From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 15:04:44 +0000 (+0000)
Subject: debugged mappings and translated sequence recovery
X-Git-Tag: Release_2_4~350
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=385e63c78d289d4beae9c1ad2b187c0ea311ffbc;p=jalview.git

debugged mappings and translated sequence recovery
---

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index e5eecbb..8bbb5f7 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -102,4 +102,18 @@ public Mapping getMap() {
 public void setMap(Mapping map) {
     this.map = map;
 }
+public boolean hasMap()
+{
+  // TODO Auto-generated method stub
+  return map!=null;
+}
+/**
+ * 
+ * @return source+":"+accessionId
+ */
+public String getSrcAccString()
+{
+  return ((source!=null) ? source : "")
+    + ":" + ((accessionId!=null) ? accessionId : "");
+}
 }
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 0063faa..e54b53e 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,121 +1,157 @@
 package jalview.datamodel;
 
+import java.util.Vector;
+
 import jalview.util.MapList;
 
-public class Mapping {
+public class Mapping
+{
   /**
-   * Contains the
-   * start-end pairs mapping from
-   * the associated sequence to the
-   * sequence in the database
-   * coordinate system
-   * it also takes care of step difference between coordinate systems
+   * Contains the start-end pairs mapping from the associated sequence to the
+   * sequence in the database coordinate system it also takes care of step
+   * difference between coordinate systems
    */
-  MapList map=null;
+  MapList map = null;
+
   /**
    * The seuqence that map maps the associated seuqence to (if any).
    */
-  SequenceI to=null;
-  public Mapping(MapList map) {
+  SequenceI to = null;
+
+  public Mapping(MapList map)
+  {
     super();
     this.map = map;
   }
-  public Mapping(SequenceI to, MapList map) {
+
+  public Mapping(SequenceI to, MapList map)
+  {
     this(map);
     this.to = to;
   }
+
   /**
    * create a new mapping from
-   * @param to the sequence being mapped
-   * @param exon int[] {start,end,start,end} series on associated sequence
-   * @param is int[] {start,end,...} ranges on the reference frame being mapped to
-   * @param i step size on associated sequence
-   * @param j step size on mapped frame
+   * 
+   * @param to
+   *          the sequence being mapped
+   * @param exon
+   *          int[] {start,end,start,end} series on associated sequence
+   * @param is
+   *          int[] {start,end,...} ranges on the reference frame being mapped
+   *          to
+   * @param i
+   *          step size on associated sequence
+   * @param j
+   *          step size on mapped frame
    */
   public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
   {
     this(to, new MapList(exon, is, i, j));
   }
+
   /**
-   * create a duplicate (and independent) mapping object with
-   * the same reference to any SequenceI being mapped to.
+   * create a duplicate (and independent) mapping object with the same reference
+   * to any SequenceI being mapped to.
+   * 
    * @param map2
    */
   public Mapping(Mapping map2)
   {
-    if (map2!=this && map2!=null) {
-      if (map2.map!=null)
+    if (map2 != this && map2 != null)
+    {
+      if (map2.map != null)
       {
-        map=new MapList(map2.map);
+        map = new MapList(map2.map);
       }
       to = map2.to;
     }
   }
+
   /**
    * @return the map
    */
-  public MapList getMap() {
+  public MapList getMap()
+  {
     return map;
   }
 
   /**
-   * @param map the map to set
+   * @param map
+   *          the map to set
    */
-  public void setMap(MapList map) {
+  public void setMap(MapList map)
+  {
     this.map = map;
   }
+
   /**
    * Equals that compares both the to references and MapList mappings.
