src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
   3  * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26
  27 import MCview.*;
  28 import jalview.analysis.*;
  29 import jalview.commands.*;
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.schemes.*;
  33 import jalview.util.UrlLink;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class PopupMenu extends JPopupMenu
  42 {
  43   JMenu groupMenu = new JMenu();
  44
  45   JMenuItem groupName = new JMenuItem();
  46
  47   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  48
  49   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  50
  51   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  52
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54
  55   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  56
  57   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  58
  59   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  60
  61   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  62
  63   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  64
  65   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  66
  67   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  68
  69   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  70
  71   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  72
  73   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  74
  75   AlignmentPanel ap;
  76
  77   JMenu sequenceMenu = new JMenu();
  78
  79   JMenuItem sequenceName = new JMenuItem();
  80
  81   Sequence sequence;
  82
  83   JMenuItem unGroupMenuItem = new JMenuItem();
  84
  85   JMenuItem outline = new JMenuItem();
  86
  87   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  88
  89   JMenu colourMenu = new JMenu();
  90
  91   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  92
  93   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  94
  95   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  96
  97   JMenu editMenu = new JMenu();
  98
  99   JMenuItem cut = new JMenuItem();
 100
 101   JMenuItem copy = new JMenuItem();
 102
 103   JMenuItem upperCase = new JMenuItem();
 104
 105   JMenuItem lowerCase = new JMenuItem();
 106
 107   JMenuItem toggle = new JMenuItem();
 108
 109   JMenu pdbMenu = new JMenu();
 110
 111   JMenuItem pdbFromFile = new JMenuItem();
 112
 113   JMenuItem enterPDB = new JMenuItem();
 114
 115   JMenuItem discoverPDB = new JMenuItem();
 116
 117   JMenu outputMenu = new JMenu();
 118
 119   JMenuItem sequenceFeature = new JMenuItem();
 120
 121   JMenuItem textColour = new JMenuItem();
 122
 123   JMenu jMenu1 = new JMenu();
 124
 125   JMenu structureMenu = new JMenu();
 126
 127   JMenu viewStructureMenu = new JMenu();
 128
 129   // JMenu colStructureMenu = new JMenu();
 130   JMenuItem editSequence = new JMenuItem();
 131
 132   // JMenuItem annotationMenuItem = new JMenuItem();
 133
 134   /**
 135    * Creates a new PopupMenu object.
 136    *
 137    * @param ap
 138    *                DOCUMENT ME!
 139    * @param seq
 140    *                DOCUMENT ME!
 141    */
 142   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 143   {
 144     // /////////////////////////////////////////////////////////
 145     // If this is activated from the sequence panel, the user may want to
 146     // edit or annotate a particular residue. Therefore display the residue menu
 147     //
 148     // If from the IDPanel, we must display the sequence menu
 149     // ////////////////////////////////////////////////////////
 150     this.ap = ap;
 151     sequence = seq;
 152
 153     ButtonGroup colours = new ButtonGroup();
 154     colours.add(noColourmenuItem);
 155     colours.add(clustalColour);
 156     colours.add(zappoColour);
 157     colours.add(taylorColour);
 158     colours.add(hydrophobicityColour);
 159     colours.add(helixColour);
 160     colours.add(strandColour);
 161     colours.add(turnColour);
 162     colours.add(buriedColour);
 163     colours.add(abovePIDColour);
 164     colours.add(userDefinedColour);
 165     colours.add(PIDColour);
 166     colours.add(BLOSUM62Colour);
 167
 168     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 169     {
 170       JMenuItem item = new JMenuItem(
 171               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 172
 173       item.addActionListener(new java.awt.event.ActionListener()
 174       {
 175         public void actionPerformed(ActionEvent e)
 176         {
 177           outputText_actionPerformed(e);
 178         }
 179       });
 180
 181       outputMenu.add(item);
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception e)
 188     {
 189       e.printStackTrace();
 190     }
 191
 192     if (seq != null)
 193     {
 194       sequenceMenu.setText(sequence.getName());
 195
 196       JMenuItem menuItem;
 197       if (seq.getDatasetSequence().getPDBId() != null
 198               && seq.getDatasetSequence().getPDBId().size() > 0)
 199       {
 200         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 201                 .elements();
 202
 203         while (e.hasMoreElements())
 204         {
 205           final PDBEntry pdb = (PDBEntry) e.nextElement();
 206
 207           menuItem = new JMenuItem();
 208           menuItem.setText(pdb.getId());
 209           menuItem.addActionListener(new java.awt.event.ActionListener()
 210           {
 211             public void actionPerformed(ActionEvent e)
 212             {
 213               Vector seqs = new Vector();
 214               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 215               {
 216                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 217                         .getDatasetSequence().getPDBId();
 218                 if (pdbs == null)
 219                   continue;
 220
 221                 for (int p = 0; p < pdbs.size(); p++)
 222                 {
 223                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 224                   if (p1.getId().equals(pdb.getId()))
 225                   {
