X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d778125ad4c104d4950a81e4cd58b69fbed782ce;hb=7c28880430765f06ccd5ec8ad3caf17871336e97;hp=457638a2f3ad147bee4e007db8a5c73691900d56;hpb=298ac6df4e5542ba4d5aa635831537e8dd887084;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
old mode 100755
new mode 100644
index 457638a..d778125
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -22,6 +21,7 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
 import MCview.*;
@@ -31,13 +31,14 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
 import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.118 $
  */
 public class PopupMenu extends JPopupMenu
 {
@@ -140,14 +141,15 @@ public class PopupMenu extends JPopupMenu
    * Creates a new PopupMenu object.
    * 
    * @param ap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) 
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
   {
     this(ap, seq, links, null);
   }
+
   /**
    * 
    * @param ap
@@ -155,7 +157,8 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
+          Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -205,11 +208,11 @@ public class PopupMenu extends JPopupMenu
       e.printStackTrace();
     }
 
+    JMenuItem menuItem;
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
 
-      JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
       {
@@ -226,33 +229,11 @@ public class PopupMenu extends JPopupMenu
           {
             public void actionPerformed(ActionEvent e)
             {
-              Vector seqs = new Vector();
-              for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-              {
-                Vector pdbs = ap.av.alignment.getSequenceAt(i)
-                        .getDatasetSequence().getPDBId();
-                if (pdbs == null)
-                  continue;
-
-                for (int p = 0; p < pdbs.size(); p++)
-                {
-                  PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
-                  if (p1.getId().equals(pdb.getId()))
-                  {
-                    if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
-                      seqs.addElement(ap.av.alignment.getSequenceAt(i));
-
-                    continue;
-                  }
-                }
-              }
-
-              SequenceI[] seqs2 = new SequenceI[seqs.size()];
-              seqs.toArray(seqs2);
-
-              new AppJmol(pdb, seqs2, null, ap);
+            	// TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
+              new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
             }
+
           });
           viewStructureMenu.add(menuItem);
 
@@ -316,7 +297,11 @@ public class PopupMenu extends JPopupMenu
           });
           add(menuItem);
         }
-
+      }
+    }
+    // for the case when no sequences are even visible
+    if (ap.av.hasHiddenRows) {
+      {
         menuItem = new JMenuItem("Reveal All");
         menuItem.addActionListener(new ActionListener()
         {
@@ -337,9 +322,10 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = ap.av.getSelectionGroup();
 
-    if (sg != null)
+    if (sg != null&& sg.getSize()>0)
     {
-      groupName.setText(sg.getName());
+      groupName.setText("Name: "+sg.getName());
+      groupName.setText("Edit name and description of current group.");
 
       if (sg.cs instanceof ZappoColourScheme)
       {
@@ -394,14 +380,53 @@ public class PopupMenu extends JPopupMenu
       {
         conservationMenuItem.setSelected(true);
       }
-      displayNonconserved.setSelected(sg.getShowunconserved());
+      displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
       // add any groupURLs to the groupURL submenu and make it visible
-      if (groupLinks!=null && groupLinks.size()>0) {
+      if (groupLinks != null && groupLinks.size() > 0)
+      {
         buildGroupURLMenu(sg, groupLinks);
       }
+      // Add a 'show all structures' for the current selection
+      Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
+      SequenceI sqass=null;
+      for (SequenceI sq: ap.av.getSequenceSelection())
+      {
+        Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
+        if (pes!=null) {
+          for (PDBEntry pe: pes)
+          {
+            pdbe.put(pe.getId(),  pe);
+            if (sqass==null)
+            {
+              sqass = sq;
+            }
+          }
+        }
+      }
+      if (pdbe.size()>0)
+      {
+        final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
+        final JMenuItem gpdbview;
+        if (pdbe.size()==1)
+        {
+          structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
+        } else {
+          structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
+        }
+        gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+        gpdbview.addActionListener(new ActionListener()
+        {
+          
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+          }
+        });
+      }
     }
     else
     {
@@ -420,9 +445,9 @@ public class PopupMenu extends JPopupMenu
       structureMenu.setVisible(false);
     }
 
