src/jalview/gui/PopupMenu.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
   3  * Copyright (C) 2009 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.GroupUrlLink;
  34 import jalview.util.UrlLink;
  35
  36 /**
  37  * DOCUMENT ME!
  38  *
  39  * @author $author$
  40  * @version $Revision$
  41  */
  42 public class PopupMenu extends JPopupMenu
  43 {
  44   JMenu groupMenu = new JMenu();
  45
  46   JMenuItem groupName = new JMenuItem();
  47
  48   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  49
  50   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  51
  52   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  53
  54   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  55
  56   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  57
  58   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  59
  60   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  61
  62   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  63
  64   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
  65
  66   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  67
  68   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  69
  70   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  71
  72   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  73
  74   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  75
  76   AlignmentPanel ap;
  77
  78   JMenu sequenceMenu = new JMenu();
  79
  80   JMenuItem sequenceName = new JMenuItem();
  81
  82   Sequence sequence;
  83
  84   JMenuItem unGroupMenuItem = new JMenuItem();
  85
  86   JMenuItem outline = new JMenuItem();
  87
  88   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
  89
  90   JMenu colourMenu = new JMenu();
  91
  92   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
  93
  94   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
  95
  96   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
  97
  98   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
  99
 100   JMenu editMenu = new JMenu();
 101
 102   JMenuItem cut = new JMenuItem();
 103
 104   JMenuItem copy = new JMenuItem();
 105
 106   JMenuItem upperCase = new JMenuItem();
 107
 108   JMenuItem lowerCase = new JMenuItem();
 109
 110   JMenuItem toggle = new JMenuItem();
 111
 112   JMenu pdbMenu = new JMenu();
 113
 114   JMenuItem pdbFromFile = new JMenuItem();
 115
 116   JMenuItem enterPDB = new JMenuItem();
 117
 118   JMenuItem discoverPDB = new JMenuItem();
 119
 120   JMenu outputMenu = new JMenu();
 121
 122   JMenuItem sequenceFeature = new JMenuItem();
 123
 124   JMenuItem textColour = new JMenuItem();
 125
 126   JMenu jMenu1 = new JMenu();
 127
 128   JMenu structureMenu = new JMenu();
 129
 130   JMenu viewStructureMenu = new JMenu();
 131
 132   // JMenu colStructureMenu = new JMenu();
 133   JMenuItem editSequence = new JMenuItem();
 134
 135   // JMenuItem annotationMenuItem = new JMenuItem();
 136
 137   JMenu groupLinksMenu;
 138
 139   /**
 140    * Creates a new PopupMenu object.
 141    *
 142    * @param ap
 143    *                DOCUMENT ME!
 144    * @param seq
 145    *                DOCUMENT ME!
 146    */
 147   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
 148   {
 149     this(ap, seq, links, null);
 150   }
 151   /**
 152    *
 153    * @param ap
 154    * @param seq
 155    * @param links
 156    * @param groupLinks
 157    */
 158   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
 159   {
 160     // /////////////////////////////////////////////////////////
 161     // If this is activated from the sequence panel, the user may want to
 162     // edit or annotate a particular residue. Therefore display the residue menu
 163     //
 164     // If from the IDPanel, we must display the sequence menu
 165     // ////////////////////////////////////////////////////////
 166     this.ap = ap;
 167     sequence = seq;
 168
 169     ButtonGroup colours = new ButtonGroup();
 170     colours.add(noColourmenuItem);
 171     colours.add(clustalColour);
 172     colours.add(zappoColour);
 173     colours.add(taylorColour);
 174     colours.add(hydrophobicityColour);
 175     colours.add(helixColour);
 176     colours.add(strandColour);
 177     colours.add(turnColour);
 178     colours.add(buriedColour);
 179     colours.add(abovePIDColour);
 180     colours.add(userDefinedColour);
 181     colours.add(PIDColour);
 182     colours.add(BLOSUM62Colour);
 183
 184     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
 185     {
 186       JMenuItem item = new JMenuItem(
 187               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 188
 189       item.addActionListener(new java.awt.event.ActionListener()
 190       {
 191         public void actionPerformed(ActionEvent e)
 192         {
 193           outputText_actionPerformed(e);
 194         }
 195       });
 196
 197       outputMenu.add(item);
 198     }
 199
 200     try
 201     {
 202       jbInit();
 203     } catch (Exception e)
 204     {
 205       e.printStackTrace();
 206     }
 207
 208     if (seq != null)
 209     {
 210       sequenceMenu.setText(sequence.getName());
 211
 212       JMenuItem menuItem;
 213       if (seq.getDatasetSequence().getPDBId() != null
 214               && seq.getDatasetSequence().getPDBId().size() > 0)
 215       {
 216         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
 217                 .elements();
 218
 219         while (e.hasMoreElements())
 220         {
 221           final PDBEntry pdb = (PDBEntry) e.nextElement();
 222
 223           menuItem = new JMenuItem();
 224           menuItem.setText(pdb.getId());
 225           menuItem.addActionListener(new java.awt.event.ActionListener()
 226           {
 227             public void actionPerformed(ActionEvent e)
 228             {
 229               Vector seqs = new Vector();
 230               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
 231               {
 232                 Vector pdbs = ap.av.alignment.getSequenceAt(i)
 233                         .getDatasetSequence().getPDBId();
 234                 if (pdbs == null)
 235                   continue;
 236
 237                 for (int p = 0; p < pdbs.size(); p++)
 238                 {
 239                   PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
 240                   if (p1.getId().equals(pdb.getId()))
 241                   {
 242                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
 243                       seqs.addElement(ap.av.alignment.getSequenceAt(i));
 244
 245                     continue;
 246                   }
 247                 }
 248               }
 249
 250               SequenceI[] seqs2 = new SequenceI[seqs.size()];
 251               seqs.toArray(seqs2);
 252
 253               new AppJmol(pdb, seqs2, null, ap);
 254               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 255             }
 256           });
 257           viewStructureMenu.add(menuItem);
 258
 259           /*
 260            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
 261            * menuItem.addActionListener(new java.awt.event.ActionListener() {
 262            * public void actionPerformed(ActionEvent e) {
 263            * colourByStructure(pdb.getId()); } });
 264            * colStructureMenu.add(menuItem);
 265            */
 266         }
 267       }
