335    */
1336   public void showText_actionPerformed()
1337   {
1338     getGroup().setDisplayText(showText.isSelected());
1339     refresh();
1340   }
1341
1342   /**
1343    * DOCUMENT ME!
1344    *
1345    * @param e
1346    *                DOCUMENT ME!
1347    */
1348   public void showColourText_actionPerformed()
1349   {
1350     getGroup().setColourText(showColourText.isSelected());
1351     refresh();
1352   }
1353
1354   public void showLink(String url)
1355   {
1356     try
1357     {
1358       jalview.util.BrowserLauncher.openURL(url);
1359     } catch (Exception ex)
1360     {
1361       JOptionPane
1362               .showInternalMessageDialog(
1363                       Desktop.desktop,
1364                       "Unixers: Couldn't find default web browser."
1365                               + "\nAdd the full path to your browser in Preferences.",
1366                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1367
1368       ex.printStackTrace();
1369     }
1370   }
1371
1372   void hideSequences(boolean representGroup)
1373   {
1374     SequenceGroup sg = ap.av.getSelectionGroup();
1375     if (sg == null || sg.getSize() < 1)
1376     {
1377       ap.av.hideSequence(new SequenceI[]
1378       { sequence });
1379       return;
1380     }
1381
1382     ap.av.setSelectionGroup(null);
1383
1384     if (representGroup)
1385     {
1386       ap.av.hideRepSequences(sequence, sg);
1387
1388       return;
1389     }
1390
1391     int gsize = sg.getSize();
1392     SequenceI[] hseqs;
1393
1394     hseqs = new SequenceI[gsize];
1395
1396     int index = 0;
1397     for (int i = 0; i < gsize; i++)
1398     {
1399       hseqs[index++] = sg.getSequenceAt(i);
1400     }
1401
1402     ap.av.hideSequence(hseqs);
1403     ap.av.sendSelection();
1404   }
1405
1406   public void copy_actionPerformed()
1407   {
1408     ap.alignFrame.copy_actionPerformed(null);
1409   }
1410
1411   public void cut_actionPerformed()
1412   {
1413     ap.alignFrame.cut_actionPerformed(null);
1414   }
1415
1416   void changeCase(ActionEvent e)
1417   {
1418     Object source = e.getSource();
1419     SequenceGroup sg = ap.av.getSelectionGroup();
1420
1421     if (sg != null)
1422     {
1423       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1424               sg.getEndRes() + 1);
1425
1426       String description;
1427       int caseChange;
1428
1429       if (source == toggle)
1430       {
1431         description = "Toggle Case";
1432         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1433       }
1434       else if (source == upperCase)
1435       {
1436         description = "To Upper Case";
1437         caseChange = ChangeCaseCommand.TO_UPPER;
1438       }
1439       else
1440       {
1441         description = "To Lower Case";
1442         caseChange = ChangeCaseCommand.TO_LOWER;
1443       }
1444
1445       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1446               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1447               caseChange);
1448
1449       ap.alignFrame.addHistoryItem(caseCommand);
1450
1451       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1452               .getSequences());
1453
1454     }
1455   }
1456
1457   public void outputText_actionPerformed(ActionEvent e)
1458   {
1459     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1460     cap.setForInput(null);
1461     Desktop.addInternalFrame(cap, "Alignment output - "
1462             + e.getActionCommand(), 600, 500);
1463
1464     String[] omitHidden = null;
1465
1466     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1467                                             // or we simply trust the user wants
1468                                             // wysiwig behaviour
1469     SequenceGroup sg = ap.av.getSelectionGroup();
1470     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1471     omitHidden = ap.av.getViewAsString(true);
1472     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1473     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1474     for (int i = 0; i < nala.length; i++)
1475     {
1476       AlignmentAnnotation na = nala[i];
1477       oal.addAnnotation(na);
1478     }
1479     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1480             oal, omitHidden, csel, sg));
1481     oal = null;
1482   }
1483
1484   public void pdbFromFile_actionPerformed()
1485   {
1486     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1487             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1488     chooser.setFileView(new jalview.io.JalviewFileView());
1489     chooser.setDialogTitle("Select a PDB file");
1490     chooser.setToolTipText("Load a PDB file");
1491
1492     int value = chooser.showOpenDialog(null);
1493
1494     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1495     {
1496       PDBEntry entry = new PDBEntry();
1497       String choice = chooser.getSelectedFile().getPath();
1498       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1499       try
1500       {
1501         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1502                 jalview.io.AppletFormatAdapter.FILE);
1503
1504         if (pdbfile.id == null)
1505         {
1506           String reply = JOptionPane
1507                   .showInternalInputDialog(
1508                           Desktop.desktop,
1509                           "Couldn't find a PDB id in the file supplied."