 226                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 227                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 228
 229                     continue;
 230                   }
 231                 }
 232               }
 233
 234               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 235               seqs.toArray(seqs2);
 236
 237               new AppJmol(pdb, seqs2, null, ap);
 238               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 239             }
 240           });
 241           viewStructureMenu.add(menuItem);
 242
 243           /*
 244            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 245            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 246            * public void actionPerformed(ActionEvent e) {
 247            * colourByStructure(pdb.getId()); } });
 248            * colStructureMenu.add(menuItem);
 249            */
 250         }
 251       }
 252       else
 253       {
 254         structureMenu.remove(viewStructureMenu);
 255         // structureMenu.remove(colStructureMenu);
 256       }
 257
 258       menuItem = new JMenuItem("Hide Sequences");
 259       menuItem.addActionListener(new java.awt.event.ActionListener()
 260       {
 261         public void actionPerformed(ActionEvent e)
 262         {
 263           hideSequences(false);
 264         }
 265       });
 266       add(menuItem);
 267
 268       if (ap.av.getSelectionGroup() != null
 269               && ap.av.getSelectionGroup().getSize() > 1)
 270       {
 271         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 272         menuItem.addActionListener(new java.awt.event.ActionListener()
 273         {
 274           public void actionPerformed(ActionEvent e)
 275           {
 276             hideSequences(true);
 277           }
 278         });
 279         sequenceMenu.add(menuItem);
 280       }
 281
 282       if (ap.av.hasHiddenRows)
 283       {
 284         final int index = ap.av.alignment.findIndex(seq);
 285
 286         if (ap.av.adjustForHiddenSeqs(index)
 287                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 288         {
 289           menuItem = new JMenuItem("Reveal Sequences");
 290           menuItem.addActionListener(new ActionListener()
 291           {
 292             public void actionPerformed(ActionEvent e)
 293             {
 294               ap.av.showSequence(index);
 295               if (ap.overviewPanel != null)
 296               {
 297                 ap.overviewPanel.updateOverviewImage();
 298               }
 299             }
 300           });
 301           add(menuItem);
 302         }
 303
 304         menuItem = new JMenuItem("Reveal All");
 305         menuItem.addActionListener(new ActionListener()
 306         {
 307           public void actionPerformed(ActionEvent e)
 308           {
 309             ap.av.showAllHiddenSeqs();
 310             if (ap.overviewPanel != null)
 311             {
 312               ap.overviewPanel.updateOverviewImage();
 313             }
 314           }
 315         });
 316
 317         add(menuItem);
 318       }
 319
 320     }
 321
 322     SequenceGroup sg = ap.av.getSelectionGroup();
 323
 324     if (sg != null)
 325     {
 326       groupName.setText(sg.getName());
 327
 328       if (sg.cs instanceof ZappoColourScheme)
 329       {
 330         zappoColour.setSelected(true);
 331       }
 332       else if (sg.cs instanceof TaylorColourScheme)
 333       {
 334         taylorColour.setSelected(true);
 335       }
 336       else if (sg.cs instanceof PIDColourScheme)
 337       {
 338         PIDColour.setSelected(true);
 339       }
 340       else if (sg.cs instanceof Blosum62ColourScheme)
 341       {
 342         BLOSUM62Colour.setSelected(true);
 343       }
 344       else if (sg.cs instanceof UserColourScheme)
 345       {
 346         userDefinedColour.setSelected(true);
 347       }
 348       else if (sg.cs instanceof HydrophobicColourScheme)
 349       {
 350         hydrophobicityColour.setSelected(true);
 351       }
 352       else if (sg.cs instanceof HelixColourScheme)
 353       {
 354         helixColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof StrandColourScheme)
 357       {
 358         strandColour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof TurnColourScheme)
 361       {
 362         turnColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof BuriedColourScheme)
 365       {
 366         buriedColour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof ClustalxColourScheme)
 369       {
 370         clustalColour.setSelected(true);
 371       }
 372       else
 373       {
 374         noColourmenuItem.setSelected(true);
 375       }
 376
 377       if (sg.cs != null && sg.cs.conservationApplied())
 378       {
 379         conservationMenuItem.setSelected(true);
 380       }
 381
 382       showText.setSelected(sg.getDisplayText());
 383       showColourText.setSelected(sg.getColourText());
 384       showBoxes.setSelected(sg.getDisplayBoxes());
 385     }
 386     else
 387     {
 388       groupMenu.setVisible(false);
 389       editMenu.setVisible(false);
 390     }
 391
 392     if (!ap.av.alignment.getGroups().contains(sg))
 393     {
 394       unGroupMenuItem.setVisible(false);
 395     }
 396
 397     if (seq == null)
 398     {
 399       sequenceMenu.setVisible(false);
 400       structureMenu.setVisible(false);
 401     }
 402
 403     if (links != null && links.size() > 0)
 404     {
 405       JMenu linkMenu = new JMenu("Link");
 406
 407       for (int i = 0; i < links.size(); i++)
 408       {
 409         String link = links.elementAt(i).toString();
 410         UrlLink urlLink = null;
 411         try
 412         {
 413           urlLink = new UrlLink(link);
 414         } catch (Exception foo)
 415         {
 416           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 417                   + "'", foo);
 418           continue;
 419         }
 420         ;
