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