1510                                   + "Please enter an Id to identify this structure.",
1511                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1512           if (reply == null)
1513           {
1514             return;
1515           }
1516
1517           entry.setId(reply);
1518         }
1519         else
1520         {
1521           entry.setId(pdbfile.id);
1522         }
1523       } catch (java.io.IOException ex)
1524       {
1525         ex.printStackTrace();
1526       }
1527
1528       entry.setFile(choice);
1529       sequence.getDatasetSequence().addPDBId(entry);
1530     }
1531
1532   }
1533
1534   public void enterPDB_actionPerformed()
1535   {
1536     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1537             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1538
1539     if (id != null && id.length() > 0)
1540     {
1541       PDBEntry entry = new PDBEntry();
1542       entry.setId(id.toUpperCase());
1543       sequence.getDatasetSequence().addPDBId(entry);
1544     }
1545   }
1546
1547   public void discoverPDB_actionPerformed()
1548   {
1549
1550     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1551     { sequence }
1552             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1553     Thread discpdb = new Thread(new Runnable()
1554     {
1555       public void run()
1556       {
1557
1558         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1559                 .fetchDBRefs(false);
1560       }
1561
1562     });
1563     discpdb.start();
1564   }
1565
1566   public void sequenceFeature_actionPerformed()
1567   {
1568     SequenceGroup sg = ap.av.getSelectionGroup();
1569     if (sg == null)
1570     {
1571       return;
1572     }
1573
1574     int gSize = sg.getSize();
1575     SequenceI[] seqs = new SequenceI[gSize];
1576     SequenceFeature[] features = new SequenceFeature[gSize];
1577
1578     for (int i = 0; i < gSize; i++)
1579     {
1580       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1581       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1582       int end = sg.findEndRes(sg.getSequenceAt(i));
1583       features[i] = new SequenceFeature(null, null, null, start, end,
1584               "Jalview");
1585     }
1586
1587     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1588             features, true, ap))
1589     {
1590       ap.alignFrame.setShowSeqFeatures(true);
1591       ap.highlightSearchResults(null);
1592     }
1593   }
1594
1595   public void textColour_actionPerformed()
1596   {
1597     SequenceGroup sg = getGroup();
1598     if (sg != null)
1599     {
1600       new TextColourChooser().chooseColour(ap, sg);
1601     }
1602   }
1603
1604   public void colourByStructure(String pdbid)
1605   {
1606     Annotation[] anots = jalview.structure.StructureSelectionManager
1607             .getStructureSelectionManager().colourSequenceFromStructure(
1608                     sequence, pdbid);
1609
1610     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1611             "Coloured by " + pdbid, anots);
1612
1613     ap.av.alignment.addAnnotation(an);
1614     an.createSequenceMapping(sequence, 0, true);
1615     // an.adjustForAlignment();
1616     ap.av.alignment.setAnnotationIndex(an, 0);
1617
1618     ap.adjustAnnotationHeight();
1619
1620     sequence.addAlignmentAnnotation(an);
1621
1622   }
1623
1624   public void editSequence_actionPerformed(ActionEvent actionEvent)
1625   {
1626     SequenceGroup sg = ap.av.getSelectionGroup();
1627
1628     if (sg != null)
1629     {
1630       if (sequence == null)
1631         sequence = (Sequence) sg.getSequenceAt(0);
1632
1633       EditNameDialog dialog = new EditNameDialog(sequence
1634               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1635               null, "Edit Sequence ", null, "Edit Sequence");
1636
1637       if (dialog.accept)
1638       {
1639         EditCommand editCommand = new EditCommand("Edit Sequences",
1640                 EditCommand.REPLACE, dialog.getName().replace(' ',
1641                         ap.av.getGapCharacter()), sg
1642                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1643                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1644
1645         ap.alignFrame.addHistoryItem(editCommand);
1646
1647         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1648                 .getSequences());
1649       }
1650     }
1651   }
1652
1653 }