 421         if (!urlLink.isValid())
 422         {
 423           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 424           continue;
 425         }
 426         final String label = urlLink.getLabel();
 427         if (urlLink.isDynamic())
 428         {
 429
 430           // collect matching db-refs
 431           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 432                   .getDBRef(), new String[]
 433           { urlLink.getTarget() });
 434           // collect id string too
 435           String id = seq.getName();
 436           String descr = seq.getDescription();
 437           if (descr!=null && descr.length()<1)
 438           {
 439             descr = null;
 440           }
 441
 442           if (dbr != null)
 443           {
 444             for (int r = 0; r < dbr.length; r++)
 445             {
 446               if (id != null && dbr[r].getAccessionId().equals(id))
 447               {
 448                 // suppress duplicate link creation for the bare sequence ID
 449                 // string with this link
 450                 id = null;
 451               }
 452               // create Bare ID link for this RUL
 453               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 454                       true);
 455               if (urls != null)
 456               {
 457                 for (int u = 0; u < urls.length; u += 2)
 458                 {
 459                   addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 460                 }
 461               }
 462             }
 463           }
 464           if (id != null)
 465           {
 466             // create Bare ID link for this RUL
 467             String[] urls = urlLink.makeUrls(id, true);
 468             if (urls != null)
 469             {
 470               for (int u = 0; u < urls.length; u += 2)
 471               {
 472                 addshowLink(linkMenu, label, urls[u + 1]);
 473               }
 474             }
 475           }
 476           // hard-disable construction of URLs from regexes that match the description
 477           // TODO: introduce a Cache preferences option to dis/en/able URl generation from description
 478 //          if (descr != null)
 479 //          {
 480 //            // create link for this URL from description where regex matches
 481 //            String[] urls = urlLink.makeUrls(descr, false);
 482 //            if (urls != null)
 483 //            {
 484 //              for (int u = 0; u < urls.length; u += 2)
 485 //              {
 486 //                addshowLink(linkMenu, label, urls[u + 1]);
 487 //              }
 488 //            }
 489 //          }
 490         }
 491         else
 492         {
 493           // Add a non-dynamic link
 494           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 495         }
 496       }
 497       if (sequence != null)
 498       {
 499         sequenceMenu.add(linkMenu);
 500       }
 501       else
 502       {
 503         add(linkMenu);
 504       }
 505     }
 506   }
 507
 508   /**
 509    * add a show URL menu item to the given linkMenu
 510    *
 511    * @param linkMenu
 512    * @param label -
 513    *                menu label string
 514    * @param url -
 515    *                url to open
 516    */
 517   private void addshowLink(JMenu linkMenu, String label, final String url)
 518   {
 519     JMenuItem item = new JMenuItem(label);
 520     item.setToolTipText("open URL: " + url);
 521     item.addActionListener(new java.awt.event.ActionListener()
 522     {
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         new Thread(new Runnable()
 526         {
 527
 528           public void run()
 529           {
 530             showLink(url);
 531           }
 532
 533         }).start();
 534       }
 535     });
 536
 537     linkMenu.add(item);
 538   }
 539
 540   /**
 541    * DOCUMENT ME!
 542    *
 543    * @throws Exception
 544    *                 DOCUMENT ME!
 545    */
 546   private void jbInit() throws Exception
 547   {
 548     groupMenu.setText("Group");
 549     groupMenu.setText("Selection");
 550     groupName.setText("Name");
 551     groupName.addActionListener(new java.awt.event.ActionListener()
 552     {
 553       public void actionPerformed(ActionEvent e)
 554       {
 555         groupName_actionPerformed();
 556       }
 557     });
 558     sequenceMenu.setText("Sequence");
 559     sequenceName.setText("Edit Name/Description");
 560     sequenceName.addActionListener(new java.awt.event.ActionListener()
 561     {
 562       public void actionPerformed(ActionEvent e)
 563       {
 564         sequenceName_actionPerformed();
 565       }
 566     });
 567     PIDColour.setFocusPainted(false);
 568     unGroupMenuItem.setText("Remove Group");
 569     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 570     {
 571       public void actionPerformed(ActionEvent e)
 572       {
 573         unGroupMenuItem_actionPerformed();
 574       }
 575     });
 576
 577     outline.setText("Border colour");
 578     outline.addActionListener(new java.awt.event.ActionListener()
 579     {
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         outline_actionPerformed();
 583       }
 584     });
 585     nucleotideMenuItem.setText("Nucleotide");
 586     nucleotideMenuItem.addActionListener(new ActionListener()
 587     {
 588       public void actionPerformed(ActionEvent e)
 589       {
 590         nucleotideMenuItem_actionPerformed();
 591       }
 592     });
 593     colourMenu.setText("Group Colour");
 594     showBoxes.setText("Boxes");
 595     showBoxes.setState(true);
 596     showBoxes.addActionListener(new ActionListener()
 597     {
 598       public void actionPerformed(ActionEvent e)
 599       {
 600         showBoxes_actionPerformed();
 601       }
 602     });
 603     showText.setText("Text");
 604     showText.setState(true);
 605     showText.addActionListener(new ActionListener()
 606     {
 607       public void actionPerformed(ActionEvent e)
 608       {