 268       else
 269       {
 270         structureMenu.remove(viewStructureMenu);
 271         // structureMenu.remove(colStructureMenu);
 272       }
 273
 274       menuItem = new JMenuItem("Hide Sequences");
 275       menuItem.addActionListener(new java.awt.event.ActionListener()
 276       {
 277         public void actionPerformed(ActionEvent e)
 278         {
 279           hideSequences(false);
 280         }
 281       });
 282       add(menuItem);
 283
 284       if (ap.av.getSelectionGroup() != null
 285               && ap.av.getSelectionGroup().getSize() > 1)
 286       {
 287         menuItem = new JMenuItem("Represent Group with " + seq.getName());
 288         menuItem.addActionListener(new java.awt.event.ActionListener()
 289         {
 290           public void actionPerformed(ActionEvent e)
 291           {
 292             hideSequences(true);
 293           }
 294         });
 295         sequenceMenu.add(menuItem);
 296       }
 297
 298       if (ap.av.hasHiddenRows)
 299       {
 300         final int index = ap.av.alignment.findIndex(seq);
 301
 302         if (ap.av.adjustForHiddenSeqs(index)
 303                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
 304         {
 305           menuItem = new JMenuItem("Reveal Sequences");
 306           menuItem.addActionListener(new ActionListener()
 307           {
 308             public void actionPerformed(ActionEvent e)
 309             {
 310               ap.av.showSequence(index);
 311               if (ap.overviewPanel != null)
 312               {
 313                 ap.overviewPanel.updateOverviewImage();
 314               }
 315             }
 316           });
 317           add(menuItem);
 318         }
 319
 320         menuItem = new JMenuItem("Reveal All");
 321         menuItem.addActionListener(new ActionListener()
 322         {
 323           public void actionPerformed(ActionEvent e)
 324           {
 325             ap.av.showAllHiddenSeqs();
 326             if (ap.overviewPanel != null)
 327             {
 328               ap.overviewPanel.updateOverviewImage();
 329             }
 330           }
 331         });
 332
 333         add(menuItem);
 334       }
 335
 336     }
 337
 338     SequenceGroup sg = ap.av.getSelectionGroup();
 339
 340     if (sg != null)
 341     {
 342       groupName.setText(sg.getName());
 343
 344       if (sg.cs instanceof ZappoColourScheme)
 345       {
 346         zappoColour.setSelected(true);
 347       }
 348       else if (sg.cs instanceof TaylorColourScheme)
 349       {
 350         taylorColour.setSelected(true);
 351       }
 352       else if (sg.cs instanceof PIDColourScheme)
 353       {
 354         PIDColour.setSelected(true);
 355       }
 356       else if (sg.cs instanceof Blosum62ColourScheme)
 357       {
 358         BLOSUM62Colour.setSelected(true);
 359       }
 360       else if (sg.cs instanceof UserColourScheme)
 361       {
 362         userDefinedColour.setSelected(true);
 363       }
 364       else if (sg.cs instanceof HydrophobicColourScheme)
 365       {
 366         hydrophobicityColour.setSelected(true);
 367       }
 368       else if (sg.cs instanceof HelixColourScheme)
 369       {
 370         helixColour.setSelected(true);
 371       }
 372       else if (sg.cs instanceof StrandColourScheme)
 373       {
 374         strandColour.setSelected(true);
 375       }
 376       else if (sg.cs instanceof TurnColourScheme)
 377       {
 378         turnColour.setSelected(true);
 379       }
 380       else if (sg.cs instanceof BuriedColourScheme)
 381       {
 382         buriedColour.setSelected(true);
 383       }
 384       else if (sg.cs instanceof ClustalxColourScheme)
 385       {
 386         clustalColour.setSelected(true);
 387       }
 388       else
 389       {
 390         noColourmenuItem.setSelected(true);
 391       }
 392
 393       if (sg.cs != null && sg.cs.conservationApplied())
 394       {
 395         conservationMenuItem.setSelected(true);
 396       }
 397       displayNonconserved.setSelected(sg.getShowunconserved());
 398       showText.setSelected(sg.getDisplayText());
 399       showColourText.setSelected(sg.getColourText());
 400       showBoxes.setSelected(sg.getDisplayBoxes());
 401       // add any groupURLs to the groupURL submenu and make it visible
 402       if (groupLinks!=null && groupLinks.size()>0) {
 403         buildGroupURLMenu(sg, groupLinks);
 404       }
 405     }
 406     else
 407     {
 408       groupMenu.setVisible(false);
 409       editMenu.setVisible(false);
 410     }
 411
 412     if (!ap.av.alignment.getGroups().contains(sg))
 413     {
 414       unGroupMenuItem.setVisible(false);
 415     }
 416
 417     if (seq == null)
 418     {
 419       sequenceMenu.setVisible(false);
 420       structureMenu.setVisible(false);
 421     }
 422
 423     if (links != null && links.size() > 0)
 424     {
 425
 426       JMenu linkMenu = new JMenu("Link");
 427       Vector linkset = new Vector();
 428       for (int i = 0; i < links.size(); i++)
 429       {
 430         String link = links.elementAt(i).toString();
 431         UrlLink urlLink = null;
 432         try
 433         {
 434           urlLink = new UrlLink(link);
 435         } catch (Exception foo)
 436         {
 437           jalview.bin.Cache.log.error("Exception for URLLink '" + link
 438                   + "'", foo);
 439           continue;
 440         }
 441         ;
 442         if (!urlLink.isValid())
 443         {
 444           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 445           continue;
 446         }
 447         final String label = urlLink.getLabel();
 448         if (urlLink.isDynamic())
 449         {
 450
 451           // collect matching db-refs
 452           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
 453                   .getDBRef(), new String[]
 454           { urlLink.getTarget() });
 455           // collect id string too
 456           String id = seq.getName();
 457           String descr = seq.getDescription();
 458           if (descr!=null && descr.length()<1)
 459           {
 460             descr = null;
 461           }
 462
 463           if (dbr != null)
 464           {
 465             for (int r = 0; r < dbr.length; r++)
 466             {
 467               if (id != null && dbr[r].getAccessionId().equals(id))
 468               {
 469                 // suppress duplicate link creation for the bare sequence ID
 470                 // string with this link
 471                 id = null;
 472               }
 473               // create Bare ID link for this RUL
 474               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
 475                       true);
 476               if (urls != null)
 477               {
 478                 for (int u = 0; u < urls.length; u += 2)
 479                 {
 480                   if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 481                   {
 482                     linkset.addElement(urls[u]+"|"+urls[u+1]);
 483                     addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
 484                   }
 485                 }
 486               }
 487             }
 488           }
 489           if (id != null)
 490           {
 491             // create Bare ID link for this RUL
 492             String[] urls = urlLink.makeUrls(id, true);