+   * 
    * @param other
    * @return
    */
-  public boolean equals(Mapping other) {
-    if (other==null)
+  public boolean equals(Mapping other)
+  {
+    if (other == null)
       return false;
-    if (other==this)
+    if (other == this)
       return true;
-    if (other.to!=to)
+    if (other.to != to)
       return false;
-    if ((map!=null && other.map==null) || (map==null && other.map!=null))
+    if ((map != null && other.map == null)
+            || (map == null && other.map != null))
       return false;
     if (map.equals(other.map))
       return true;
     return false;
   }
+
   /**
-   * get the 'initial' position in the associated
-   * sequence for a position in the mapped reference frame
+   * get the 'initial' position in the associated sequence for a position in the
+   * mapped reference frame
+   * 
    * @param mpos
    * @return
    */
   public int getPosition(int mpos)
   {
-    if (map!=null) {
+    if (map != null)
+    {
       int[] mp = map.shiftTo(mpos);
-      if (mp!=null)
+      if (mp != null)
       {
         return mp[0];
       }
     }
     return mpos;
   }
+
   /**
-   * gets boundary in direction of mapping 
-   * @param position in mapped reference frame
-   * @return int{start, end} positions in associated sequence (in direction of mapped word)
+   * gets boundary in direction of mapping
+   * 
+   * @param position
+   *          in mapped reference frame
+   * @return int{start, end} positions in associated sequence (in direction of
+   *         mapped word)
    */
-  public int[] getWord(int mpos) {
-    if (map!=null) {
+  public int[] getWord(int mpos)
+  {
+    if (map != null)
+    {
       return map.getToWord(mpos);
     }
     return null;
   }
+
   /**
    * width of mapped unit in associated sequence
-   *
+   * 
    */
-  public int getWidth() {
-    if (map!=null) {
+  public int getWidth()
+  {
+    if (map != null)
+    {
       return map.getFromRatio();
     }
     return 1;
@@ -123,103 +159,263 @@ public class Mapping {
 
   /**
    * width of unit in mapped reference frame
+   * 
    * @return
    */
-  public int getMappedWidth() {
-    if (map!=null) {
+  public int getMappedWidth()
+  {
+    if (map != null)
+    {
       return map.getToRatio();
     }
     return 1;
   }
+
   /**
-   * get mapped position in the associated
-   * reference frame for position pos in the
-   * associated sequence.
+   * get mapped position in the associated reference frame for position pos in
+   * the associated sequence.
+   * 
    * @param pos
    * @return
    */
-  public int getMappedPosition(int pos) {
-    if (map!=null) {
+  public int getMappedPosition(int pos)
+  {
+    if (map != null)
+    {
       int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
+      if (mp != null)
       {
         return mp[0];
       }
     }
     return pos;
   }
-  public int[] getMappedWord(int pos) {
-    if (map!=null) {
+
+  public int[] getMappedWord(int pos)
+  {
+    if (map != null)
+    {
       int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
+      if (mp != null)
       {
-        return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};
+        return new int[]
+        { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
       }
     }
     return null;
   }
+
   /**
-   * locates the region of feature f in the associated sequence's reference frame
+   * locates the region of feature f in the associated sequence's reference
+   * frame
+   * 
    * @param f
    * @return one or more features corresponding to f
    */
   public SequenceFeature[] locateFeature(SequenceFeature f)
   {
-    if (true) { // f.getBegin()!=f.getEnd()) {
-      if (map!=null) {
+    if (true)
+    { // f.getBegin()!=f.getEnd()) {
+      if (map != null)
+      {
         int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
-        SequenceFeature[] vf = new SequenceFeature[frange.length/2];
-        for (int i=0,v=0;i<frange.length;i+=2,v++) {
+        SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
+        for (int i = 0, v = 0; i < frange.length; i += 2, v++)
+        {
           vf[v] = new SequenceFeature(f);
           vf[v].setBegin(frange[i]);
-          vf[v].setEnd(frange[i+1]);
-          if (frange.length>2)
-            vf[v].setDescription(f.getDescription() +"\nPart "+v);
+          vf[v].setEnd(frange[i + 1]);
+          if (frange.length > 2)
+            vf[v].setDescription(f.getDescription() + "\nPart " + v);
         }
         return vf;
       }
     }
-    if (false) //else
+    if (false) // else
     {
       int[] word = getWord(f.getBegin());
-      if (word[0]<word[1])
+      if (word[0] < word[1])
       {
         f.setBegin(word[0]);
-      } else {
+      }
+      else
+      {
         f.setBegin(word[1]);
       }
       word = getWord(f.getEnd());
-      if (word[0]>word[1])
+      if (word[0] > word[1])
       {
         f.setEnd(word[0]);
-      } else {
+      }
+      else
+      {
         f.setEnd(word[1]);
       }
     }
     // give up and just return the feature.