-    if (links != null && links.size() > 0)
+    if (seq !=null && links != null && links.size() > 0)
     {
-      
+
       JMenu linkMenu = new JMenu("Link");
       Vector linkset = new Vector();
       for (int i = 0; i < links.size(); i++)
@@ -449,13 +474,13 @@ public class PopupMenu extends JPopupMenu
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
-                  .getDBRef(), new String[]
-          { urlLink.getTarget() });
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+                  seq.getDBRef(), new String[]
+                  { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
-          if (descr!=null && descr.length()<1)
+          if (descr != null && descr.length() < 1)
           {
             descr = null;
           }
@@ -477,10 +502,11 @@ public class PopupMenu extends JPopupMenu
               {
                 for (int u = 0; u < urls.length; u += 2)
                 {
-                  if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                  if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                   {
-                    linkset.addElement(urls[u]+"|"+urls[u+1]);
-                    addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+                    linkset.addElement(urls[u] + "|" + urls[u + 1]);
+                    addshowLink(linkMenu, label + "|" + urls[u],
+                            urls[u + 1]);
                   }
                 }
               }
@@ -494,16 +520,17 @@ public class PopupMenu extends JPopupMenu
             {
               for (int u = 0; u < urls.length; u += 2)
               {
-                if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u]+"|"+urls[u+1]);
+                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
             }
           }
-          // Create urls from description but only for URL links which are regex links
-          if (descr != null && urlLink.getRegexReplace()!=null)
+          // Create urls from description but only for URL links which are regex
+          // links
+          if (descr != null && urlLink.getRegexReplace() != null)
           {
             // create link for this URL from description where regex matches
             String[] urls = urlLink.makeUrls(descr, true);
@@ -511,9 +538,9 @@ public class PopupMenu extends JPopupMenu
             {
               for (int u = 0; u < urls.length; u += 2)
               {
-                if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
                 {
-                  linkset.addElement(urls[u]+"|"+urls[u+1]);
+                  linkset.addElement(urls[u] + "|" + urls[u + 1]);
                   addshowLink(linkMenu, label, urls[u + 1]);
                 }
               }
@@ -522,9 +549,9 @@ public class PopupMenu extends JPopupMenu
         }
         else
         {
-          if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+          if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
           {
-            linkset.addElement(label+"|"+urlLink.getUrl_prefix());
+            linkset.addElement(label + "|" + urlLink.getUrl_prefix());
             // Add a non-dynamic link
             addshowLink(linkMenu, label, urlLink.getUrl_prefix());
           }
@@ -540,119 +567,150 @@ public class PopupMenu extends JPopupMenu
       }
     }
   }
-  
+
   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
   {
-    
-    // TODO: usability: thread off the generation of group url content so root menu appears asap
+
+    // TODO: usability: thread off the generation of group url content so root
+    // menu appears asap
     // sequence only URLs
     // ID/regex match URLs
     groupLinksMenu = new JMenu("Group Link");
-    JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
-    SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); 
+    JMenu[] linkMenus = new JMenu[]
+    { null, new JMenu("IDS"), new JMenu("Sequences"),
+        new JMenu("IDS and Sequences") }; // three types of url that might be
+                                          // created.
+    SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
     Hashtable commonDbrefs = new Hashtable();
-    for (int sq = 0; sq<seqs.length;sq++) {
+    for (int sq = 0; sq < seqs.length; sq++)
+    {
 