 493             if (urls != null)
 494             {
 495               for (int u = 0; u < urls.length; u += 2)
 496               {
 497                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 498                 {
 499                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 500                   addshowLink(linkMenu, label, urls[u + 1]);
 501                 }
 502               }
 503             }
 504           }
 505           // Create urls from description but only for URL links which are regex links
 506           if (descr != null && urlLink.getRegexReplace()!=null)
 507           {
 508             // create link for this URL from description where regex matches
 509             String[] urls = urlLink.makeUrls(descr, true);
 510             if (urls != null)
 511             {
 512               for (int u = 0; u < urls.length; u += 2)
 513               {
 514                 if (!linkset.contains(urls[u]+"|"+urls[u+1]))
 515                 {
 516                   linkset.addElement(urls[u]+"|"+urls[u+1]);
 517                   addshowLink(linkMenu, label, urls[u + 1]);
 518                 }
 519               }
 520             }
 521           }
 522         }
 523         else
 524         {
 525           if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
 526           {
 527             linkset.addElement(label+"|"+urlLink.getUrl_prefix());
 528             // Add a non-dynamic link
 529             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
 530           }
 531         }
 532       }
 533       if (sequence != null)
 534       {
 535         sequenceMenu.add(linkMenu);
 536       }
 537       else
 538       {
 539         add(linkMenu);
 540       }
 541     }
 542   }
 543
 544   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
 545   {
 546
 547     // TODO: usability: thread off the generation of group url content so root menu appears asap
 548     // sequence only URLs
 549     // ID/regex match URLs
 550     groupLinksMenu = new JMenu("Group Link");
 551     JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
 552     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
 553     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
 554     Hashtable commonDbrefs = new Hashtable();
 555     for (int sq = 0; sq<seqs.length;sq++) {
 556
 557       int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes());
 558       // just collect ids from dataset sequence
 559       // TODO: check if IDs collected from selecton group intersects with the current selection, too
 560       SequenceI sqi = seqs[sq];
 561       while (sqi.getDatasetSequence()!=null) {
 562         sqi = sqi.getDatasetSequence(); }
 563       DBRefEntry[] dbr = sqi.getDBRef();
 564       if (dbr!=null && dbr.length>0)
 565       {
 566         for (int d=0;d<dbr.length;d++)
 567         {
 568           String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
 569           Object[] sarray = (Object[]) commonDbrefs.get(src);
 570           if (sarray==null)
 571           {
 572             sarray = new Object[2];
 573             sarray[0] = new int[] { 0 };
 574             sarray[1] = new String[seqs.length];
 575
 576             commonDbrefs.put(src,sarray);
 577           }
 578
 579           if (((String[])sarray[1])[sq]==null) {
 580             if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
 581               ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
 582               ((int[])sarray[0])[0]++;
 583             }
 584           }
 585         }
 586       }
 587     }
 588     // now create group links for all distinct ID/sequence sets.
 589     boolean addMenu = false; // indicates if there are any group links to give to user
 590     for (int i = 0; i < groupLinks.size(); i++) {
 591         String link = groupLinks.elementAt(i).toString();
 592         GroupUrlLink urlLink = null;
 593         try
 594         {
 595           urlLink = new GroupUrlLink(link);
 596         } catch (Exception foo)
 597         {
 598           jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
 599                   + "'", foo);
 600           continue;
 601         }
 602         ;
 603         if (!urlLink.isValid())
 604         {
 605           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
 606           continue;
 607         }
 608         final String label = urlLink.getLabel();
 609         boolean usingNames = false;
 610         // Now see which parts of the group apply for this URL
 611         String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
 612         Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
 613         String[] seqstr,ids; // input to makeUrl
 614         if (idset!=null)
 615         {
 616           int numinput = ((int[])idset[0])[0];
 617           String[] allids = ((String[])idset[1]);
 618           seqstr = new String[numinput];
 619           ids = new String[numinput];
 620           for (int sq=0,idcount=0;sq<seqs.length;sq++)
 621           {
 622             if (allids[sq]!=null) {
 623               ids[idcount] = allids[sq];
 624               seqstr[idcount++] = idandseqs[1][sq];
 625             }
 626           }
 627         } else {
 628           // just use the id/seq set
 629           seqstr = idandseqs[1];
 630           ids = idandseqs[0];
 631           usingNames=true;
 632         }
 633         // and try and make the groupURL!
 634
 635         Object[] urlset = urlLink.makeUrls(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
 636         if (urlset!=null)
 637         {
 638           System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
 639           // first two bits ofurlLink type bitfield are sequenceids and sequences
 640           // TODO: FUTURE: ensure the groupURL menu structure can be generalised
 641           addshowLink(linkMenus[urlLink.getGroupURLType() & 3], label + "("+(usingNames ? "Names" : ltarget)+")", ((String[])urlset[3])[0]);
 642           addMenu = true;
 643         }
 644       }
 645     if (addMenu)
 646     {
 647       groupLinksMenu = new JMenu("Group Links");
 648       for (int m=0;m<linkMenus.length; m++)
 649       {
 650         if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
 651         {
 652           groupLinksMenu.add(linkMenus[m]);
 653         }
 654       }
 655
 656       groupMenu.add(groupLinksMenu);
 657     }
 658   }
 659
 660   /**
 661    * add a show URL menu item to the given linkMenu
 662    *
 663    * @param linkMenu
 664    * @param label -
 665    *                menu label string
 666    * @param url -
 667    *                url to open
 668    */
 669   private void addshowLink(JMenu linkMenu, String label, final String url)
 670   {
 671     JMenuItem item = new JMenuItem(label);
 672     item.setToolTipText("open URL: " + url);
 673     item.addActionListener(new java.awt.event.ActionListener()
 674     {
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         new Thread(new Runnable()
 678         {
 679
 680           public void run()
 681           {
 682             showLink(url);
 683           }
 684
 685         }).start();
 686       }
 687     });
 688
 689     linkMenu.add(item);
 690   }
 691
 692   /**
 693    * DOCUMENT ME!
 694    *
 695    * @throws Exception
 696    *                 DOCUMENT ME!
