src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class PopupMenu
  41     extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44   JMenuItem groupName = new JMenuItem();
  45   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  46   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  47   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  48   protected JRadioButtonMenuItem hydrophobicityColour = new
  49       JRadioButtonMenuItem();
  50   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  54   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  55   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  58   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  59   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  60   AlignmentPanel ap;
  61   JMenu sequenceMenu = new JMenu();
  62   JMenuItem sequenceName = new JMenuItem();
  63   Sequence sequence;
  64   JMenuItem unGroupMenuItem = new JMenuItem();
  65   JMenuItem outline = new JMenuItem();
  66   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  67   JMenu colourMenu = new JMenu();
  68   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  69   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  70   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  71   JMenu editMenu = new JMenu();
  72   JMenuItem cut = new JMenuItem();
  73   JMenuItem copy = new JMenuItem();
  74   JMenuItem upperCase = new JMenuItem();
  75   JMenuItem lowerCase = new JMenuItem();
  76   JMenuItem toggle = new JMenuItem();
  77   JMenu pdbMenu = new JMenu();
  78   JMenuItem pdbFromFile = new JMenuItem();
  79   JMenuItem enterPDB = new JMenuItem();
  80   JMenuItem discoverPDB = new JMenuItem();
  81   JMenu outputMenu = new JMenu();
  82   JMenuItem sequenceFeature = new JMenuItem();
  83   JMenuItem textColour = new JMenuItem();
  84   JMenu jMenu1 = new JMenu();
  85   JMenu structureMenu = new JMenu();
  86   JMenu viewStructureMenu = new JMenu();
  87  // JMenu colStructureMenu = new JMenu();
  88   JMenuItem editSequence = new JMenuItem();
  89  // JMenuItem annotationMenuItem = new JMenuItem();
  90
  91   /**
  92    * Creates a new PopupMenu object.
  93    *
  94    * @param ap DOCUMENT ME!
  95    * @param seq DOCUMENT ME!
  96    */
  97   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
  98   {
  99     ///////////////////////////////////////////////////////////
 100     // If this is activated from the sequence panel, the user may want to
 101     // edit or annotate a particular residue. Therefore display the residue menu
 102     //
 103     // If from the IDPanel, we must display the sequence menu
 104     //////////////////////////////////////////////////////////
 105     this.ap = ap;
 106     sequence = seq;
 107
 108     ButtonGroup colours = new ButtonGroup();
 109     colours.add(noColourmenuItem);
 110     colours.add(clustalColour);
 111     colours.add(zappoColour);
 112     colours.add(taylorColour);
 113     colours.add(hydrophobicityColour);
 114     colours.add(helixColour);
 115     colours.add(strandColour);
 116     colours.add(turnColour);
 117     colours.add(buriedColour);
 118     colours.add(abovePIDColour);
 119     colours.add(userDefinedColour);
 120     colours.add(PIDColour);
 121     colours.add(BLOSUM62Colour);
 122
 123     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 124     {
 125       JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
 126                                      i]);
 127
 128       item.addActionListener(new java.awt.event.ActionListener()
 129       {
 130         public void actionPerformed(ActionEvent e)
 131         {
 132           outputText_actionPerformed(e);
 133         }
 134       });
 135
 136       outputMenu.add(item);
 137     }
 138
 139     try
 140     {
 141       jbInit();
 142     }
 143     catch (Exception e)
 144     {
 145       e.printStackTrace();
 146     }
 147
 148     if (seq != null)
 149     {
 150       sequenceMenu.setText(sequence.getName());
 151
 152       JMenuItem menuItem;
 153       if (seq.getDatasetSequence().getPDBId() != null
 154           && seq.getDatasetSequence().getPDBId().size()>0)
 155       {
 156         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
 157             elements();
 158
 159         while (e.hasMoreElements())
 160         {
 161           final PDBEntry pdb = (PDBEntry) e.nextElement();
 162
 163           menuItem = new JMenuItem();
 164           menuItem.setText(pdb.getId());
 165           menuItem.addActionListener(new java.awt.event.ActionListener()
 166           {
 167             public void actionPerformed(ActionEvent e)
 168             {
 169               Vector seqs = new Vector();
 170               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 171               {
 172                 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
 173                 if(pdbs==null)
 174                   continue;
 175
 176                 for(int p=0; p<pdbs.size(); p++)
 177                 {
 178                   PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
 179                   if(p1.getId().equals(pdb.getId()))
 180                   {
 181                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 182                         seqs.addElement(ap.av.alignment.getSequenceAt(i));
 183
 184                       continue;
 185                   }
 186                 }
 187               }
 188
 189               SequenceI [] seqs2 = new SequenceI[seqs.size()];
 190               seqs.toArray(seqs2);
 191
 192               new AppJmol(pdb, seqs2, null, ap);
 193               //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 194             }
 195           });
 196           viewStructureMenu.add(menuItem);
 197
 198        /*   menuItem = new JMenuItem();
 199           menuItem.setText(pdb.getId());
 200           menuItem.addActionListener(new java.awt.event.ActionListener()
 201           {
 202             public void actionPerformed(ActionEvent e)
 203             {
 204               colourByStructure(pdb.getId());
 205             }
 206           });
 207           colStructureMenu.add(menuItem);*/
 208         }
 209       }
 210       else
 211       {
 212         structureMenu.remove(viewStructureMenu);
 213        // structureMenu.remove(colStructureMenu);
 214       }
 215
 216       menuItem = new JMenuItem("Hide Sequences");
 217       menuItem.addActionListener(new java.awt.event.ActionListener()
 218       {
 219         public void actionPerformed(ActionEvent e)
 220         {
 221           hideSequences(false);
 222         }
 223       });
 224       add(menuItem);
 225
 226       if (ap.av.getSelectionGroup() != null
 227           && ap.av.getSelectionGroup().getSize() > 1)
 228       {