 609         showText_actionPerformed();
 610       }
 611     });
 612     showColourText.setText("Colour Text");
 613     showColourText.addActionListener(new ActionListener()
 614     {
 615       public void actionPerformed(ActionEvent e)
 616       {
 617         showColourText_actionPerformed();
 618       }
 619     });
 620     editMenu.setText("Edit");
 621     cut.setText("Cut");
 622     cut.addActionListener(new ActionListener()
 623     {
 624       public void actionPerformed(ActionEvent e)
 625       {
 626         cut_actionPerformed();
 627       }
 628     });
 629     upperCase.setText("To Upper Case");
 630     upperCase.addActionListener(new ActionListener()
 631     {
 632       public void actionPerformed(ActionEvent e)
 633       {
 634         changeCase(e);
 635       }
 636     });
 637     copy.setText("Copy");
 638     copy.addActionListener(new ActionListener()
 639     {
 640       public void actionPerformed(ActionEvent e)
 641       {
 642         copy_actionPerformed();
 643       }
 644     });
 645     lowerCase.setText("To Lower Case");
 646     lowerCase.addActionListener(new ActionListener()
 647     {
 648       public void actionPerformed(ActionEvent e)
 649       {
 650         changeCase(e);
 651       }
 652     });
 653     toggle.setText("Toggle Case");
 654     toggle.addActionListener(new ActionListener()
 655     {
 656       public void actionPerformed(ActionEvent e)
 657       {
 658         changeCase(e);
 659       }
 660     });
 661     pdbMenu.setText("Associate Structure with Sequence");
 662     pdbFromFile.setText("From File");
 663     pdbFromFile.addActionListener(new ActionListener()
 664     {
 665       public void actionPerformed(ActionEvent e)
 666       {
 667         pdbFromFile_actionPerformed();
 668       }
 669     });
 670     enterPDB.setText("Enter PDB Id");
 671     enterPDB.addActionListener(new ActionListener()
 672     {
 673       public void actionPerformed(ActionEvent e)
 674       {
 675         enterPDB_actionPerformed();
 676       }
 677     });
 678     discoverPDB.setText("Discover PDB ids");
 679     discoverPDB.addActionListener(new ActionListener()
 680     {
 681       public void actionPerformed(ActionEvent e)
 682       {
 683         discoverPDB_actionPerformed();
 684       }
 685     });
 686     outputMenu.setText("Output to Textbox...");
 687     sequenceFeature.setText("Create Sequence Feature");
 688     sequenceFeature.addActionListener(new ActionListener()
 689     {
 690       public void actionPerformed(ActionEvent e)
 691       {
 692         sequenceFeature_actionPerformed();
 693       }
 694     });
 695     textColour.setText("Text Colour");
 696     textColour.addActionListener(new ActionListener()
 697     {
 698       public void actionPerformed(ActionEvent e)
 699       {
 700         textColour_actionPerformed();
 701       }
 702     });
 703     jMenu1.setText("Group");
 704     structureMenu.setText("Structure");
 705     viewStructureMenu.setText("View Structure");
 706     // colStructureMenu.setText("Colour By Structure");
 707     editSequence.setText("Edit Sequence...");
 708     editSequence.addActionListener(new ActionListener()
 709     {
 710       public void actionPerformed(ActionEvent actionEvent)
 711       {
 712         editSequence_actionPerformed(actionEvent);
 713       }
 714     });
 715     /*
 716      * annotationMenuItem.setText("By Annotation");
 717      * annotationMenuItem.addActionListener(new ActionListener() { public void
 718      * actionPerformed(ActionEvent actionEvent) {
 719      * annotationMenuItem_actionPerformed(actionEvent); } });
 720      */
 721
 722     add(groupMenu);
 723
 724     add(sequenceMenu);
 725     this.add(structureMenu);
 726     groupMenu.add(editMenu);
 727     groupMenu.add(outputMenu);
 728     groupMenu.add(sequenceFeature);
 729     groupMenu.add(jMenu1);
 730     sequenceMenu.add(sequenceName);
 731     colourMenu.add(textColour);
 732     colourMenu.add(noColourmenuItem);
 733     colourMenu.add(clustalColour);
 734     colourMenu.add(BLOSUM62Colour);
 735     colourMenu.add(PIDColour);
 736     colourMenu.add(zappoColour);
 737     colourMenu.add(taylorColour);
 738     colourMenu.add(hydrophobicityColour);
 739     colourMenu.add(helixColour);
 740     colourMenu.add(strandColour);
 741     colourMenu.add(turnColour);
 742     colourMenu.add(buriedColour);
 743     colourMenu.add(nucleotideMenuItem);
 744     colourMenu.add(userDefinedColour);
 745
 746     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 747     {
 748       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 749               .getUserColourSchemes().keys();
 750
 751       while (userColours.hasMoreElements())
 752       {
 753         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 754         item.addActionListener(new ActionListener()
 755         {
 756           public void actionPerformed(ActionEvent evt)
 757           {
 758             userDefinedColour_actionPerformed(evt);
 759           }
 760         });
 761         colourMenu.add(item);
 762       }
 763     }
 764
 765     colourMenu.addSeparator();
 766     colourMenu.add(abovePIDColour);
 767     colourMenu.add(conservationMenuItem);
 768     // colourMenu.add(annotationMenuItem);
 769     editMenu.add(copy);
 770     editMenu.add(cut);
 771     editMenu.add(editSequence);
 772     editMenu.add(upperCase);
 773     editMenu.add(lowerCase);
 774     editMenu.add(toggle);
 775     pdbMenu.add(pdbFromFile);
 776     pdbMenu.add(enterPDB);
 777     pdbMenu.add(discoverPDB);
 778     jMenu1.add(groupName);
 779     jMenu1.add(unGroupMenuItem);
 780     jMenu1.add(colourMenu);
 781     jMenu1.add(showBoxes);
 782     jMenu1.add(showText);
 783     jMenu1.add(showColourText);
 784     jMenu1.add(outline);
 785     structureMenu.add(pdbMenu);
 786     structureMenu.add(viewStructureMenu);
 787     // structureMenu.add(colStructureMenu);
 788     noColourmenuItem.setText("None");
 789     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 790     {