 697    */
 698   private void jbInit() throws Exception
 699   {
 700     groupMenu.setText("Group");
 701     groupMenu.setText("Selection");
 702     groupName.setText("Name");
 703     groupName.addActionListener(new java.awt.event.ActionListener()
 704     {
 705       public void actionPerformed(ActionEvent e)
 706       {
 707         groupName_actionPerformed();
 708       }
 709     });
 710     sequenceMenu.setText("Sequence");
 711     sequenceName.setText("Edit Name/Description");
 712     sequenceName.addActionListener(new java.awt.event.ActionListener()
 713     {
 714       public void actionPerformed(ActionEvent e)
 715       {
 716         sequenceName_actionPerformed();
 717       }
 718     });
 719     PIDColour.setFocusPainted(false);
 720     unGroupMenuItem.setText("Remove Group");
 721     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 722     {
 723       public void actionPerformed(ActionEvent e)
 724       {
 725         unGroupMenuItem_actionPerformed();
 726       }
 727     });
 728
 729     outline.setText("Border colour");
 730     outline.addActionListener(new java.awt.event.ActionListener()
 731     {
 732       public void actionPerformed(ActionEvent e)
 733       {
 734         outline_actionPerformed();
 735       }
 736     });
 737     nucleotideMenuItem.setText("Nucleotide");
 738     nucleotideMenuItem.addActionListener(new ActionListener()
 739     {
 740       public void actionPerformed(ActionEvent e)
 741       {
 742         nucleotideMenuItem_actionPerformed();
 743       }
 744     });
 745     colourMenu.setText("Group Colour");
 746     showBoxes.setText("Boxes");
 747     showBoxes.setState(true);
 748     showBoxes.addActionListener(new ActionListener()
 749     {
 750       public void actionPerformed(ActionEvent e)
 751       {
 752         showBoxes_actionPerformed();
 753       }
 754     });
 755     showText.setText("Text");
 756     showText.setState(true);
 757     showText.addActionListener(new ActionListener()
 758     {
 759       public void actionPerformed(ActionEvent e)
 760       {
 761         showText_actionPerformed();
 762       }
 763     });
 764     showColourText.setText("Colour Text");
 765     showColourText.addActionListener(new ActionListener()
 766     {
 767       public void actionPerformed(ActionEvent e)
 768       {
 769         showColourText_actionPerformed();
 770       }
 771     });
 772     displayNonconserved.setText("Show Nonconserved");
 773     displayNonconserved.setState(true);
 774     displayNonconserved.addActionListener(new ActionListener()
 775     {
 776       public void actionPerformed(ActionEvent e)
 777       {
 778         showNonconserved_actionPerformed();
 779       }
 780     });
 781     editMenu.setText("Edit");
 782     cut.setText("Cut");
 783     cut.addActionListener(new ActionListener()
 784     {
 785       public void actionPerformed(ActionEvent e)
 786       {
 787         cut_actionPerformed();
 788       }
 789     });
 790     upperCase.setText("To Upper Case");
 791     upperCase.addActionListener(new ActionListener()
 792     {
 793       public void actionPerformed(ActionEvent e)
 794       {
 795         changeCase(e);
 796       }
 797     });
 798     copy.setText("Copy");
 799     copy.addActionListener(new ActionListener()
 800     {
 801       public void actionPerformed(ActionEvent e)
 802       {
 803         copy_actionPerformed();
 804       }
 805     });
 806     lowerCase.setText("To Lower Case");
 807     lowerCase.addActionListener(new ActionListener()
 808     {
 809       public void actionPerformed(ActionEvent e)
 810       {
 811         changeCase(e);
 812       }
 813     });
 814     toggle.setText("Toggle Case");
 815     toggle.addActionListener(new ActionListener()
 816     {
 817       public void actionPerformed(ActionEvent e)
 818       {
 819         changeCase(e);
 820       }
 821     });
 822     pdbMenu.setText("Associate Structure with Sequence");
 823     pdbFromFile.setText("From File");
 824     pdbFromFile.addActionListener(new ActionListener()
 825     {
 826       public void actionPerformed(ActionEvent e)
 827       {
 828         pdbFromFile_actionPerformed();
 829       }
 830     });
 831     enterPDB.setText("Enter PDB Id");
 832     enterPDB.addActionListener(new ActionListener()
 833     {
 834       public void actionPerformed(ActionEvent e)
 835       {
 836         enterPDB_actionPerformed();
 837       }
 838     });
 839     discoverPDB.setText("Discover PDB ids");
 840     discoverPDB.addActionListener(new ActionListener()
 841     {
 842       public void actionPerformed(ActionEvent e)
 843       {
 844         discoverPDB_actionPerformed();
 845       }
 846     });
 847     outputMenu.setText("Output to Textbox...");
 848     sequenceFeature.setText("Create Sequence Feature");
 849     sequenceFeature.addActionListener(new ActionListener()
 850     {
 851       public void actionPerformed(ActionEvent e)
 852       {
 853         sequenceFeature_actionPerformed();
 854       }
 855     });
 856     textColour.setText("Text Colour");
 857     textColour.addActionListener(new ActionListener()
 858     {
 859       public void actionPerformed(ActionEvent e)
 860       {
 861         textColour_actionPerformed();
 862       }
 863     });
 864     jMenu1.setText("Group");
 865     structureMenu.setText("Structure");
 866     viewStructureMenu.setText("View Structure");
 867     // colStructureMenu.setText("Colour By Structure");
 868     editSequence.setText("Edit Sequence...");
 869     editSequence.addActionListener(new ActionListener()
 870     {
 871       public void actionPerformed(ActionEvent actionEvent)
 872       {
 873         editSequence_actionPerformed(actionEvent);
 874       }
 875     });
 876     /*
 877      * annotationMenuItem.setText("By Annotation");
 878      * annotationMenuItem.addActionListener(new ActionListener() { public void
 879      * actionPerformed(ActionEvent actionEvent) {
 880      * annotationMenuItem_actionPerformed(actionEvent); } });
 881      */
 882
 883     add(groupMenu);
 884
 885     add(sequenceMenu);
 886     this.add(structureMenu);
 887     groupMenu.add(editMenu);
 888     groupMenu.add(outputMenu);
 889     groupMenu.add(sequenceFeature);
 890     groupMenu.add(jMenu1);
 891     sequenceMenu.add(sequenceName);
 892     colourMenu.add(textColour);
 893     colourMenu.add(noColourmenuItem);
 894     colourMenu.add(clustalColour);