 229         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 230         menuItem.addActionListener(new java.awt.event.ActionListener()
 231         {
 232           public void actionPerformed(ActionEvent e)
 233           {
 234             hideSequences(true);
 235           }
 236         });
 237         sequenceMenu.add(menuItem);
 238       }
 239
 240       if (ap.av.hasHiddenRows)
 241       {
 242         final int index = ap.av.alignment.findIndex(seq);
 243
 244         if (ap.av.adjustForHiddenSeqs(index) -
 245             ap.av.adjustForHiddenSeqs(index - 1) > 1)
 246         {
 247           menuItem = new JMenuItem("Reveal Sequences");
 248           menuItem.addActionListener(new ActionListener()
 249           {
 250             public void actionPerformed(ActionEvent e)
 251             {
 252               ap.av.showSequence(index);
 253               if (ap.overviewPanel != null)
 254               {
 255                 ap.overviewPanel.updateOverviewImage();
 256               }
 257             }
 258           });
 259           add(menuItem);
 260         }
 261
 262         menuItem = new JMenuItem("Reveal All");
 263         menuItem.addActionListener(new ActionListener()
 264         {
 265           public void actionPerformed(ActionEvent e)
 266           {
 267             ap.av.showAllHiddenSeqs();
 268             if (ap.overviewPanel != null)
 269             {
 270               ap.overviewPanel.updateOverviewImage();
 271             }
 272           }
 273         });
 274
 275         add(menuItem);
 276       }
 277
 278     }
 279
 280     SequenceGroup sg = ap.av.getSelectionGroup();
 281
 282     if (sg != null)
 283     {
 284       groupName.setText(sg.getName());
 285
 286       if (sg.cs instanceof ZappoColourScheme)
 287       {
 288         zappoColour.setSelected(true);
 289       }
 290       else if (sg.cs instanceof TaylorColourScheme)
 291       {
 292         taylorColour.setSelected(true);
 293       }
 294       else if (sg.cs instanceof PIDColourScheme)
 295       {
 296         PIDColour.setSelected(true);
 297       }
 298       else if (sg.cs instanceof Blosum62ColourScheme)
 299       {
 300         BLOSUM62Colour.setSelected(true);
 301       }
 302       else if (sg.cs instanceof UserColourScheme)
 303       {
 304         userDefinedColour.setSelected(true);
 305       }
 306       else if (sg.cs instanceof HydrophobicColourScheme)
 307       {
 308         hydrophobicityColour.setSelected(true);
 309       }
 310       else if (sg.cs instanceof HelixColourScheme)
 311       {
 312         helixColour.setSelected(true);
 313       }
 314       else if (sg.cs instanceof StrandColourScheme)
 315       {
 316         strandColour.setSelected(true);
 317       }
 318       else if (sg.cs instanceof TurnColourScheme)
 319       {
 320         turnColour.setSelected(true);
 321       }
 322       else if (sg.cs instanceof BuriedColourScheme)
 323       {
 324         buriedColour.setSelected(true);
 325       }
 326       else if (sg.cs instanceof ClustalxColourScheme)
 327       {
 328         clustalColour.setSelected(true);
 329       }
 330       else
 331       {
 332         noColourmenuItem.setSelected(true);
 333       }
 334
 335       if (sg.cs != null && sg.cs.conservationApplied())
 336       {
 337         conservationMenuItem.setSelected(true);
 338       }
 339
 340       showText.setSelected(sg.getDisplayText());
 341       showColourText.setSelected(sg.getColourText());
 342       showBoxes.setSelected(sg.getDisplayBoxes());
 343     }
 344     else
 345     {
 346       groupMenu.setVisible(false);
 347       editMenu.setVisible(false);
 348     }
 349
 350     if (!ap.av.alignment.getGroups().contains(sg))
 351     {
 352       unGroupMenuItem.setVisible(false);
 353     }
 354
 355     if (seq == null)
 356     {
 357       sequenceMenu.setVisible(false);
 358       structureMenu.setVisible(false);
 359     }
 360
 361     if (links != null && links.size() > 0)
 362     {
 363       JMenu linkMenu = new JMenu("Link");
 364
 365       for (int i = 0; i < links.size(); i++)
 366       {
 367         String link = links.elementAt(i).toString();
 368         final String label = link.substring(0, link.indexOf("|"));
 369
 370
 371         if (link.indexOf("$SEQUENCE_ID$") > -1)
 372         {
 373           // Substitute SEQUENCE_ID string and any matching database reference accessions
 374           String url_pref = link.substring(link.indexOf("|") + 1,
 375                   link.indexOf("$SEQUENCE_ID$"));
 376
 377           String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
 378
 379           // collect matching db-refs
 380           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{label});
 381           // collect id string too
 382           String id = seq.getName();
 383           if (id.indexOf("|") > -1)
 384           {
 385             id = id.substring(id.lastIndexOf("|") + 1);
 386           }
 387
 388           if (dbr!=null)
 389           {
 390             for (int r=0;r<dbr.length; r++)
 391             {
 392               if (dbr[r].getAccessionId().equals(id))
 393               {
 394                 // suppress duplicate link creation for the bare sequence ID string with this link
 395                 id = null;
 396               }
 397               addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
 398                       url_pref+dbr[r].getAccessionId()+url_suff);
 399             }
 400           }
 401           if (id!=null)
 402           {
 403             // create Bare ID link for this RUL
 404             addshowLink(linkMenu, label,  url_pref + id + url_suff);
 405           }
 406         }
 407         else
 408         {
 409           // Add a non-dynamic link
 410           addshowLink(linkMenu, label, link.substring(link.lastIndexOf("|") + 1));
 411         }
 412       }
 413       if (sequence != null)
 414       {
 415         sequenceMenu.add(linkMenu);
 416       }
 417       else
 418       {
 419         add(linkMenu);
 420       }
 421     }
 422   }
 423
 424   /**
 425    * add a show URL menu item to the given linkMenu
 426    * @param linkMenu
 427    * @param label - menu label string
 428    * @param url - url to open
 429    */
 430   private void addshowLink(JMenu linkMenu, String label, final String url)
 431   {
 432     JMenuItem item = new JMenuItem(label);
 433     item.addActionListener(new java.awt.event.ActionListener()
 434     {
 435       public void actionPerformed(ActionEvent e)
 436       {
 437         new Thread(new Runnable() {
 438
 439           public void run()
 440           {
 441             showLink(url);
 442           }
 443
 444         }).start();
 445       }
 446     });
 447
 448     linkMenu.add(item);
 449   }
 450
 451   /**
 452    * DOCUMENT ME!