-    return new SequenceFeature[] { f };
+    return new SequenceFeature[]
+    { f };
   }
 
-    /**
-   * return a series of contigs on the associated sequence corresponding to
-   * the from,to interval on the mapped reference frame
+  /**
+   * return a series of contigs on the associated sequence corresponding to the
+   * from,to interval on the mapped reference frame
+   * 
    * @param from
    * @param to
-   * @return
+   * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+   *         associated sequence}
    */
-  public int[] locateRange(int from, int to) {
-    //TODO
-    return null;
+  public int[] locateRange(int from, int to)
+  {
+    if (map != null)
+    {
+      if (from <= to)
+      {
+        from = (map.getToLowest() < from) ? from : map.getToLowest();
+        to = (map.getToHighest() > to) ? to : map.getToHighest();
+        if (from > to)
+          return null;
+      }
+      else
+      {
+        from = (map.getToHighest() > from) ? from : map.getToHighest();
+        to = (map.getToLowest() < to) ? to : map.getToLowest();
+        if (from < to)
+          return null;
+      }
+      return map.locateInFrom(from, to);
+    }
+    return new int[]
+    { from, to };
   }
+
   /**
-   * return a series of contigs on the mapped reference frame corresponding to
-   * the from,to interval on the associated sequence
+   * return a series of mapped contigs mapped from a range on the associated
+   * sequence
+   * 
    * @param from
    * @param to
    * @return
    */
-  public int[] locateMappedRange(int from, int to) {
-    //TODO
-    return null;
+  public int[] locateMappedRange(int from, int to)
+  {
+    if (map != null)
+    {
+
+      if (from <= to)
+      {
+        from = (map.getFromLowest() < from) ? from : map.getFromLowest();
+        to = (map.getFromHighest() > to) ? to : map.getFromHighest();
+        if (from > to)
+          return null;
+      }
+      else
+      {
+        from = (map.getFromHighest() > from) ? from : map.getFromHighest();
+        to = (map.getFromLowest() < to) ? to : map.getFromLowest();
+        if (from < to)
+          return null;
+      }
+      return map.locateInTo(from, to);
+    }
+    return new int[]
+    { from, to };
+  }
+
+  /**
+   * return a new mapping object with a maplist modifed to only map the visible
+   * regions defined by viscontigs.
+   * 
+   * @param viscontigs
+   * @return
+   */
+  public Mapping intersectVisContigs(int[] viscontigs)
+  {
+    Mapping copy = new Mapping(this);
+    if (map != null)
+    {
+      int vpos = 0;
+      int apos = 0;
+      Vector toRange = new Vector();
+      Vector fromRange = new Vector();
+      for (int vc = 0; vc < viscontigs.length; vc += 2)
+      {
+        // find a mapped range in this visible region
+        int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+        if (mpr != null)
+        {
+          for (int m = 0; m < mpr.length; m += 2)
+          {
+            toRange.addElement(new int[]
+            { mpr[m], mpr[m + 1] });
+            int[] xpos = locateRange(mpr[m], mpr[m + 1]);
+            for (int x = 0; x < xpos.length; x += 2)
+            {
+              fromRange.addElement(new int[]
+              { xpos[x], xpos[x + 1] });
+            }
+          }
+        }
+      }
+      int[] from = new int[fromRange.size()*2];
+      int[] to = new int[toRange.size()*2];
+      int[] r;
+      for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+      {
+        r = (int[]) fromRange.elementAt(f);
+        from[f*2] = r[0];
+        from[f*2+1] = r[1];
+      }
+      for (int f=0,fSize=toRange.size(); f<fSize; f++)
+      {
+        r = (int[]) toRange.elementAt(f);
+        to[f*2] = r[0];
+        to[f*2+1] = r[1];
+      }
+      copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+    }
+    return copy;
+  }
+  public static void main(String[] args)
+  {
+    /**
+     * trite test of the intersectVisContigs method
+     * for a simple DNA -> Protein exon map and a range of visContigs
+     */
+    MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+    Mapping m = new Mapping(fk);
+    Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
+    Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
+    System.out.println(""+m_1.map.getFromRanges());
+    
+    
+  }
+  /**
+   * get the sequence being mapped to - if any
+   * @return null or a dataset sequence
+   */
+  public SequenceI getTo()
+  {
+    return to;
+  }
+  /**
+   * set the dataset sequence being mapped to if any
+   * @param tto
+   */
+  public void setTo(SequenceI tto)
+  {
+    to = tto;
+  }
+
+  /* (non-Javadoc)
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    map = null;