 895     colourMenu.add(BLOSUM62Colour);
 896     colourMenu.add(PIDColour);
 897     colourMenu.add(zappoColour);
 898     colourMenu.add(taylorColour);
 899     colourMenu.add(hydrophobicityColour);
 900     colourMenu.add(helixColour);
 901     colourMenu.add(strandColour);
 902     colourMenu.add(turnColour);
 903     colourMenu.add(buriedColour);
 904     colourMenu.add(nucleotideMenuItem);
 905     colourMenu.add(userDefinedColour);
 906
 907     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
 908     {
 909       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
 910               .getUserColourSchemes().keys();
 911
 912       while (userColours.hasMoreElements())
 913       {
 914         JMenuItem item = new JMenuItem(userColours.nextElement().toString());
 915         item.addActionListener(new ActionListener()
 916         {
 917           public void actionPerformed(ActionEvent evt)
 918           {
 919             userDefinedColour_actionPerformed(evt);
 920           }
 921         });
 922         colourMenu.add(item);
 923       }
 924     }
 925
 926     colourMenu.addSeparator();
 927     colourMenu.add(abovePIDColour);
 928     colourMenu.add(conservationMenuItem);
 929     // colourMenu.add(annotationMenuItem);
 930     editMenu.add(copy);
 931     editMenu.add(cut);
 932     editMenu.add(editSequence);
 933     editMenu.add(upperCase);
 934     editMenu.add(lowerCase);
 935     editMenu.add(toggle);
 936     pdbMenu.add(pdbFromFile);
 937     pdbMenu.add(enterPDB);
 938     pdbMenu.add(discoverPDB);
 939     jMenu1.add(groupName);
 940     jMenu1.add(unGroupMenuItem);
 941     jMenu1.add(colourMenu);
 942     jMenu1.add(showBoxes);
 943     jMenu1.add(showText);
 944     jMenu1.add(showColourText);
 945     jMenu1.add(outline);
 946     jMenu1.add(displayNonconserved);
 947     structureMenu.add(pdbMenu);
 948     structureMenu.add(viewStructureMenu);
 949     // structureMenu.add(colStructureMenu);
 950     noColourmenuItem.setText("None");
 951     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 952     {
 953       public void actionPerformed(ActionEvent e)
 954       {
 955         noColourmenuItem_actionPerformed();
 956       }
 957     });
 958
 959     clustalColour.setText("Clustalx colours");
 960     clustalColour.addActionListener(new java.awt.event.ActionListener()
 961     {
 962       public void actionPerformed(ActionEvent e)
 963       {
 964         clustalColour_actionPerformed();
 965       }
 966     });
 967     zappoColour.setText("Zappo");
 968     zappoColour.addActionListener(new java.awt.event.ActionListener()
 969     {
 970       public void actionPerformed(ActionEvent e)
 971       {
 972         zappoColour_actionPerformed();
 973       }
 974     });
 975     taylorColour.setText("Taylor");
 976     taylorColour.addActionListener(new java.awt.event.ActionListener()
 977     {
 978       public void actionPerformed(ActionEvent e)
 979       {
 980         taylorColour_actionPerformed();
 981       }
 982     });
 983     hydrophobicityColour.setText("Hydrophobicity");
 984     hydrophobicityColour
 985             .addActionListener(new java.awt.event.ActionListener()
 986             {
 987               public void actionPerformed(ActionEvent e)
 988               {
 989                 hydrophobicityColour_actionPerformed();
 990               }
 991             });
 992     helixColour.setText("Helix propensity");
 993     helixColour.addActionListener(new java.awt.event.ActionListener()
 994     {
 995       public void actionPerformed(ActionEvent e)
 996       {
 997         helixColour_actionPerformed();
 998       }
 999     });
1000     strandColour.setText("Strand propensity");
1001     strandColour.addActionListener(new java.awt.event.ActionListener()
1002     {
1003       public void actionPerformed(ActionEvent e)
1004       {
1005         strandColour_actionPerformed();
1006       }
1007     });
1008     turnColour.setText("Turn propensity");
1009     turnColour.addActionListener(new java.awt.event.ActionListener()
1010     {
1011       public void actionPerformed(ActionEvent e)
1012       {
1013         turnColour_actionPerformed();
1014       }
1015     });
1016     buriedColour.setText("Buried Index");
1017     buriedColour.addActionListener(new java.awt.event.ActionListener()
1018     {
1019       public void actionPerformed(ActionEvent e)
1020       {
1021         buriedColour_actionPerformed();
1022       }
1023     });
1024     abovePIDColour.setText("Above % Identity");
1025     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1026     {
1027       public void actionPerformed(ActionEvent e)
1028       {
1029         abovePIDColour_actionPerformed();
1030       }
1031     });
1032     userDefinedColour.setText("User Defined...");
1033     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1034     {
1035       public void actionPerformed(ActionEvent e)
1036       {
1037         userDefinedColour_actionPerformed(e);
1038       }
1039     });
1040     PIDColour.setText("Percentage Identity");
1041     PIDColour.addActionListener(new java.awt.event.ActionListener()
1042     {
1043       public void actionPerformed(ActionEvent e)
1044       {
1045         PIDColour_actionPerformed();
1046       }
1047     });
1048     BLOSUM62Colour.setText("BLOSUM62");
1049     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1050     {
1051       public void actionPerformed(ActionEvent e)
1052       {
1053         BLOSUM62Colour_actionPerformed();
1054       }
1055     });
1056     conservationMenuItem.setText("Conservation");
1057     conservationMenuItem
1058             .addActionListener(new java.awt.event.ActionListener()
1059             {
1060               public void actionPerformed(ActionEvent e)
1061               {
1062                 conservationMenuItem_actionPerformed();
1063               }
1064             });
1065   }
1066
1067   protected void showNonconserved_actionPerformed()
1068   {
1069     getGroup().setShowunconserved(displayNonconserved.isSelected());
1070     refresh();
1071   }
1072
1073   /**
1074    * call to refresh view after settings change
1075    */
1076   void refresh()
1077   {
1078     ap.updateAnnotation();
1079     ap.paintAlignment(true);
1080
1081     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1082   }
1083
1084   /**
1085    * DOCUMENT ME!
1086    *
1087    * @param e
1088    *                DOCUMENT ME!