 453    *
 454    * @throws Exception DOCUMENT ME!
 455    */
 456   private void jbInit()
 457       throws Exception
 458   {
 459     groupMenu.setText("Group");
 460     groupMenu.setText("Selection");
 461     groupName.setText("Name");
 462     groupName.addActionListener(new java.awt.event.ActionListener()
 463     {
 464       public void actionPerformed(ActionEvent e)
 465       {
 466         groupName_actionPerformed();
 467       }
 468     });
 469     sequenceMenu.setText("Sequence");
 470     sequenceName.setText("Edit Name/Description");
 471     sequenceName.addActionListener(new java.awt.event.ActionListener()
 472     {
 473       public void actionPerformed(ActionEvent e)
 474       {
 475         sequenceName_actionPerformed();
 476       }
 477     });
 478     PIDColour.setFocusPainted(false);
 479     unGroupMenuItem.setText("Remove Group");
 480     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 481     {
 482       public void actionPerformed(ActionEvent e)
 483       {
 484         unGroupMenuItem_actionPerformed();
 485       }
 486     });
 487
 488     outline.setText("Border colour");
 489     outline.addActionListener(new java.awt.event.ActionListener()
 490     {
 491       public void actionPerformed(ActionEvent e)
 492       {
 493         outline_actionPerformed();
 494       }
 495     });
 496     nucleotideMenuItem.setText("Nucleotide");
 497     nucleotideMenuItem.addActionListener(new ActionListener()
 498     {
 499       public void actionPerformed(ActionEvent e)
 500       {
 501         nucleotideMenuItem_actionPerformed();
 502       }
 503     });
 504     colourMenu.setText("Group Colour");
 505     showBoxes.setText("Boxes");
 506     showBoxes.setState(true);
 507     showBoxes.addActionListener(new ActionListener()
 508     {
 509       public void actionPerformed(ActionEvent e)
 510       {
 511         showBoxes_actionPerformed();
 512       }
 513     });
 514     showText.setText("Text");
 515     showText.setState(true);
 516     showText.addActionListener(new ActionListener()
 517     {
 518       public void actionPerformed(ActionEvent e)
 519       {
 520         showText_actionPerformed();
 521       }
 522     });
 523     showColourText.setText("Colour Text");
 524     showColourText.addActionListener(new ActionListener()
 525     {
 526       public void actionPerformed(ActionEvent e)
 527       {
 528         showColourText_actionPerformed();
 529       }
 530     });
 531     editMenu.setText("Edit");
 532     cut.setText("Cut");
 533     cut.addActionListener(new ActionListener()
 534     {
 535       public void actionPerformed(ActionEvent e)
 536       {
 537         cut_actionPerformed();
 538       }
 539     });
 540     upperCase.setText("To Upper Case");
 541     upperCase.addActionListener(new ActionListener()
 542     {
 543       public void actionPerformed(ActionEvent e)
 544       {
 545         changeCase(e);
 546       }
 547     });
 548     copy.setText("Copy");
 549     copy.addActionListener(new ActionListener()
 550     {
 551       public void actionPerformed(ActionEvent e)
 552       {
 553         copy_actionPerformed();
 554       }
 555     });
 556     lowerCase.setText("To Lower Case");
 557     lowerCase.addActionListener(new ActionListener()
 558     {
 559       public void actionPerformed(ActionEvent e)
 560       {
 561         changeCase(e);
 562       }
 563     });
 564     toggle.setText("Toggle Case");
 565     toggle.addActionListener(new ActionListener()
 566     {
 567       public void actionPerformed(ActionEvent e)
 568       {
 569         changeCase(e);
 570       }
 571     });
 572     pdbMenu.setText("Associate Structure with Sequence");
 573     pdbFromFile.setText("From File");
 574     pdbFromFile.addActionListener(new ActionListener()
 575     {
 576       public void actionPerformed(ActionEvent e)
 577       {
 578         pdbFromFile_actionPerformed();
 579       }
 580     });
 581     enterPDB.setText("Enter PDB Id");
 582     enterPDB.addActionListener(new ActionListener()
 583     {
 584       public void actionPerformed(ActionEvent e)
 585       {
 586         enterPDB_actionPerformed();
 587       }
 588     });
 589     discoverPDB.setText("Discover PDB ids");
 590     discoverPDB.addActionListener(new ActionListener()
 591     {
 592       public void actionPerformed(ActionEvent e)
 593       {
 594         discoverPDB_actionPerformed();
 595       }
 596     });
 597     outputMenu.setText("Output to Textbox...");
 598     sequenceFeature.setText("Create Sequence Feature");
 599     sequenceFeature.addActionListener(new ActionListener()
 600     {
 601       public void actionPerformed(ActionEvent e)
 602       {
 603         sequenceFeature_actionPerformed();
 604       }
 605     });