 791       public void actionPerformed(ActionEvent e)
 792       {
 793         noColourmenuItem_actionPerformed();
 794       }
 795     });
 796
 797     clustalColour.setText("Clustalx colours");
 798     clustalColour.addActionListener(new java.awt.event.ActionListener()
 799     {
 800       public void actionPerformed(ActionEvent e)
 801       {
 802         clustalColour_actionPerformed();
 803       }
 804     });
 805     zappoColour.setText("Zappo");
 806     zappoColour.addActionListener(new java.awt.event.ActionListener()
 807     {
 808       public void actionPerformed(ActionEvent e)
 809       {
 810         zappoColour_actionPerformed();
 811       }
 812     });
 813     taylorColour.setText("Taylor");
 814     taylorColour.addActionListener(new java.awt.event.ActionListener()
 815     {
 816       public void actionPerformed(ActionEvent e)
 817       {
 818         taylorColour_actionPerformed();
 819       }
 820     });
 821     hydrophobicityColour.setText("Hydrophobicity");
 822     hydrophobicityColour
 823             .addActionListener(new java.awt.event.ActionListener()
 824             {
 825               public void actionPerformed(ActionEvent e)
 826               {
 827                 hydrophobicityColour_actionPerformed();
 828               }
 829             });
 830     helixColour.setText("Helix propensity");
 831     helixColour.addActionListener(new java.awt.event.ActionListener()
 832     {
 833       public void actionPerformed(ActionEvent e)
 834       {
 835         helixColour_actionPerformed();
 836       }
 837     });
 838     strandColour.setText("Strand propensity");
 839     strandColour.addActionListener(new java.awt.event.ActionListener()
 840     {
 841       public void actionPerformed(ActionEvent e)
 842       {
 843         strandColour_actionPerformed();
 844       }
 845     });
 846     turnColour.setText("Turn propensity");
 847     turnColour.addActionListener(new java.awt.event.ActionListener()
 848     {
 849       public void actionPerformed(ActionEvent e)
 850       {
 851         turnColour_actionPerformed();
 852       }
 853     });
 854     buriedColour.setText("Buried Index");
 855     buriedColour.addActionListener(new java.awt.event.ActionListener()
 856     {
 857       public void actionPerformed(ActionEvent e)
 858       {
 859         buriedColour_actionPerformed();
 860       }
 861     });
 862     abovePIDColour.setText("Above % Identity");
 863     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
 864     {
 865       public void actionPerformed(ActionEvent e)
 866       {
 867         abovePIDColour_actionPerformed();
 868       }
 869     });
 870     userDefinedColour.setText("User Defined...");
 871     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 872     {
 873       public void actionPerformed(ActionEvent e)
 874       {
 875         userDefinedColour_actionPerformed(e);
 876       }
 877     });
 878     PIDColour.setText("Percentage Identity");
 879     PIDColour.addActionListener(new java.awt.event.ActionListener()
 880     {
 881       public void actionPerformed(ActionEvent e)
 882       {
 883         PIDColour_actionPerformed();
 884       }
 885     });
 886     BLOSUM62Colour.setText("BLOSUM62");
 887     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 888     {
 889       public void actionPerformed(ActionEvent e)
 890       {
 891         BLOSUM62Colour_actionPerformed();
 892       }
 893     });
 894     conservationMenuItem.setText("Conservation");
 895     conservationMenuItem
 896             .addActionListener(new java.awt.event.ActionListener()
 897             {
 898               public void actionPerformed(ActionEvent e)
 899               {
 900                 conservationMenuItem_actionPerformed();
 901               }
 902             });
 903   }
 904
 905   /**
 906    * DOCUMENT ME!
 907    */
 908   void refresh()
 909   {
 910     ap.paintAlignment(true);
 911
 912     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
 913   }
 914
 915   /**
 916    * DOCUMENT ME!
 917    *
 918    * @param e
 919    *                DOCUMENT ME!
 920    */
 921   protected void clustalColour_actionPerformed()
 922   {
 923     SequenceGroup sg = getGroup();
 924     sg.cs = new ClustalxColourScheme(sg
 925             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
 926             .getWidth());
 927     refresh();
 928   }
 929
 930   /**
 931    * DOCUMENT ME!
 932    *
 933    * @param e
 934    *                DOCUMENT ME!
 935    */
 936   protected void zappoColour_actionPerformed()
 937   {
 938     getGroup().cs = new ZappoColourScheme();
 939     refresh();
 940   }
 941
 942   /**
 943    * DOCUMENT ME!
 944    *
 945    * @param e
 946    *                DOCUMENT ME!
 947    */
 948   protected void taylorColour_actionPerformed()
 949   {
 950     getGroup().cs = new TaylorColourScheme();
 951     refresh();
 952   }
 953
 954   /**
 955    * DOCUMENT ME!
 956    *
 957    * @param e
 958    *                DOCUMENT ME!
 959    */
 960   protected void hydrophobicityColour_actionPerformed()
 961   {
 962     getGroup().cs = new HydrophobicColourScheme();
 963     refresh();
 964   }
 965
 966   /**
 967    * DOCUMENT ME!
 968    *
 969    * @param e
 970    *                DOCUMENT ME!
 971    */
 972   protected void helixColour_actionPerformed()
 973   {
 974     getGroup().cs = new HelixColourScheme();
 975     refresh();
 976   }
 977
 978   /**
 979    * DOCUMENT ME!
 980    *
 981    * @param e
 982    *                DOCUMENT ME!
 983    */
 984   protected void strandColour_actionPerformed()
 985   {
 986     getGroup().cs = new StrandColourScheme();
 987     refresh();
 988   }
 989
 990   /**
 991    * DOCUMENT ME!
 992    *
 993    * @param e
 994    *                DOCUMENT ME!
 995    */
 996   protected void turnColour_actionPerformed()
 997   {
 998     getGroup().cs = new TurnColourScheme();
 999     refresh();
1000   }
1001
1002   /**
1003    * DOCUMENT ME!