+    to = null;
+    super.finalize();
   }
+  
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index a22eff7..906122d 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -3,6 +3,7 @@ package jalview.datamodel.xdb.embl;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -405,7 +406,6 @@ public class EmblEntry
     {
       for (Iterator i = features.iterator(); i.hasNext();)
       {
-        boolean nextFeature=false;
         EmblFeature feature = (EmblFeature) i.next();
         if (!noNa)
         {
@@ -416,133 +416,9 @@ public class EmblEntry
               ;
           }
         }
-        if (FeatureProperties.isCodingFeature(DBRefSource.EMBL, "CDS"))
+        if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
         {
-          // extract coding region(s)
-          jalview.datamodel.Mapping map = null;
-          int[] exon = null;
-          if (feature.locations != null && feature.locations.size() > 0)
-          {
-            for (Enumeration locs = feature.locations.elements(); locs
-                    .hasMoreElements();)
-            {
-              EmblFeatureLocations loc = (EmblFeatureLocations) locs
-                      .nextElement();
-              int[] se = loc.getElementRanges(accession);
-              if (exon == null)
-              {
-                exon = se;
-              }
-              else
-              {
-                int[] t = new int[exon.length + se.length];
-                System.arraycopy(exon, 0, t, 0, exon.length);
-                System.arraycopy(se, 0, t, exon.length, se.length);
-                exon = t;
-              }
-            }
-          }
-          String prseq = null;
-          String prname = new String();
-          String prid = null;
-          Hashtable vals = new Hashtable();
-          int prstart = 1;
-          // get qualifiers
-          if (feature.getQualifiers() != null
-                  && feature.getQualifiers().size() > 0)
-          {
-            for (Iterator quals = feature.getQualifiers().iterator(); quals
-                    .hasNext();)
-            {
-              Qualifier q = (Qualifier) quals.next();
-              if (q.getName().equals("translation"))
-              {
-                prseq = q.getValues()[0];
-              }
-              else if (q.getName().equals("protein_id"))
-              {
-                prid = q.getValues()[0];
-              }
-              else if (q.getName().equals("codon_start"))
-              {
-                prstart = Integer.parseInt(q.getValues()[0]);
-              }
-              else if (q.getName().equals("product"))
-              {
-                prname = q.getValues()[0];
-              }
-              else
-              {
-                // throw anything else into the additional properties hash
-                vals.put(q.getName(), q.getValues().toString());
-              }
-            }
-          }
-          Sequence product = null;
-          if (prseq != null && prname != null && prid != null)
-          {
-            // extract proteins.
-            if (!noPeptide)
-            {
-              product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
-                      + "|" + prname, prseq, prstart, prstart
-                      + prseq.length() - 1);
-              product.setDescription("Protein Product from " + sourceDb);
-              seqs.add(product);
-            }
-            // we have everything - create the mapping and perhaps the protein
-            // sequence
-            map = new jalview.datamodel.Mapping(product, exon, new int[]
-            { prstart, prstart + prseq.length() - 1 }, 3, 1);
-            // add cds feature to dna seq - this may include the stop codon
-            for (int xint = 0; xint < exon.length; xint += 2)
-            {
-              SequenceFeature sf = new SequenceFeature();
-              sf.setBegin(exon[xint]);
-              sf.setEnd(exon[xint + 1]);
-              sf.setType(feature.getName());
-              sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);
-              sf.setDescription("Exon " + (1 + xint) + " for protein '"
-                      + prname + "' EMBLCDS:" + prid);
-              sf.setValue(FeatureProperties.EXONPOS, new Integer(1+xint));
-              sf.setValue(FeatureProperties.EXONPRODUCT, prname);
-              if (vals != null && vals.size() > 0)
-              {
-                Enumeration kv = vals.elements();
-                while (kv.hasMoreElements())
-                {
-                  Object key = kv.nextElement();
-                  if (key != null)
-                    sf.setValue(key.toString(), vals.get(key));
-                }