 606     textColour.setText("Text Colour");
 607     textColour.addActionListener(new ActionListener()
 608     {
 609       public void actionPerformed(ActionEvent e)
 610       {
 611         textColour_actionPerformed();
 612       }
 613     });
 614     jMenu1.setText("Group");
 615     structureMenu.setText("Structure");
 616     viewStructureMenu.setText("View Structure");
 617   //  colStructureMenu.setText("Colour By Structure");
 618     editSequence.setText("Edit Sequence...");
 619     editSequence.addActionListener(new ActionListener()
 620     {
 621       public void actionPerformed(ActionEvent actionEvent)
 622       {
 623         editSequence_actionPerformed(actionEvent);
 624       }
 625     });
 626    /* annotationMenuItem.setText("By Annotation");
 627     annotationMenuItem.addActionListener(new ActionListener()
 628     {
 629       public void actionPerformed(ActionEvent actionEvent)
 630       {
 631         annotationMenuItem_actionPerformed(actionEvent);
 632       }
 633     });*/
 634
 635     add(groupMenu);
 636
 637     add(sequenceMenu);
 638     this.add(structureMenu);
 639     groupMenu.add(editMenu);
 640     groupMenu.add(outputMenu);
 641     groupMenu.add(sequenceFeature);
 642     groupMenu.add(jMenu1);
 643     sequenceMenu.add(sequenceName);
 644     colourMenu.add(textColour);
 645     colourMenu.add(noColourmenuItem);
 646     colourMenu.add(clustalColour);
 647     colourMenu.add(BLOSUM62Colour);
 648     colourMenu.add(PIDColour);
 649     colourMenu.add(zappoColour);
 650     colourMenu.add(taylorColour);
 651     colourMenu.add(hydrophobicityColour);
 652     colourMenu.add(helixColour);
 653     colourMenu.add(strandColour);
 654     colourMenu.add(turnColour);
 655     colourMenu.add(buriedColour);
 656     colourMenu.add(nucleotideMenuItem);
 657     colourMenu.add(userDefinedColour);
 658
 659     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 660     {
 661       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
 662           getUserColourSchemes().keys();
 663
 664       while (userColours.hasMoreElements())
 665       {
 666         JMenuItem item = new JMenuItem(userColours.
 667                                        nextElement().toString());
 668         item.addActionListener(new ActionListener()
 669         {
 670           public void actionPerformed(ActionEvent evt)
 671           {
 672             userDefinedColour_actionPerformed(evt);
 673           }
 674         });
 675         colourMenu.add(item);
 676       }
 677     }
 678
 679     colourMenu.addSeparator();
 680     colourMenu.add(abovePIDColour);
 681     colourMenu.add(conservationMenuItem);
 682     //colourMenu.add(annotationMenuItem);
 683     editMenu.add(copy);
 684     editMenu.add(cut);
 685     editMenu.add(editSequence);
 686     editMenu.add(upperCase);
 687     editMenu.add(lowerCase);
 688     editMenu.add(toggle);
 689     pdbMenu.add(pdbFromFile);
 690     pdbMenu.add(enterPDB);
 691     pdbMenu.add(discoverPDB);
 692     jMenu1.add(groupName);
 693     jMenu1.add(unGroupMenuItem);
 694     jMenu1.add(colourMenu);
 695     jMenu1.add(showBoxes);
 696     jMenu1.add(showText);
 697     jMenu1.add(showColourText);
 698     jMenu1.add(outline);
 699     structureMenu.add(pdbMenu);
 700     structureMenu.add(viewStructureMenu);
 701    // structureMenu.add(colStructureMenu);
 702     noColourmenuItem.setText("None");
 703     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 704     {
 705       public void actionPerformed(ActionEvent e)
 706       {
 707         noColourmenuItem_actionPerformed();
 708       }
 709     });
 710
 711     clustalColour.setText("Clustalx colours");
 712     clustalColour.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         clustalColour_actionPerformed();
 717       }
 718     });
 719     zappoColour.setText("Zappo");
 720     zappoColour.addActionListener(new java.awt.event.ActionListener()
 721     {
 722       public void actionPerformed(ActionEvent e)
 723       {
 724         zappoColour_actionPerformed();
 725       }
 726     });
 727     taylorColour.setText("Taylor");
 728     taylorColour.addActionListener(new java.awt.event.ActionListener()
 729     {
 730       public void actionPerformed(ActionEvent e)
 731       {
 732         taylorColour_actionPerformed();
 733       }
 734     });
 735     hydrophobicityColour.setText("Hydrophobicity");
 736     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 737     {
 738       public void actionPerformed(ActionEvent e)
 739       {
 740         hydrophobicityColour_actionPerformed();
 741       }
 742     });
 743     helixColour.setText("Helix propensity");
 744     helixColour.addActionListener(new java.awt.event.ActionListener()
 745     {