1004    *
1005    * @param e
1006    *                DOCUMENT ME!
1007    */
1008   protected void buriedColour_actionPerformed()
1009   {
1010     getGroup().cs = new BuriedColourScheme();
1011     refresh();
1012   }
1013
1014   /**
1015    * DOCUMENT ME!
1016    *
1017    * @param e
1018    *                DOCUMENT ME!
1019    */
1020   public void nucleotideMenuItem_actionPerformed()
1021   {
1022     getGroup().cs = new NucleotideColourScheme();
1023     refresh();
1024   }
1025
1026   /**
1027    * DOCUMENT ME!
1028    *
1029    * @param e
1030    *                DOCUMENT ME!
1031    */
1032   protected void abovePIDColour_actionPerformed()
1033   {
1034     SequenceGroup sg = getGroup();
1035     if (sg.cs == null)
1036     {
1037       return;
1038     }
1039
1040     if (abovePIDColour.isSelected())
1041     {
1042       sg.cs.setConsensus(AAFrequency.calculate(sg
1043               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1044               .getEndRes() + 1));
1045
1046       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1047               .getName());
1048
1049       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1050
1051       SliderPanel.showPIDSlider();
1052     }
1053     else
1054     // remove PIDColouring
1055     {
1056       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1057     }
1058
1059     refresh();
1060   }
1061
1062   /**
1063    * DOCUMENT ME!
1064    *
1065    * @param e
1066    *                DOCUMENT ME!
1067    */
1068   protected void userDefinedColour_actionPerformed(ActionEvent e)
1069   {
1070     SequenceGroup sg = getGroup();
1071
1072     if (e.getActionCommand().equals("User Defined..."))
1073     {
1074       new UserDefinedColours(ap, sg);
1075     }
1076     else
1077     {
1078       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1079               .getUserColourSchemes().get(e.getActionCommand());
1080
1081       sg.cs = udc;
1082     }
1083     refresh();
1084   }
1085
1086   /**
1087    * DOCUMENT ME!
1088    *
1089    * @param e
1090    *                DOCUMENT ME!
1091    */
1092   protected void PIDColour_actionPerformed()
1093   {
1094     SequenceGroup sg = getGroup();
1095     sg.cs = new PIDColourScheme();
1096     sg.cs.setConsensus(AAFrequency.calculate(sg
1097             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1098             .getEndRes() + 1));
1099     refresh();
1100   }
1101
1102   /**
1103    * DOCUMENT ME!
1104    *
1105    * @param e
1106    *                DOCUMENT ME!
1107    */
1108   protected void BLOSUM62Colour_actionPerformed()
1109   {
1110     SequenceGroup sg = getGroup();
1111
1112     sg.cs = new Blosum62ColourScheme();
1113
1114     sg.cs.setConsensus(AAFrequency.calculate(sg
1115             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1116             .getEndRes() + 1));
1117
1118     refresh();
1119   }
1120
1121   /**
1122    * DOCUMENT ME!
1123    *
1124    * @param e
1125    *                DOCUMENT ME!
1126    */
1127   protected void noColourmenuItem_actionPerformed()
1128   {
1129     getGroup().cs = null;
1130     refresh();
1131   }
1132
1133   /**
1134    * DOCUMENT ME!
1135    *
1136    * @param e
1137    *                DOCUMENT ME!
1138    */
1139   protected void conservationMenuItem_actionPerformed()
1140   {
1141     SequenceGroup sg = getGroup();
1142     if (sg.cs == null)
1143     {
1144       return;
1145     }
1146
1147     if (conservationMenuItem.isSelected())
1148     {
1149       Conservation c = new Conservation("Group",
1150               ResidueProperties.propHash, 3, sg
1151                       .getSequences(ap.av.hiddenRepSequences), sg
1152                       .getStartRes(), sg.getEndRes() + 1);
1153
1154       c.calculate();
1155       c.verdict(false, ap.av.ConsPercGaps);
1156
1157       sg.cs.setConservation(c);
1158
1159       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1160       SliderPanel.showConservationSlider();
1161     }
1162     else
1163     // remove ConservationColouring
1164     {
1165       sg.cs.setConservation(null);
1166     }
1167
1168     refresh();
1169   }
1170
1171   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1172   {
1173     SequenceGroup sg = getGroup();
1174     if (sg == null)
1175     {
1176       return;
1177     }
1178
1179     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1180             .getAnnotation()[0], null,
1181             AnnotationColourGradient.NO_THRESHOLD);
1182
1183     acg.predefinedColours = true;
1184     sg.cs = acg;
1185
1186     refresh();
1187   }
1188
1189   /**
1190    * DOCUMENT ME!
1191    *
1192    * @param e
1193    *                DOCUMENT ME!
1194    */
1195   protected void groupName_actionPerformed()
1196   {
1197
1198     SequenceGroup sg = getGroup();
1199     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1200             .getDescription(), "       Group Name ", "Group Description ",
1201             "Edit Group Name/Description");
1202
1203     if (!dialog.accept)
1204     {
1205       return;
1206     }
1207
1208     sg.setName(dialog.getName());
1209     sg.setDescription(dialog.getDescription());
1210   }
1211
1212   /**
1213    * DOCUMENT ME!
1214    *
1215    * @return DOCUMENT ME!
1216    */
1217   SequenceGroup getGroup()
1218   {
1219     SequenceGroup sg = ap.av.getSelectionGroup();
1220     // this method won't add a new group if it already exists
1221     if (sg != null)
1222     {
1223       ap.av.alignment.addGroup(sg);
1224     }
1225
1226     return sg;
1227   }
1228
1229   /**
1230    * DOCUMENT ME!