-      int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes()); 
+      int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
+              .findPosition(sg.getEndRes());
       // just collect ids from dataset sequence
-      // TODO: check if IDs collected from selecton group intersects with the current selection, too
+      // TODO: check if IDs collected from selecton group intersects with the
+      // current selection, too
       SequenceI sqi = seqs[sq];
-      while (sqi.getDatasetSequence()!=null) {
-        sqi = sqi.getDatasetSequence(); }
+      while (sqi.getDatasetSequence() != null)
+      {
+        sqi = sqi.getDatasetSequence();
+      }
       DBRefEntry[] dbr = sqi.getDBRef();
-      if (dbr!=null && dbr.length>0)
+      if (dbr != null && dbr.length > 0)
       {
-        for (int d=0;d<dbr.length;d++)
+        for (int d = 0; d < dbr.length; d++)
         {
-          String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
           Object[] sarray = (Object[]) commonDbrefs.get(src);
-          if (sarray==null)
+          if (sarray == null)
           {
             sarray = new Object[2];
-            sarray[0] = new int[] { 0 };
+            sarray[0] = new int[]
+            { 0 };
             sarray[1] = new String[seqs.length];
-            
-            commonDbrefs.put(src,sarray);
+
+            commonDbrefs.put(src, sarray);
           }
-          
-          if (((String[])sarray[1])[sq]==null) {
-            if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
-              ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
-              ((int[])sarray[0])[0]++;
+
+          if (((String[]) sarray[1])[sq] == null)
+          {
+            if (!dbr[d].hasMap()
+                    || (dbr[d].getMap().locateMappedRange(start, end) != null))
+            {
+              ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+              ((int[]) sarray[0])[0]++;
             }
           }
         }
       }
     }
     // now create group links for all distinct ID/sequence sets.
-    boolean addMenu = false; // indicates if there are any group links to give to user  
-    for (int i = 0; i < groupLinks.size(); i++) {
-        String link = groupLinks.elementAt(i).toString();
-        GroupUrlLink urlLink = null;
-        try
-        {
-          urlLink = new GroupUrlLink(link);
-        } catch (Exception foo)
-        {
-          jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
-                  + "'", foo);
-          continue;
-        }
-        ;
-        if (!urlLink.isValid())
-        {
-          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
-          continue;
-        }
-        final String label = urlLink.getLabel();
-        boolean usingNames = false;
-        // Now see which parts of the group apply for this URL
-        String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-        Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
-        String[] seqstr,ids; // input to makeUrl
-        if (idset!=null)
+    boolean addMenu = false; // indicates if there are any group links to give
+                             // to user
+    for (int i = 0; i < groupLinks.size(); i++)
+    {
+      String link = groupLinks.elementAt(i).toString();
+      GroupUrlLink urlLink = null;
+      try
+      {
+        urlLink = new GroupUrlLink(link);
+      } catch (Exception foo)
+      {
+        jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+                + "'", foo);
+        continue;
+      }
+      ;
+      if (!urlLink.isValid())
+      {
+        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        continue;
+      }
+      final String label = urlLink.getLabel();
+      boolean usingNames = false;
+      // Now see which parts of the group apply for this URL
+      String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+      Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+      String[] seqstr, ids; // input to makeUrl
+      if (idset != null)
+      {
+        int numinput = ((int[]) idset[0])[0];
+        String[] allids = ((String[]) idset[1]);
+        seqstr = new String[numinput];
+        ids = new String[numinput];
+        for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
         {
-          int numinput = ((int[])idset[0])[0];
-          String[] allids = ((String[])idset[1]);
-          seqstr = new String[numinput];
-          ids = new String[numinput];
-          for (int sq=0,idcount=0;sq<seqs.length;sq++)
+          if (allids[sq] != null)
           {
-            if (allids[sq]!=null) {
-              ids[idcount] = allids[sq];
-              seqstr[idcount++] = idandseqs[1][sq];
-            }
+            ids[idcount] = allids[sq];
+            seqstr[idcount++] = idandseqs[1][sq];
           }
-        } else {
-          // just use the id/seq set
-          seqstr = idandseqs[1];
-          ids = idandseqs[0];
-          usingNames=true;
-        }
-        // and try and make the groupURL!
-        
-        Object[] urlset = urlLink.makeUrls(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
-        if (urlset!=null)
-        {
-          System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
-          // first two bits ofurlLink type bitfield are sequenceids and sequences
-          // TODO: FUTURE: ensure the groupURL menu structure can be generalised
-          addshowLink(linkMenus[urlLink.getGroupURLType() & 3], label + "("+(usingNames ? "Names" : ltarget)+")", ((String[])urlset[3])[0]);
-          addMenu = true;
         }
       }
+      else
+      {
+        // just use the id/seq set
+        seqstr = idandseqs[1];
+        ids = idandseqs[0];
+        usingNames = true;
+      }
+      // and try and make the groupURL!
+
+      Object[] urlset = null;
+      try
+      {
+        urlset = urlLink.makeUrlStubs(ids, seqstr,
+                "FromJalview" + System.currentTimeMillis(), false);
+      } catch (UrlStringTooLongException e)
+      {
+      }
+      if (urlset != null)
+      {
+        int type = urlLink.getGroupURLType() & 3;
+        // System.out.println(urlLink.getGroupURLType()
+        // +" "+((String[])urlset[3])[0]);
+        // first two bits ofurlLink type bitfield are sequenceids and sequences
+        // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+        addshowLink(linkMenus[type], label
+                + (((type & 1) == 1) ? ("("
+                        + (usingNames ? "Names" : ltarget) + ")") : ""),
+                urlLink, urlset);
+        addMenu = true;
+      }
+    }
     if (addMenu)
     {
       groupLinksMenu = new JMenu("Group Links");
-      for (int m=0;m<linkMenus.length; m++)
+      for (int m = 0; m < linkMenus.length; m++)
       {
-        if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+        if (linkMenus[m] != null
+                && linkMenus[m].getMenuComponentCount() > 0)
         {
           groupLinksMenu.add(linkMenus[m]);
         }
       }
-      
+
       groupMenu.add(groupLinksMenu);
     }
   }
@@ -661,10 +719,10 @@ public class PopupMenu extends JPopupMenu
    * add a show URL menu item to the given linkMenu
    * 
    * @param linkMenu
-   * @param label -
-   *                menu label string
-   * @param url -
-   *                url to open
+   * @param label
+   *          - menu label string
+   * @param url
+   *          - url to open
    */
   private void addshowLink(JMenu linkMenu, String label, final String url)
   {
@@ -690,10 +748,59 @@ public class PopupMenu extends JPopupMenu
   }
 