 746       public void actionPerformed(ActionEvent e)
 747       {
 748         helixColour_actionPerformed();
 749       }
 750     });
 751     strandColour.setText("Strand propensity");
 752     strandColour.addActionListener(new java.awt.event.ActionListener()
 753     {
 754       public void actionPerformed(ActionEvent e)
 755       {
 756         strandColour_actionPerformed();
 757       }
 758     });
 759     turnColour.setText("Turn propensity");
 760     turnColour.addActionListener(new java.awt.event.ActionListener()
 761     {
 762       public void actionPerformed(ActionEvent e)
 763       {
 764         turnColour_actionPerformed();
 765       }
 766     });
 767     buriedColour.setText("Buried Index");
 768     buriedColour.addActionListener(new java.awt.event.ActionListener()
 769     {
 770       public void actionPerformed(ActionEvent e)
 771       {
 772         buriedColour_actionPerformed();
 773       }
 774     });
 775     abovePIDColour.setText("Above % Identity");
 776     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 777     {
 778       public void actionPerformed(ActionEvent e)
 779       {
 780         abovePIDColour_actionPerformed();
 781       }
 782     });
 783     userDefinedColour.setText("User Defined...");
 784     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 785     {
 786       public void actionPerformed(ActionEvent e)
 787       {
 788         userDefinedColour_actionPerformed(e);
 789       }
 790     });
 791     PIDColour.setText("Percentage Identity");
 792     PIDColour.addActionListener(new java.awt.event.ActionListener()
 793     {
 794       public void actionPerformed(ActionEvent e)
 795       {
 796         PIDColour_actionPerformed();
 797       }
 798     });
 799     BLOSUM62Colour.setText("BLOSUM62");
 800     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 801     {
 802       public void actionPerformed(ActionEvent e)
 803       {
 804         BLOSUM62Colour_actionPerformed();
 805       }
 806     });
 807     conservationMenuItem.setText("Conservation");
 808     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 809     {
 810       public void actionPerformed(ActionEvent e)
 811       {
 812         conservationMenuItem_actionPerformed();
 813       }
 814     });
 815   }
 816
 817   /**
 818    * DOCUMENT ME!
 819    */
 820   void refresh()
 821   {
 822     ap.paintAlignment(true);
 823
 824     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 825   }
 826
 827   /**
 828    * DOCUMENT ME!
 829    *
 830    * @param e DOCUMENT ME!
 831    */
 832   protected void clustalColour_actionPerformed()
 833   {
 834     SequenceGroup sg = getGroup();
 835     sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
 836                                      ap.av.alignment.getWidth());
 837     refresh();
 838   }
 839
 840   /**
 841    * DOCUMENT ME!
 842    *
 843    * @param e DOCUMENT ME!
 844    */
 845   protected void zappoColour_actionPerformed()
 846   {
 847     getGroup().cs = new ZappoColourScheme();
 848     refresh();
 849   }
 850
 851   /**
 852    * DOCUMENT ME!
 853    *
 854    * @param e DOCUMENT ME!
 855    */
 856   protected void taylorColour_actionPerformed()
 857   {
 858     getGroup().cs = new TaylorColourScheme();
 859     refresh();
 860   }
 861
 862   /**
 863    * DOCUMENT ME!
 864    *
 865    * @param e DOCUMENT ME!
 866    */
 867   protected void hydrophobicityColour_actionPerformed()
 868   {
 869     getGroup().cs = new HydrophobicColourScheme();
 870     refresh();
 871   }
 872
 873   /**
 874    * DOCUMENT ME!
 875    *
 876    * @param e DOCUMENT ME!
 877    */
 878   protected void helixColour_actionPerformed()
 879   {
 880     getGroup().cs = new HelixColourScheme();
 881     refresh();
 882   }
 883
 884   /**
 885    * DOCUMENT ME!
 886    *
 887    * @param e DOCUMENT ME!
 888    */
 889   protected void strandColour_actionPerformed()
 890   {
 891     getGroup().cs = new StrandColourScheme();
 892     refresh();
 893   }
 894
 895   /**
 896    * DOCUMENT ME!
 897    *
 898    * @param e DOCUMENT ME!
 899    */
 900   protected void turnColour_actionPerformed()
 901   {
 902     getGroup().cs = new TurnColourScheme();
 903     refresh();
 904   }
 905
 906   /**
 907    * DOCUMENT ME!
 908    *
 909    * @param e DOCUMENT ME!
 910    */
 911   protected void buriedColour_actionPerformed()
 912   {
 913     getGroup().cs = new BuriedColourScheme();
 914     refresh();
 915   }
 916
 917   /**
 918    * DOCUMENT ME!
 919    *
 920    * @param e DOCUMENT ME!
 921    */
 922   public void nucleotideMenuItem_actionPerformed()
 923   {
 924     getGroup().cs = new NucleotideColourScheme();
 925     refresh();
 926   }
 927
 928   /**
 929    * DOCUMENT ME!
 930    *
 931    * @param e DOCUMENT ME!