1231    *
1232    * @param e
1233    *                DOCUMENT ME!
1234    */
1235   void sequenceName_actionPerformed()
1236   {
1237     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1238             .getDescription(), "       Sequence Name ",
1239             "Sequence Description ", "Edit Sequence Name/Description");
1240
1241     if (!dialog.accept)
1242     {
1243       return;
1244     }
1245
1246     if (dialog.getName() != null)
1247     {
1248       if (dialog.getName().indexOf(" ") > -1)
1249       {
1250         JOptionPane.showMessageDialog(ap,
1251                 "Spaces have been converted to \"_\"",
1252                 "No spaces allowed in Sequence Name",
1253                 JOptionPane.WARNING_MESSAGE);
1254       }
1255
1256       sequence.setName(dialog.getName().replace(' ', '_'));
1257       ap.paintAlignment(false);
1258     }
1259
1260     sequence.setDescription(dialog.getDescription());
1261
1262     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1263             .getSequences());
1264
1265   }
1266
1267   /**
1268    * DOCUMENT ME!
1269    *
1270    * @param e
1271    *                DOCUMENT ME!
1272    */
1273   void unGroupMenuItem_actionPerformed()
1274   {
1275     SequenceGroup sg = ap.av.getSelectionGroup();
1276     ap.av.alignment.deleteGroup(sg);
1277     ap.av.setSelectionGroup(null);
1278     refresh();
1279   }
1280
1281   /**
1282    * DOCUMENT ME!
1283    *
1284    * @param e
1285    *                DOCUMENT ME!
1286    */
1287   protected void outline_actionPerformed()
1288   {
1289     SequenceGroup sg = getGroup();
1290     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1291             Color.BLUE);
1292
1293     if (col != null)
1294     {
1295       sg.setOutlineColour(col);
1296     }
1297
1298     refresh();
1299   }
1300
1301   /**
1302    * DOCUMENT ME!
1303    *
1304    * @param e
1305    *                DOCUMENT ME!
1306    */
1307   public void showBoxes_actionPerformed()
1308   {
1309     getGroup().setDisplayBoxes(showBoxes.isSelected());
1310     refresh();
1311   }
1312
1313   /**
1314    * DOCUMENT ME!
1315    *
1316    * @param e
1317    *                DOCUMENT ME!
1318    */
1319   public void showText_actionPerformed()
1320   {
1321     getGroup().setDisplayText(showText.isSelected());
1322     refresh();
1323   }
1324
1325   /**
1326    * DOCUMENT ME!
1327    *
1328    * @param e
1329    *                DOCUMENT ME!
1330    */
1331   public void showColourText_actionPerformed()
1332   {
1333     getGroup().setColourText(showColourText.isSelected());
1334     refresh();
1335   }
1336
1337   public void showLink(String url)
1338   {
1339     try
1340     {
1341       jalview.util.BrowserLauncher.openURL(url);
1342     } catch (Exception ex)
1343     {
1344       JOptionPane
1345               .showInternalMessageDialog(
1346                       Desktop.desktop,
1347                       "Unixers: Couldn't find default web browser."
1348                               + "\nAdd the full path to your browser in Preferences.",
1349                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1350
1351       ex.printStackTrace();
1352     }
1353   }
1354
1355   void hideSequences(boolean representGroup)
1356   {
1357     SequenceGroup sg = ap.av.getSelectionGroup();
1358     if (sg == null || sg.getSize() < 1)
1359     {
1360       ap.av.hideSequence(new SequenceI[]
1361       { sequence });
1362       return;
1363     }
1364
1365     ap.av.setSelectionGroup(null);
1366
1367     if (representGroup)
1368     {
1369       ap.av.hideRepSequences(sequence, sg);
1370
1371       return;
1372     }
1373
1374     int gsize = sg.getSize();
1375     SequenceI[] hseqs;
1376
1377     hseqs = new SequenceI[gsize];
1378
1379     int index = 0;
1380     for (int i = 0; i < gsize; i++)
1381     {
1382       hseqs[index++] = sg.getSequenceAt(i);
1383     }
1384
1385     ap.av.hideSequence(hseqs);
1386   }
1387
1388   public void copy_actionPerformed()
1389   {
1390     ap.alignFrame.copy_actionPerformed(null);
1391   }
1392
1393   public void cut_actionPerformed()
1394   {
1395     ap.alignFrame.cut_actionPerformed(null);
1396   }
1397
1398   void changeCase(ActionEvent e)
1399   {
1400     Object source = e.getSource();
1401     SequenceGroup sg = ap.av.getSelectionGroup();
1402
1403     if (sg != null)
1404     {
1405       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1406               sg.getEndRes() + 1);
1407
1408       String description;
1409       int caseChange;
1410
1411       if (source == toggle)
1412       {
1413         description = "Toggle Case";
1414         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1415       }
1416       else if (source == upperCase)
1417       {
1418         description = "To Upper Case";
1419         caseChange = ChangeCaseCommand.TO_UPPER;
1420       }
1421       else
1422       {
1423         description = "To Lower Case";
1424         caseChange = ChangeCaseCommand.TO_LOWER;
1425       }
1426
1427       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1428               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1429               caseChange);
1430
1431       ap.alignFrame.addHistoryItem(caseCommand);
1432
1433       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1434               .getSequences());
1435
1436     }
1437   }
1438
1439   public void outputText_actionPerformed(ActionEvent e)
1440   {
1441     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1442     cap.setForInput(null);
1443     Desktop.addInternalFrame(cap, "Alignment output - "
1444             + e.getActionCommand(), 600, 500);
1445
1446     String[] omitHidden = null;
1447
1448     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1449                                             // or we simply trust the user wants
1450                                             // wysiwig behaviour
1451     SequenceGroup sg = ap.av.getSelectionGroup();
1452     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1453     omitHidden = ap.av.getViewAsString(true);
1454     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1455     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1456     for (int i = 0; i < nala.length; i++)
1457     {
1458       AlignmentAnnotation na = nala[i];
1459       oal.addAnnotation(na);
1460     }
1461     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1462             oal, omitHidden, csel, sg));
1463     oal = null;
1464   }
1465
1466   public void pdbFromFile_actionPerformed()
1467   {
1468     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1469             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1470     chooser.setFileView(new jalview.io.JalviewFileView());
1471     chooser.setDialogTitle("Select a PDB file");
1472     chooser.setToolTipText("Load a PDB file");
1473
1474     int value = chooser.showOpenDialog(null);
1475
1476     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1477     {
1478       PDBEntry entry = new PDBEntry();
1479       String choice = chooser.getSelectedFile().getPath();
1480       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1481       try
1482       {
1483         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1484                 jalview.io.AppletFormatAdapter.FILE);
1485
1486         if (pdbfile.id == null)
1487         {
1488           String reply = JOptionPane
1489                   .showInternalInputDialog(
1490                           Desktop.desktop,
1491                           "Couldn't find a PDB id in the file supplied."