1089    */
1090   protected void clustalColour_actionPerformed()
1091   {
1092     SequenceGroup sg = getGroup();
1093     sg.cs = new ClustalxColourScheme(sg
1094             .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
1095             .getWidth());
1096     refresh();
1097   }
1098
1099   /**
1100    * DOCUMENT ME!
1101    *
1102    * @param e
1103    *                DOCUMENT ME!
1104    */
1105   protected void zappoColour_actionPerformed()
1106   {
1107     getGroup().cs = new ZappoColourScheme();
1108     refresh();
1109   }
1110
1111   /**
1112    * DOCUMENT ME!
1113    *
1114    * @param e
1115    *                DOCUMENT ME!
1116    */
1117   protected void taylorColour_actionPerformed()
1118   {
1119     getGroup().cs = new TaylorColourScheme();
1120     refresh();
1121   }
1122
1123   /**
1124    * DOCUMENT ME!
1125    *
1126    * @param e
1127    *                DOCUMENT ME!
1128    */
1129   protected void hydrophobicityColour_actionPerformed()
1130   {
1131     getGroup().cs = new HydrophobicColourScheme();
1132     refresh();
1133   }
1134
1135   /**
1136    * DOCUMENT ME!
1137    *
1138    * @param e
1139    *                DOCUMENT ME!
1140    */
1141   protected void helixColour_actionPerformed()
1142   {
1143     getGroup().cs = new HelixColourScheme();
1144     refresh();
1145   }
1146
1147   /**
1148    * DOCUMENT ME!
1149    *
1150    * @param e
1151    *                DOCUMENT ME!
1152    */
1153   protected void strandColour_actionPerformed()
1154   {
1155     getGroup().cs = new StrandColourScheme();
1156     refresh();
1157   }
1158
1159   /**
1160    * DOCUMENT ME!
1161    *
1162    * @param e
1163    *                DOCUMENT ME!
1164    */
1165   protected void turnColour_actionPerformed()
1166   {
1167     getGroup().cs = new TurnColourScheme();
1168     refresh();
1169   }
1170
1171   /**
1172    * DOCUMENT ME!
1173    *
1174    * @param e
1175    *                DOCUMENT ME!
1176    */
1177   protected void buriedColour_actionPerformed()
1178   {
1179     getGroup().cs = new BuriedColourScheme();
1180     refresh();
1181   }
1182
1183   /**
1184    * DOCUMENT ME!
1185    *
1186    * @param e
1187    *                DOCUMENT ME!
1188    */
1189   public void nucleotideMenuItem_actionPerformed()
1190   {
1191     getGroup().cs = new NucleotideColourScheme();
1192     refresh();
1193   }
1194
1195   /**
1196    * DOCUMENT ME!
1197    *
1198    * @param e
1199    *                DOCUMENT ME!
1200    */
1201   protected void abovePIDColour_actionPerformed()
1202   {
1203     SequenceGroup sg = getGroup();
1204     if (sg.cs == null)
1205     {
1206       return;
1207     }
1208
1209     if (abovePIDColour.isSelected())
1210     {
1211       sg.cs.setConsensus(AAFrequency.calculate(sg
1212               .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1213               .getEndRes() + 1));
1214
1215       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1216               .getName());
1217
1218       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1219
1220       SliderPanel.showPIDSlider();
1221     }
1222     else
1223     // remove PIDColouring
1224     {
1225       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1226     }
1227
1228     refresh();
1229   }
1230
1231   /**
1232    * DOCUMENT ME!
1233    *
1234    * @param e
1235    *                DOCUMENT ME!
1236    */
1237   protected void userDefinedColour_actionPerformed(ActionEvent e)
1238   {
1239     SequenceGroup sg = getGroup();
1240
1241     if (e.getActionCommand().equals("User Defined..."))
1242     {
1243       new UserDefinedColours(ap, sg);
1244     }
1245     else
1246     {
1247       UserColourScheme udc = (UserColourScheme) UserDefinedColours
1248               .getUserColourSchemes().get(e.getActionCommand());
1249
1250       sg.cs = udc;
1251     }
1252     refresh();
1253   }
1254
1255   /**
1256    * DOCUMENT ME!
1257    *
1258    * @param e
1259    *                DOCUMENT ME!
1260    */
1261   protected void PIDColour_actionPerformed()
1262   {
1263     SequenceGroup sg = getGroup();
1264     sg.cs = new PIDColourScheme();
1265     sg.cs.setConsensus(AAFrequency.calculate(sg
1266             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1267             .getEndRes() + 1));
1268     refresh();
1269   }
1270
1271   /**
1272    * DOCUMENT ME!
1273    *
1274    * @param e
1275    *                DOCUMENT ME!
1276    */
1277   protected void BLOSUM62Colour_actionPerformed()
1278   {
1279     SequenceGroup sg = getGroup();
1280
1281     sg.cs = new Blosum62ColourScheme();
1282
1283     sg.cs.setConsensus(AAFrequency.calculate(sg
1284             .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
1285             .getEndRes() + 1));
1286
1287     refresh();
1288   }
1289
1290   /**
1291    * DOCUMENT ME!
1292    *
1293    * @param e
1294    *                DOCUMENT ME!
1295    */
1296   protected void noColourmenuItem_actionPerformed()
1297   {
1298     getGroup().cs = null;
1299     refresh();
1300   }
1301
1302   /**
1303    * DOCUMENT ME!
1304    *
1305    * @param e
1306    *                DOCUMENT ME!
1307    */
1308   protected void conservationMenuItem_actionPerformed()
1309   {
1310     SequenceGroup sg = getGroup();
1311     if (sg.cs == null)
1312     {
1313       return;
1314     }
1315
1316     if (conservationMenuItem.isSelected())
1317     {
1318       Conservation c = new Conservation("Group",
1319               ResidueProperties.propHash, 3, sg
1320                       .getSequences(ap.av.hiddenRepSequences), sg
1321                       .getStartRes(), sg.getEndRes() + 1);
1322
1323       c.calculate();
1324       c.verdict(false, ap.av.ConsPercGaps);
1325
1326       sg.cs.setConservation(c);
1327
1328       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1329       SliderPanel.showConservationSlider();
1330     }
1331     else
1332     // remove ConservationColouring
1333     {
1334       sg.cs.setConservation(null);
1335     }
1336
1337     refresh();
1338   }
1339
1340   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1341   {
1342     SequenceGroup sg = getGroup();
1343     if (sg == null)
1344     {
1345       return;
1346     }
1347
1348     AnnotationColourGradient acg = new AnnotationColourGradient(sequence
1349             .getAnnotation()[0], null,
1350             AnnotationColourGradient.NO_THRESHOLD);
1351
1352     acg.predefinedColours = true;
1353     sg.cs = acg;
1354
1355     refresh();
1356   }
1357
1358   /**
1359    * DOCUMENT ME!