 932    */
 933   protected void abovePIDColour_actionPerformed()
 934   {
 935     SequenceGroup sg = getGroup();
 936     if (sg.cs == null)
 937     {
 938       return;
 939     }
 940
 941     if (abovePIDColour.isSelected())
 942     {
 943       sg.cs.setConsensus(AAFrequency.calculate(
 944           sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
 945           sg.getEndRes() + 1));
 946
 947       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
 948           getGroup().getName());
 949
 950       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 951
 952       SliderPanel.showPIDSlider();
 953     }
 954     else // remove PIDColouring
 955     {
 956       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 957     }
 958
 959     refresh();
 960   }
 961
 962   /**
 963    * DOCUMENT ME!
 964    *
 965    * @param e DOCUMENT ME!
 966    */
 967   protected void userDefinedColour_actionPerformed(ActionEvent e)
 968   {
 969     SequenceGroup sg = getGroup();
 970
 971     if (e.getActionCommand().equals("User Defined..."))
 972     {
 973       new UserDefinedColours(ap, sg);
 974     }
 975     else
 976     {
 977       UserColourScheme udc = (UserColourScheme) UserDefinedColours.
 978           getUserColourSchemes().get(e.getActionCommand());
 979
 980       sg.cs = udc;
 981     }
 982     refresh();
 983   }
 984
 985   /**
 986    * DOCUMENT ME!
 987    *
 988    * @param e DOCUMENT ME!
 989    */
 990   protected void PIDColour_actionPerformed()
 991   {
 992     SequenceGroup sg = getGroup();
 993     sg.cs = new PIDColourScheme();
 994     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
 995         hiddenRepSequences),
 996                                              sg.getStartRes(),
 997                                              sg.getEndRes() + 1));
 998     refresh();
 999   }
1000
1001   /**
1002    * DOCUMENT ME!
1003    *
1004    * @param e DOCUMENT ME!
1005    */
1006   protected void BLOSUM62Colour_actionPerformed()
1007   {
1008     SequenceGroup sg = getGroup();
1009
1010     sg.cs = new Blosum62ColourScheme();
1011
1012     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1013         hiddenRepSequences),
1014                                              sg.getStartRes(),
1015                                              sg.getEndRes() + 1));
1016
1017     refresh();
1018   }
1019
1020   /**
1021    * DOCUMENT ME!
1022    *
1023    * @param e DOCUMENT ME!
1024    */
1025   protected void noColourmenuItem_actionPerformed()
1026   {
1027     getGroup().cs = null;
1028     refresh();
1029   }
1030
1031   /**
1032    * DOCUMENT ME!
1033    *
1034    * @param e DOCUMENT ME!
1035    */
1036   protected void conservationMenuItem_actionPerformed()
1037   {
1038     SequenceGroup sg = getGroup();
1039     if (sg.cs == null)
1040     {
1041       return;
1042     }
1043
1044     if (conservationMenuItem.isSelected())
1045     {
1046       Conservation c = new Conservation("Group",
1047                                         ResidueProperties.propHash, 3,
1048                                         sg.getSequences(ap.av.
1049           hiddenRepSequences),
1050                                         sg.getStartRes(),
1051                                         sg.getEndRes() + 1);
1052
1053       c.calculate();
1054       c.verdict(false, ap.av.ConsPercGaps);
1055
1056       sg.cs.setConservation(c);
1057
1058       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1059       SliderPanel.showConservationSlider();
1060     }
1061     else // remove ConservationColouring
1062     {
1063       sg.cs.setConservation(null);
1064     }
1065
1066     refresh();
1067   }
1068
1069   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1070   {
1071     SequenceGroup sg = getGroup();
1072     if (sg == null)
1073     {
1074       return;
1075     }
1076
1077     AnnotationColourGradient acg = new AnnotationColourGradient(
1078         sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
1079
1080     acg.predefinedColours = true;
1081     sg.cs = acg;
1082
1083     refresh();
1084   }
1085
1086   /**
1087    * DOCUMENT ME!
1088    *
1089    * @param e DOCUMENT ME!
1090    */
1091   protected void groupName_actionPerformed()
1092   {
1093
1094     SequenceGroup sg = getGroup();
1095     EditNameDialog dialog = new EditNameDialog(sg.getName(),
1096                                                sg.getDescription(),
1097                                                "       Group Name ",
1098                                                "Group Description ",
1099                                                "Edit Group Name/Description");
1100
1101     if (!dialog.accept)
1102     {
1103       return;
1104     }
1105
1106     sg.setName(dialog.getName());
1107     sg.setDescription(dialog.getDescription());
1108   }
1109
1110   /**
1111    * DOCUMENT ME!
1112    *
1113    * @return DOCUMENT ME!
1114    */
1115   SequenceGroup getGroup()
1116   {
1117     SequenceGroup sg = ap.av.getSelectionGroup();
1118     // this method won't add a new group if it already exists
1119     if (sg != null)
1120     {
1121       ap.av.alignment.addGroup(sg);
1122     }
1123
1124     return sg;
1125   }
1126
1127   /**
1128    * DOCUMENT ME!
1129    *
1130    * @param e DOCUMENT ME!
1131    */
1132   void sequenceName_actionPerformed()
1133   {
1134     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1135                                                sequence.getDescription(),
1136                                                "       Sequence Name ",
1137                                                "Sequence Description ",
1138                                                "Edit Sequence Name/Description");
1139
1140     if (!dialog.accept)
1141     {
1142       return;
1143     }
1144
1145     if (dialog.getName() != null)
1146     {
1147       if (dialog.getName().indexOf(" ") > -1)
1148       {
1149         JOptionPane.showMessageDialog(ap,
1150                                       "Spaces have been converted to \"_\"",
1151                                       "No spaces allowed in Sequence Name",
1152                                       JOptionPane.WARNING_MESSAGE);
1153       }
1154
1155       sequence.setName(dialog.getName().replace(' ', '_'));
1156       ap.paintAlignment(false);
1157     }
1158
1159     sequence.setDescription(dialog.getDescription());
1160
1161     ap.av.firePropertyChange("alignment", null,
1162                              ap.av.getAlignment().getSequences());
1163
1164   }
1165
1166   /**
1167    * DOCUMENT ME!