   /**
+   * add a late bound groupURL item to the given linkMenu
+   * 
+   * @param linkMenu
+   * @param label
+   *          - menu label string
+   * @param urlgenerator
+   *          GroupURLLink used to generate URL
+   * @param urlstub
+   *          Object array returned from the makeUrlStubs function.
+   */
+  private void addshowLink(JMenu linkMenu, String label,
+          final GroupUrlLink urlgenerator, final Object[] urlstub)
+  {
+    JMenuItem item = new JMenuItem(label);
+    item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
+            + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
+                                                                             // put
+                                                                             // in
+                                                                             // info
+                                                                             // about
+                                                                             // what
+                                                                             // is
+                                                                             // being
+                                                                             // sent.
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        new Thread(new Runnable()
+        {
+
+          public void run()
+          {
+            try
+            {
+              showLink(urlgenerator.constructFrom(urlstub));
+            } catch (UrlStringTooLongException e)
+            {
+            }
+          }
+
+        }).start();
+      }
+    });
+
+    linkMenu.add(item);
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @throws Exception
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   private void jbInit() throws Exception
   {
@@ -1066,7 +1173,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void showNonconserved_actionPerformed()
   {
-    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    getGroup().setShowNonconserved(displayNonconserved.isSelected());
     refresh();
   }
 