1360    *
1361    * @param e
1362    *                DOCUMENT ME!
1363    */
1364   protected void groupName_actionPerformed()
1365   {
1366
1367     SequenceGroup sg = getGroup();
1368     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
1369             .getDescription(), "       Group Name ", "Group Description ",
1370             "Edit Group Name/Description");
1371
1372     if (!dialog.accept)
1373     {
1374       return;
1375     }
1376
1377     sg.setName(dialog.getName());
1378     sg.setDescription(dialog.getDescription());
1379   }
1380
1381   /**
1382    * DOCUMENT ME!
1383    *
1384    * @return DOCUMENT ME!
1385    */
1386   SequenceGroup getGroup()
1387   {
1388     SequenceGroup sg = ap.av.getSelectionGroup();
1389     // this method won't add a new group if it already exists
1390     if (sg != null)
1391     {
1392       ap.av.alignment.addGroup(sg);
1393     }
1394
1395     return sg;
1396   }
1397
1398   /**
1399    * DOCUMENT ME!
1400    *
1401    * @param e
1402    *                DOCUMENT ME!
1403    */
1404   void sequenceName_actionPerformed()
1405   {
1406     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
1407             .getDescription(), "       Sequence Name ",
1408             "Sequence Description ", "Edit Sequence Name/Description");
1409
1410     if (!dialog.accept)
1411     {
1412       return;
1413     }
1414
1415     if (dialog.getName() != null)
1416     {
1417       if (dialog.getName().indexOf(" ") > -1)
1418       {
1419         JOptionPane.showMessageDialog(ap,
1420                 "Spaces have been converted to \"_\"",
1421                 "No spaces allowed in Sequence Name",
1422                 JOptionPane.WARNING_MESSAGE);
1423       }
1424
1425       sequence.setName(dialog.getName().replace(' ', '_'));
1426       ap.paintAlignment(false);
1427     }
1428
1429     sequence.setDescription(dialog.getDescription());
1430
1431     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1432             .getSequences());
1433
1434   }
1435
1436   /**
1437    * DOCUMENT ME!
1438    *
1439    * @param e
1440    *                DOCUMENT ME!
1441    */
1442   void unGroupMenuItem_actionPerformed()
1443   {
1444     SequenceGroup sg = ap.av.getSelectionGroup();
1445     ap.av.alignment.deleteGroup(sg);
1446     ap.av.setSelectionGroup(null);
1447     refresh();
1448   }
1449
1450   /**
1451    * DOCUMENT ME!
1452    *
1453    * @param e
1454    *                DOCUMENT ME!
1455    */
1456   protected void outline_actionPerformed()
1457   {
1458     SequenceGroup sg = getGroup();
1459     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1460             Color.BLUE);
1461
1462     if (col != null)
1463     {
1464       sg.setOutlineColour(col);
1465     }
1466
1467     refresh();
1468   }
1469
1470   /**
1471    * DOCUMENT ME!
1472    *
1473    * @param e
1474    *                DOCUMENT ME!
1475    */
1476   public void showBoxes_actionPerformed()
1477   {
1478     getGroup().setDisplayBoxes(showBoxes.isSelected());
1479     refresh();
1480   }
1481
1482   /**
1483    * DOCUMENT ME!
1484    *
1485    * @param e
1486    *                DOCUMENT ME!
1487    */
1488   public void showText_actionPerformed()
1489   {
1490     getGroup().setDisplayText(showText.isSelected());
1491     refresh();
1492   }
1493
1494   /**
1495    * DOCUMENT ME!
1496    *
1497    * @param e
1498    *                DOCUMENT ME!
1499    */
1500   public void showColourText_actionPerformed()
1501   {
1502     getGroup().setColourText(showColourText.isSelected());
1503     refresh();
1504   }
1505
1506   public void showLink(String url)
1507   {
1508     try
1509     {
1510       jalview.util.BrowserLauncher.openURL(url);
1511     } catch (Exception ex)
1512     {
1513       JOptionPane
1514               .showInternalMessageDialog(
1515                       Desktop.desktop,
1516                       "Unixers: Couldn't find default web browser."
1517                               + "\nAdd the full path to your browser in Preferences.",
1518                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
1519
1520       ex.printStackTrace();
1521     }
1522   }
1523
1524   void hideSequences(boolean representGroup)
1525   {
1526     SequenceGroup sg = ap.av.getSelectionGroup();
1527     if (sg == null || sg.getSize() < 1)
1528     {
1529       ap.av.hideSequence(new SequenceI[]
1530       { sequence });
1531       return;
1532     }
1533
1534     ap.av.setSelectionGroup(null);
1535
1536     if (representGroup)
1537     {
1538       ap.av.hideRepSequences(sequence, sg);
1539
1540       return;
1541     }
1542
1543     int gsize = sg.getSize();
1544     SequenceI[] hseqs;
1545
1546     hseqs = new SequenceI[gsize];
1547
1548     int index = 0;
1549     for (int i = 0; i < gsize; i++)
1550     {
1551       hseqs[index++] = sg.getSequenceAt(i);
1552     }
1553
1554     ap.av.hideSequence(hseqs);
1555     ap.av.sendSelection();
1556   }
1557
1558   public void copy_actionPerformed()
1559   {
1560     ap.alignFrame.copy_actionPerformed(null);
1561   }
1562
1563   public void cut_actionPerformed()
1564   {
1565     ap.alignFrame.cut_actionPerformed(null);
1566   }
1567
1568   void changeCase(ActionEvent e)
1569   {
1570     Object source = e.getSource();
1571     SequenceGroup sg = ap.av.getSelectionGroup();
1572
1573     if (sg != null)
1574     {
1575       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1576               sg.getEndRes() + 1);
1577
1578       String description;
1579       int caseChange;
1580
1581       if (source == toggle)
1582       {
1583         description = "Toggle Case";
1584         caseChange = ChangeCaseCommand.TOGGLE_CASE;
1585       }
1586       else if (source == upperCase)
1587       {
1588         description = "To Upper Case";
1589         caseChange = ChangeCaseCommand.TO_UPPER;
1590       }
1591       else
1592       {
1593         description = "To Lower Case";
1594         caseChange = ChangeCaseCommand.TO_LOWER;
1595       }
1596
1597       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
1598               .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1599               caseChange);
1600
1601       ap.alignFrame.addHistoryItem(caseCommand);
1602
1603       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1604               .getSequences());
1605
1606     }
1607   }
1608
1609   public void outputText_actionPerformed(ActionEvent e)
1610   {
1611     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1612     cap.setForInput(null);
1613     Desktop.addInternalFrame(cap, "Alignment output - "
1614             + e.getActionCommand(), 600, 500);
1615
1616     String[] omitHidden = null;
1617