1168    *
1169    * @param e DOCUMENT ME!
1170    */
1171   void unGroupMenuItem_actionPerformed()
1172   {
1173     SequenceGroup sg = ap.av.getSelectionGroup();
1174     ap.av.alignment.deleteGroup(sg);
1175     ap.av.setSelectionGroup(null);
1176     refresh();
1177   }
1178
1179   /**
1180    * DOCUMENT ME!
1181    *
1182    * @param e DOCUMENT ME!
1183    */
1184   protected void outline_actionPerformed()
1185   {
1186     SequenceGroup sg = getGroup();
1187     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1188                                          Color.BLUE);
1189
1190     if (col != null)
1191     {
1192       sg.setOutlineColour(col);
1193     }
1194
1195     refresh();
1196   }
1197
1198   /**
1199    * DOCUMENT ME!
1200    *
1201    * @param e DOCUMENT ME!
1202    */
1203   public void showBoxes_actionPerformed()
1204   {
1205     getGroup().setDisplayBoxes(showBoxes.isSelected());
1206     refresh();
1207   }
1208
1209   /**
1210    * DOCUMENT ME!
1211    *
1212    * @param e DOCUMENT ME!
1213    */
1214   public void showText_actionPerformed()
1215   {
1216     getGroup().setDisplayText(showText.isSelected());
1217     refresh();
1218   }
1219
1220   /**
1221    * DOCUMENT ME!
1222    *
1223    * @param e DOCUMENT ME!
1224    */
1225   public void showColourText_actionPerformed()
1226   {
1227     getGroup().setColourText(showColourText.isSelected());
1228     refresh();
1229   }
1230
1231   public void showLink(String url)
1232   {
1233     try
1234     {
1235       jalview.util.BrowserLauncher.openURL(url);
1236     }
1237     catch (Exception ex)
1238     {
1239       JOptionPane.showInternalMessageDialog(Desktop.desktop,
1240                                             "Unixers: Couldn't find default web browser."
1241                                             +
1242           "\nAdd the full path to your browser in Preferences.",
1243                                             "Web browser not found",
1244                                             JOptionPane.WARNING_MESSAGE);
1245
1246       ex.printStackTrace();
1247     }
1248   }
1249
1250   void hideSequences(boolean representGroup)
1251   {
1252     SequenceGroup sg = ap.av.getSelectionGroup();
1253     if (sg == null || sg.getSize() < 1)
1254     {
1255       ap.av.hideSequence(new SequenceI[]
1256                          {sequence});
1257       return;
1258     }
1259
1260     ap.av.setSelectionGroup(null);
1261
1262     if (representGroup)
1263     {
1264       ap.av.hideRepSequences(sequence, sg);
1265
1266       return;
1267     }
1268
1269     int gsize = sg.getSize();
1270     SequenceI[] hseqs;
1271
1272     hseqs = new SequenceI[gsize];
1273
1274     int index = 0;
1275     for (int i = 0; i < gsize; i++)
1276     {
1277       hseqs[index++] = sg.getSequenceAt(i);
1278     }
1279
1280     ap.av.hideSequence(hseqs);
1281   }
1282
1283   public void copy_actionPerformed()
1284   {
1285     ap.alignFrame.copy_actionPerformed(null);
1286   }
1287
1288   public void cut_actionPerformed()
1289   {
1290     ap.alignFrame.cut_actionPerformed(null);
1291   }
1292
1293   void changeCase(ActionEvent e)
1294   {
1295     Object source = e.getSource();
1296     SequenceGroup sg = ap.av.getSelectionGroup();
1297
1298     if (sg != null)
1299     {
1300       int[][] startEnd = ap.av.getVisibleRegionBoundaries(
1301           sg.getStartRes(), sg.getEndRes() + 1);
1302
1303       String description;
1304       int caseChange;
1305
1306       if (source == toggle)
1307       {
1308         description = "Toggle Case";
1309         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1310       }
1311       else if (source == upperCase)
1312       {
1313         description = "To Upper Case";
1314         caseChange = ChangeCaseCommand.TO_UPPER;
1315       }
1316       else
1317       {
1318         description = "To Lower Case";
1319         caseChange = ChangeCaseCommand.TO_LOWER;
1320       }
1321
1322       ChangeCaseCommand caseCommand = new ChangeCaseCommand(
1323           description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1324           startEnd, caseChange
1325           );
1326
1327       ap.alignFrame.addHistoryItem(caseCommand);
1328
1329       ap.av.firePropertyChange("alignment", null,
1330                                ap.av.getAlignment().getSequences());
1331
1332     }
1333   }
1334
1335   public void outputText_actionPerformed(ActionEvent e)
1336   {
1337     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1338     cap.setForInput(null);
1339     Desktop.addInternalFrame(cap,
1340                              "Alignment output - " + e.getActionCommand(), 600,
1341                              500);
1342
1343     String[] omitHidden = null;
1344
1345     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
1346     SequenceGroup sg = ap.av.getSelectionGroup();
1347     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1348     omitHidden = ap.av.getViewAsString(true);
1349     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1350     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1351     for (int i=0; i<nala.length; i++)
1352     {
1353       AlignmentAnnotation na =nala[i];
1354       oal.addAnnotation(na);
1355     }
1356     cap.setText(new FormatAdapter().formatSequences(
1357             e.getActionCommand(),
1358             oal,
1359             omitHidden, csel, sg));
1360     oal=null;
1361   }
1362
1363   public void pdbFromFile_actionPerformed()
1364   {
1365     jalview.io.JalviewFileChooser chooser
1366         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1367                                             getProperty(
1368                                                 "LAST_DIRECTORY"));
1369     chooser.setFileView(new jalview.io.JalviewFileView());
1370     chooser.setDialogTitle("Select a PDB file");
1371     chooser.setToolTipText("Load a PDB file");
1372
1373     int value = chooser.showOpenDialog(null);
1374
1375     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1376     {
1377       PDBEntry entry = new PDBEntry();
1378       String choice = chooser.getSelectedFile().getPath();
1379       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1380       try
1381       {
1382         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1383             jalview.io.AppletFormatAdapter.FILE);
1384
1385         if (pdbfile.id == null)
1386         {
1387           String reply = JOptionPane.showInternalInputDialog(
1388               Desktop.desktop,
1389               "Couldn't find a PDB id in the file supplied."