@@ -1085,14 +1192,14 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg
-            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
-            .getWidth());
+    sg.cs = new ClustalxColourScheme(
+            sg.getSequences(ap.av.hiddenRepSequences),
+            ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -1100,7 +1207,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void zappoColour_actionPerformed()
   {
@@ -1112,7 +1219,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void taylorColour_actionPerformed()
   {
@@ -1124,7 +1231,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void hydrophobicityColour_actionPerformed()
   {
@@ -1136,7 +1243,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void helixColour_actionPerformed()
   {
@@ -1148,7 +1255,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void strandColour_actionPerformed()
   {
@@ -1160,7 +1267,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void turnColour_actionPerformed()
   {
@@ -1172,7 +1279,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void buriedColour_actionPerformed()
   {
@@ -1184,7 +1291,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void nucleotideMenuItem_actionPerformed()
   {
@@ -1196,7 +1303,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void abovePIDColour_actionPerformed()
   {
@@ -1208,9 +1315,9 @@ public class PopupMenu extends JPopupMenu
 
     if (abovePIDColour.isSelected())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg
-              .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-              .getEndRes() + 1));
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
@@ -1232,7 +1339,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -1256,15 +1363,15 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-            .getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getEndRes() + 1));
     refresh();
   }
 
@@ -1272,7 +1379,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void BLOSUM62Colour_actionPerformed()
   {
@@ -1280,9 +1387,9 @@ public class PopupMenu extends JPopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-            .getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getEndRes() + 1));
 
     refresh();
   }
@@ -1291,7 +1398,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void noColourmenuItem_actionPerformed()
   {
@@ -1303,7 +1410,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void conservationMenuItem_actionPerformed()
   {
@@ -1316,9 +1423,9 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       Conservation c = new Conservation("Group",
-              ResidueProperties.propHash, 3, sg
-                      .getSequences(ap.av.hiddenRepSequences), sg
-                      .getStartRes(), sg.getEndRes() + 1);
+              ResidueProperties.propHash, 3,
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1);
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
@@ -1345,8 +1452,8 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(sequence
-            .getAnnotation()[0], null,
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+            sequence.getAnnotation()[0], null,
             AnnotationColourGradient.NO_THRESHOLD);
 
     acg.predefinedColours = true;
@@ -1359,15 +1466,16 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void groupName_actionPerformed()
   {
 
     SequenceGroup sg = getGroup();
-    EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
-            .getDescription(), "       Group Name ", "Group Description ",
-            "Edit Group Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+            sg.getDescription(), "       Group Name ",
+            "Group Description ", "Edit Group Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1376,12 +1484,13 @@ public class PopupMenu extends JPopupMenu
 
     sg.setName(dialog.getName());
     sg.setDescription(dialog.getDescription());
+    refresh();
   }
 
   /**
-   * DOCUMENT ME!
+   * Get selection group - adding it to the alignment if necessary.
    * 
-   * @return DOCUMENT ME!
+   * @return sequence group to operate on
    */
   SequenceGroup getGroup()
   {
@@ -1399,13 +1508,14 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void sequenceName_actionPerformed()
   {
-    EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
-            .getDescription(), "       Sequence Name ",
-            "Sequence Description ", "Edit Sequence Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+            sequence.getDescription(), "       Sequence Name ",
+            "Sequence Description ", "Edit Sequence Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1437,7 +1547,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void unGroupMenuItem_actionPerformed()
   {
@@ -1451,7 +1561,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void outline_actionPerformed()
   {
@@ -1471,7 +1581,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showBoxes_actionPerformed()
   {
@@ -1483,7 +1593,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showText_actionPerformed()
   {
@@ -1495,7 +1605,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showColourText_actionPerformed()
   {
@@ -1552,6 +1662,7 @@ public class PopupMenu extends JPopupMenu
     }
 
     ap.av.hideSequence(hseqs);
+    // refresh(); TODO: ? needed ?
     ap.av.sendSelection();
   }
 
@@ -1594,8 +1705,8 @@ public class PopupMenu extends JPopupMenu
         caseChange = ChangeCaseCommand.TO_LOWER;
       }
 
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
-              .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
               caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
@@ -1610,23 +1721,26 @@ public class PopupMenu extends JPopupMenu
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap, "Alignment output - "
-            + e.getActionCommand(), 600, 500);
+    Desktop.addInternalFrame(cap,
+            "Alignment output - " + e.getActionCommand(), 600, 500);
 