1618     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1619                                             // or we simply trust the user wants
1620                                             // wysiwig behaviour
1621     SequenceGroup sg = ap.av.getSelectionGroup();
1622     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1623     omitHidden = ap.av.getViewAsString(true);
1624     Alignment oal = new Alignment(ap.av.getSequenceSelection());
1625     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1626     for (int i = 0; i < nala.length; i++)
1627     {
1628       AlignmentAnnotation na = nala[i];
1629       oal.addAnnotation(na);
1630     }
1631     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1632             oal, omitHidden, csel, sg));
1633     oal = null;
1634   }
1635
1636   public void pdbFromFile_actionPerformed()
1637   {
1638     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1639             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1640     chooser.setFileView(new jalview.io.JalviewFileView());
1641     chooser.setDialogTitle("Select a PDB file");
1642     chooser.setToolTipText("Load a PDB file");
1643
1644     int value = chooser.showOpenDialog(null);
1645
1646     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1647     {
1648       PDBEntry entry = new PDBEntry();
1649       String choice = chooser.getSelectedFile().getPath();
1650       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1651       try
1652       {
1653         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1654                 jalview.io.AppletFormatAdapter.FILE);
1655
1656         if (pdbfile.id == null)
1657         {
1658           String reply = JOptionPane
1659                   .showInternalInputDialog(
1660                           Desktop.desktop,
1661                           "Couldn't find a PDB id in the file supplied."
1662                                   + "Please enter an Id to identify this structure.",
1663                           "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1664           if (reply == null)
1665           {
1666             return;
1667           }
1668
1669           entry.setId(reply);
1670         }
1671         else
1672         {
1673           entry.setId(pdbfile.id);
1674         }
1675       } catch (java.io.IOException ex)
1676       {
1677         ex.printStackTrace();
1678       }
1679
1680       entry.setFile(choice);
1681       sequence.getDatasetSequence().addPDBId(entry);
1682     }
1683
1684   }
1685
1686   public void enterPDB_actionPerformed()
1687   {
1688     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1689             "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1690
1691     if (id != null && id.length() > 0)
1692     {
1693       PDBEntry entry = new PDBEntry();
1694       entry.setId(id.toUpperCase());
1695       sequence.getDatasetSequence().addPDBId(entry);
1696     }
1697   }
1698
1699   public void discoverPDB_actionPerformed()
1700   {
1701
1702     final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1703     { sequence }
1704             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1705     Thread discpdb = new Thread(new Runnable()
1706     {
1707       public void run()
1708       {
1709
1710         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1711                 .fetchDBRefs(false);
1712       }
1713
1714     });
1715     discpdb.start();
1716   }
1717
1718   public void sequenceFeature_actionPerformed()
1719   {
1720     SequenceGroup sg = ap.av.getSelectionGroup();
1721     if (sg == null)
1722     {
1723       return;
1724     }
1725
1726     int rsize=0,gSize = sg.getSize();
1727     SequenceI[] rseqs,seqs = new SequenceI[gSize];
1728     SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
1729
1730     for (int i = 0; i < gSize; i++)
1731     {
1732       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1733       int end = sg.findEndRes(sg.getSequenceAt(i));
1734       if (start<=end)
1735       {
1736         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1737         features[rsize] = new SequenceFeature(null, null, null, start, end,
1738               "Jalview");
1739         rsize++;
1740       }
1741     }
1742     rseqs = new SequenceI[rsize];
1743     tfeatures = new SequenceFeature[rsize];
1744     System.arraycopy(seqs,0,rseqs, 0, rsize);
1745     System.arraycopy(features, 0, tfeatures, 0, rsize);
1746     features = tfeatures;
1747     seqs = rseqs;
1748     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1749             features, true, ap))
1750     {
1751       ap.alignFrame.setShowSeqFeatures(true);
1752       ap.highlightSearchResults(null);
1753     }
1754   }
1755
1756   public void textColour_actionPerformed()
1757   {
1758     SequenceGroup sg = getGroup();
1759     if (sg != null)
1760     {
1761       new TextColourChooser().chooseColour(ap, sg);
1762     }
1763   }
1764
1765   public void colourByStructure(String pdbid)
1766   {
1767     Annotation[] anots = jalview.structure.StructureSelectionManager
1768             .getStructureSelectionManager().colourSequenceFromStructure(
1769                     sequence, pdbid);
1770
1771     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1772             "Coloured by " + pdbid, anots);
1773
1774     ap.av.alignment.addAnnotation(an);
1775     an.createSequenceMapping(sequence, 0, true);
1776     // an.adjustForAlignment();
1777     ap.av.alignment.setAnnotationIndex(an, 0);
1778
1779     ap.adjustAnnotationHeight();
1780
1781     sequence.addAlignmentAnnotation(an);
1782
1783   }
1784
1785   public void editSequence_actionPerformed(ActionEvent actionEvent)
1786   {
1787     SequenceGroup sg = ap.av.getSelectionGroup();
1788
1789     if (sg != null)
1790     {
1791       if (sequence == null)
1792         sequence = (Sequence) sg.getSequenceAt(0);
1793
1794       EditNameDialog dialog = new EditNameDialog(sequence
1795               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
1796               null, "Edit Sequence ", null, "Edit Sequence");
1797
1798       if (dialog.accept)
1799       {
1800         EditCommand editCommand = new EditCommand("Edit Sequences",
1801                 EditCommand.REPLACE, dialog.getName().replace(' ',
1802                         ap.av.getGapCharacter()), sg
1803                         .getSequencesAsArray(ap.av.hiddenRepSequences), sg
1804                         .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1805
1806         ap.alignFrame.addHistoryItem(editCommand);
1807
1808         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1809                 .getSequences());
1810       }
1811     }
1812   }
1813
1814 }