1390               + "Please enter an Id to identify this structure.",
1391               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1392           if (reply == null)
1393           {
1394             return;
1395           }
1396
1397           entry.setId(reply);
1398         }
1399         else
1400         {
1401           entry.setId(pdbfile.id);
1402         }
1403       }
1404       catch (java.io.IOException ex)
1405       {
1406         ex.printStackTrace();
1407       }
1408
1409       entry.setFile(choice);
1410       sequence.getDatasetSequence().addPDBId(entry);
1411     }
1412
1413   }
1414
1415   public void enterPDB_actionPerformed()
1416   {
1417     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1418         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1419
1420     if (id != null && id.length() > 0)
1421     {
1422       PDBEntry entry = new PDBEntry();
1423       entry.setId(id.toUpperCase());
1424       sequence.getDatasetSequence()
1425           .addPDBId(entry);
1426     }
1427   }
1428
1429   public void discoverPDB_actionPerformed()
1430   {
1431     SequenceI[] sequences =
1432          ap.av.selectionGroup == null ?
1433            new Sequence[]{sequence}
1434          : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
1435
1436     new jalview.ws.DBRefFetcher(sequences,
1437         ap.alignFrame).fetchDBRefs(false);
1438   }
1439
1440   public void sequenceFeature_actionPerformed()
1441   {
1442     SequenceGroup sg = ap.av.getSelectionGroup();
1443     if (sg == null)
1444     {
1445       return;
1446     }
1447
1448     int gSize = sg.getSize();
1449     SequenceI[] seqs = new SequenceI[gSize];
1450     SequenceFeature[] features = new SequenceFeature[gSize];
1451
1452     for (int i = 0; i < gSize; i++)
1453     {
1454       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1455       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1456       int end = sg.findEndRes(sg.getSequenceAt(i));
1457       features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
1458     }
1459
1460     if (ap.seqPanel.seqCanvas.getFeatureRenderer()
1461         .amendFeatures(seqs, features, true, ap))
1462     {
1463       ap.alignFrame.showSeqFeatures.setSelected(true);
1464       ap.av.setShowSequenceFeatures(true);
1465       ap.highlightSearchResults(null);
1466     }
1467   }
1468
1469   public void textColour_actionPerformed()
1470   {
1471     SequenceGroup sg = getGroup();
1472     if (sg != null)
1473     {
1474       new TextColourChooser().chooseColour(ap, sg);
1475     }
1476   }
1477
1478   public void colourByStructure(String pdbid)
1479   {
1480     Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
1481         .colourSequenceFromStructure(sequence, pdbid);
1482
1483     AlignmentAnnotation an = new AlignmentAnnotation(
1484       "Structure", "Coloured by "+pdbid, anots);
1485
1486     ap.av.alignment.addAnnotation(an);
1487     an.createSequenceMapping(sequence, 0, true);
1488     //an.adjustForAlignment();
1489     ap.av.alignment.setAnnotationIndex(an,0);
1490
1491     ap.adjustAnnotationHeight();
1492
1493     sequence.addAlignmentAnnotation(an);
1494
1495     }
1496
1497   public void editSequence_actionPerformed(ActionEvent actionEvent)
1498   {
1499       SequenceGroup sg = ap.av.getSelectionGroup();
1500
1501       if(sg!=null)
1502       {
1503         if (sequence == null)
1504           sequence = (Sequence) sg.getSequenceAt(0);
1505
1506         EditNameDialog dialog = new EditNameDialog(
1507             sequence.getSequenceAsString(
1508                 sg.getStartRes(),
1509                 sg.getEndRes() + 1),
1510             null,
1511             "Edit Sequence ",
1512             null,
1513             "Edit Sequence");
1514
1515         if (dialog.accept)
1516         {
1517           EditCommand editCommand = new EditCommand(
1518               "Edit Sequences", EditCommand.REPLACE,
1519               dialog.getName().replace(' ', ap.av.getGapCharacter()),
1520               sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1521               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
1522               );
1523
1524           ap.alignFrame.addHistoryItem(editCommand);
1525
1526           ap.av.firePropertyChange("alignment", null,
1527                                    ap.av.getAlignment().getSequences());
1528         }
1529       }
1530   }
1531
1532
1533 }