X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9a0def1eabe77ae26d42083e6007c3894ff47ead;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=341aac2ab0f7490953a68853ced694b4c58eb20a;hpb=a4934bec020d9d80ccc0059e7cf198f8ba5a314d;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 341aac2..9a0def1 100755
--- 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;
 
@@ -31,6 +30,7 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
 import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.UrlLink;
 
 /**
@@ -140,14 +140,15 @@ 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 +156,8 @@ 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
@@ -394,12 +396,13 @@ 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);
       }
     }
@@ -422,7 +425,7 @@ public class PopupMenu extends JPopupMenu
 
     if (links != null && links.size() > 0)
     {
-      
+
       JMenu linkMenu = new JMenu("Link");
       Vector linkset = new Vector();
       for (int i = 0; i < links.size(); i++)
@@ -455,7 +458,7 @@ public class PopupMenu extends JPopupMenu
           // 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 +480,11 @@ 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 +498,17 @@ 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 +516,9 @@ 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 +527,9 @@ 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());
           }
@@ -540,120 +545,150 @@ 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.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
-        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;
         }
       }
+      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);
     }
   }
@@ -662,10 +697,10 @@ 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)
   {
@@ -689,19 +724,32 @@ public class PopupMenu extends JPopupMenu
 
     linkMenu.add(item);
   }
+
   /**
    * 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.
+   * @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)
+  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.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)
@@ -711,7 +759,12 @@ public class PopupMenu extends JPopupMenu
 
           public void run()
           {
-            showLink(urlgenerator.constructFrom(urlstub));
+            try
+            {
+              showLink(urlgenerator.constructFrom(urlstub));
+            } catch (UrlStringTooLongException e)
+            {
+            }
           }
 
         }).start();
@@ -720,11 +773,12 @@ public class PopupMenu extends JPopupMenu
 
     linkMenu.add(item);
   }
+
   /**
    * DOCUMENT ME!
    * 
    * @throws Exception
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   private void jbInit() throws Exception
   {
@@ -1097,7 +1151,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void showNonconserved_actionPerformed()
   {
-    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    getGroup().setShowNonconserved(displayNonconserved.isSelected());
     refresh();
   }
 
@@ -1116,7 +1170,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void clustalColour_actionPerformed()
   {
@@ -1131,7 +1185,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void zappoColour_actionPerformed()
   {
@@ -1143,7 +1197,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void taylorColour_actionPerformed()
   {
@@ -1155,7 +1209,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void hydrophobicityColour_actionPerformed()
   {
@@ -1167,7 +1221,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void helixColour_actionPerformed()
   {
@@ -1179,7 +1233,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void strandColour_actionPerformed()
   {
@@ -1191,7 +1245,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void turnColour_actionPerformed()
   {
@@ -1203,7 +1257,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void buriedColour_actionPerformed()
   {
@@ -1215,7 +1269,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void nucleotideMenuItem_actionPerformed()
   {
@@ -1227,7 +1281,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void abovePIDColour_actionPerformed()
   {
@@ -1263,7 +1317,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -1287,7 +1341,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void PIDColour_actionPerformed()
   {
@@ -1303,7 +1357,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void BLOSUM62Colour_actionPerformed()
   {
@@ -1322,7 +1376,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void noColourmenuItem_actionPerformed()
   {
@@ -1334,7 +1388,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void conservationMenuItem_actionPerformed()
   {
@@ -1390,7 +1444,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void groupName_actionPerformed()
   {
@@ -1398,7 +1452,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
             .getDescription(), "       Group Name ", "Group Description ",
-            "Edit Group Name/Description");
+            "Edit Group Name/Description", ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1411,7 +1465,7 @@ public class PopupMenu extends JPopupMenu
   }
 
   /**
-   * Get selection group - adding it to the alignment if necessary. 
+   * Get selection group - adding it to the alignment if necessary.
    * 
    * @return sequence group to operate on
    */
@@ -1431,13 +1485,13 @@ 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");
+            "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1469,7 +1523,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void unGroupMenuItem_actionPerformed()
   {
@@ -1483,7 +1537,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void outline_actionPerformed()
   {
@@ -1503,7 +1557,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showBoxes_actionPerformed()
   {
@@ -1515,7 +1569,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showText_actionPerformed()
   {
@@ -1527,7 +1581,7 @@ public class PopupMenu extends JPopupMenu
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void showColourText_actionPerformed()
   {
@@ -1649,17 +1703,19 @@ public class PopupMenu extends JPopupMenu
     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++)
-    {
-      AlignmentAnnotation na = nala[i];
-      oal.addAnnotation(na);
+    if (nala!=null) {
+      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));
@@ -1756,25 +1812,25 @@ 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;
@@ -1826,7 +1882,7 @@ public class PopupMenu extends JPopupMenu
 
       EditNameDialog dialog = new EditNameDialog(sequence
               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
-              null, "Edit Sequence ", null, "Edit Sequence");
+              null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame);
 
       if (dialog.accept)
       {