1492                                   + "Please enter an Id to identify this structure.",
1493                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1494           if (reply == null)
1495           {
1496             return;
1497           }
1498
1499           entry.setId(reply);
1500         }
1501         else
1502         {
1503           entry.setId(pdbfile.id);
1504         }
1505       } catch (java.io.IOException ex)
1506       {
1507         ex.printStackTrace();
1508       }
1509
1510       entry.setFile(choice);
1511       sequence.getDatasetSequence().addPDBId(entry);
1512     }
1513
1514   }
1515
1516   public void enterPDB_actionPerformed()
1517   {
1518     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1519             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1520
1521     if (id != null && id.length() > 0)
1522     {
1523       PDBEntry entry = new PDBEntry();
1524       entry.setId(id.toUpperCase());
1525       sequence.getDatasetSequence().addPDBId(entry);
1526     }
1527   }
1528
1529   public void discoverPDB_actionPerformed()
1530   {
1531
1532     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1533     { sequence }
1534             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1535     Thread discpdb = new Thread(new Runnable()
1536     {
1537       public void run()
1538       {
1539
1540         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1541                 .fetchDBRefs(false);
1542       }
1543
1544     });
1545     discpdb.start();
1546   }
1547
1548   public void sequenceFeature_actionPerformed()
1549   {
1550     SequenceGroup sg = ap.av.getSelectionGroup();
1551     if (sg == null)
1552     {
1553       return;
1554     }
1555
1556     int gSize = sg.getSize();
1557     SequenceI[] seqs = new SequenceI[gSize];
1558     SequenceFeature[] features = new SequenceFeature[gSize];
1559
1560     for (int i = 0; i < gSize; i++)
1561     {
1562       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1563       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1564       int end = sg.findEndRes(sg.getSequenceAt(i));
1565       features[i] = new SequenceFeature(null, null, null, start, end,
1566               "Jalview");
1567     }
1568
1569     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1570             features, true, ap))
1571     {
1572       ap.alignFrame.showSeqFeatures.setSelected(true);
1573       ap.av.setShowSequenceFeatures(true);
1574       ap.highlightSearchResults(null);
1575     }
1576   }
1577
1578   public void textColour_actionPerformed()
1579   {
1580     SequenceGroup sg = getGroup();
1581     if (sg != null)
1582     {
1583       new TextColourChooser().chooseColour(ap, sg);
1584     }
1585   }
1586
1587   public void colourByStructure(String pdbid)
1588   {
1589     Annotation[] anots = jalview.structure.StructureSelectionManager
1590             .getStructureSelectionManager().colourSequenceFromStructure(
1591                     sequence, pdbid);
1592
1593     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1594             "Coloured by " + pdbid, anots);
1595
1596     ap.av.alignment.addAnnotation(an);
1597     an.createSequenceMapping(sequence, 0, true);
1598     // an.adjustForAlignment();
1599     ap.av.alignment.setAnnotationIndex(an, 0);
1600
1601     ap.adjustAnnotationHeight();
1602
1603     sequence.addAlignmentAnnotation(an);
1604
1605   }
1606
1607   public void editSequence_actionPerformed(ActionEvent actionEvent)
1608   {
1609     SequenceGroup sg = ap.av.getSelectionGroup();
1610
1611     if (sg != null)
1612     {
1613       if (sequence == null)
1614         sequence = (Sequence) sg.getSequenceAt(0);
1615
1616       EditNameDialog dialog = new EditNameDialog(sequence
1617               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1618               null, "Edit Sequence ", null, "Edit Sequence");
1619
1620       if (dialog.accept)
1621       {
1622         EditCommand editCommand = new EditCommand("Edit Sequences",
1623                 EditCommand.REPLACE, dialog.getName().replace(' ',
1624                         ap.av.getGapCharacter()), sg
1625                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1626                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1627
1628         ap.alignFrame.addHistoryItem(editCommand);
1629
1630         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1631                 .getSequences());
1632       }
1633     }
1634   }
1635
1636 }