     String[] omitHidden = null;
 
     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
-                                            // or we simply trust the user wants
-                                            // wysiwig behaviour
+    // or we simply trust the user wants
+    // wysiwig behaviour
     SequenceGroup sg = ap.av.getSelectionGroup();
     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i = 0; i < nala.length; i++)
+    if (nala != null)
     {
-      AlignmentAnnotation na = nala[i];
-      oal.addAnnotation(na);
+      for (int i = 0; i < nala.length; i++)
+      {
+        AlignmentAnnotation na = nala[i];
+        oal.addAnnotation(na);
+      }
     }
     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
             oal, omitHidden, csel, sg));
@@ -1638,47 +1752,16 @@ public class PopupMenu extends JPopupMenu
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle("Select a PDB file");
-    chooser.setToolTipText("Load a PDB file");
+    chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
+    chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
 
     int value = chooser.showOpenDialog(null);
 
     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
     {
-      PDBEntry entry = new PDBEntry();
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      try
-      {
-        MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-                jalview.io.AppletFormatAdapter.FILE);
-
-        if (pdbfile.id == null)
-        {
-          String reply = JOptionPane
-                  .showInternalInputDialog(
-                          Desktop.desktop,
-                          "Couldn't find a PDB id in the file supplied."
-                                  + "Please enter an Id to identify this structure.",
-                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
-          if (reply == null)
-          {
-            return;
-          }
-
-          entry.setId(reply);
-        }
-        else
-        {
-          entry.setId(pdbfile.id);
-        }
-      } catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
-
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
+      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
     }
 
   }
@@ -1723,25 +1806,25 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    int rsize=0,gSize = sg.getSize();
-    SequenceI[] rseqs,seqs = new SequenceI[gSize];
-    SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
-    
+    int rsize = 0, gSize = sg.getSize();
+    SequenceI[] rseqs, seqs = new SequenceI[gSize];
+    SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
     for (int i = 0; i < gSize; i++)
     {
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
-      if (start<=end)
+      if (start <= end)
       {
         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
         features[rsize] = new SequenceFeature(null, null, null, start, end,
-              "Jalview");
+                "Jalview");
         rsize++;
       }
     }
     rseqs = new SequenceI[rsize];
     tfeatures = new SequenceFeature[rsize];
-    System.arraycopy(seqs,0,rseqs, 0, rsize);
+    System.arraycopy(seqs, 0, rseqs, 0, rsize);
     System.arraycopy(features, 0, tfeatures, 0, rsize);
     features = tfeatures;
     seqs = rseqs;
@@ -1764,8 +1847,7 @@ public class PopupMenu extends JPopupMenu
 
   public void colourByStructure(String pdbid)
   {
-    Annotation[] anots = jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().colourSequenceFromStructure(
+    Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
                     sequence, pdbid);
 
     AlignmentAnnotation an = new AlignmentAnnotation("Structure",
@@ -1791,17 +1873,18 @@ public class PopupMenu extends JPopupMenu
       if (sequence == null)
         sequence = (Sequence) sg.getSequenceAt(0);
 
-      EditNameDialog dialog = new EditNameDialog(sequence
-              .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
-              null, "Edit Sequence ", null, "Edit Sequence");
+      EditNameDialog dialog = new EditNameDialog(
+              sequence.getSequenceAsString(sg.getStartRes(),
+                      sg.getEndRes() + 1), null, "Edit Sequence ", null,
+              "Edit Sequence", ap.alignFrame);
 
       if (dialog.accept)
       {
         EditCommand editCommand = new EditCommand("Edit Sequences",
                 EditCommand.REPLACE, dialog.getName().replace(' ',
-                        ap.av.getGapCharacter()), sg
-                        .getSequencesAsArray(ap.av.hiddenRepSequences), sg
-                        .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+                        ap.av.getGapCharacter()),
+                sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+                sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
         ap.alignFrame.addHistoryItem(editCommand);