-              }
-              dna.addSequenceFeature(sf);
-            }
-          }
-          // add dbRefs to sequence
-          if (feature.dbRefs != null && feature.dbRefs.size() > 0)
-          {
-            for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
-            {
-              DBRefEntry ref = (DBRefEntry) dbr.next();
-              ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
-                      .getSource()));
-              // Hard code the kind of protein product accessions that EMBL cite
-              if (ref.getSource().equals(
-                      jalview.datamodel.DBRefSource.UNIPROT))
-              {
-                ref.setMap(map);
-              }
-              if (product != null)
-              {
-                DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                        .getVersion(), ref.getAccessionId());
-                pref.setMap(null); // reference is direct
-              }
-              dna.addDBRef(ref);
-            }
-          }
-
+          parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
         }
         else
         {
@@ -558,15 +434,17 @@ public class EmblEntry
           }
         }
       }
-    } catch (Exception e)
+    } 
+    catch (Exception e)
     {
       System.err.println("EMBL Record Features parsing error!");
-      System.err.println("Please report the following to help@jalview.org :");
-      System.err.println("EMBL Record "+accession);
-      System.err.println("Resulted in exception: "+e.getMessage());
+      System.err
+              .println("Please report the following to help@jalview.org :");
+      System.err.println("EMBL Record " + accession);
+      System.err.println("Resulted in exception: " + e.getMessage());
       e.printStackTrace(System.err);
     }
-    if (!noNa && dna!=null)
+    if (!noNa && dna != null)
     {
       seqs.add(dna);
     }
@@ -578,4 +456,218 @@ public class EmblEntry
     }
     return sqs;
   }
+
+  /**
+   * attempt to extract coding region and product from a feature and properly decorate it with annotations.
+   * @param feature coding feature
+   * @param sourceDb source database for the EMBLXML
+   * @param seqs place where sequences go
+   * @param dna parent dna sequence for this record
+   * @param noPeptide flag for generation of Peptide sequence objects
+   */
+  private void parseCodingFeature(EmblFeature feature, String sourceDb, Vector seqs, Sequence dna, boolean noPeptide)
+  {
+    boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+    // extract coding region(s)
+    jalview.datamodel.Mapping map = null;
+    int[] exon = null;
+    if (feature.locations != null && feature.locations.size() > 0)
+    {
+      for (Enumeration locs = feature.locations.elements(); locs
+              .hasMoreElements();)
+      {
+        EmblFeatureLocations loc = (EmblFeatureLocations) locs
+                .nextElement();
+        int[] se = loc.getElementRanges(accession);
+        if (exon == null)
+        {
+          exon = se;
+        }
+        else
+        {
+          int[] t = new int[exon.length + se.length];
+          System.arraycopy(exon, 0, t, 0, exon.length);
+          System.arraycopy(se, 0, t, exon.length, se.length);
+          exon = t;
+        }
+      }
+    }
+    String prseq = null;
+    String prname = new String();
+    String prid = null;
+    Hashtable vals = new Hashtable();
+    int prstart = 1;
+    // get qualifiers
+    if (feature.getQualifiers() != null
+            && feature.getQualifiers().size() > 0)
+    {
+      for (Iterator quals = feature.getQualifiers().iterator(); quals
+              .hasNext();)
+      {
+        Qualifier q = (Qualifier) quals.next();
+        if (q.getName().equals("translation"))
+        {
+          StringBuffer prsq = new StringBuffer(q.getValues()[0]);
+          int p = prsq.indexOf(" ");
+          while (p > -1)
+          {
+            prsq.deleteCharAt(p);
+            p = prsq.indexOf(" ", p);
+          }
+          prseq = prsq.toString();
+          prsq = null;
+
+        }
+        else if (q.getName().equals("protein_id"))
+        {
+          prid = q.getValues()[0];
+        }
+        else if (q.getName().equals("codon_start"))
+        {
+          prstart = Integer.parseInt(q.getValues()[0]);
+        }
+        else if (q.getName().equals("product"))
+        {
+          prname = q.getValues()[0];
+        }
+        else
+        {
+          // throw anything else into the additional properties hash
+          vals.put(q.getName(), q.getValues().toString());
+        }
+      }
+    }
+    Sequence product = null;
+    if (prseq != null && prname != null && prid != null)
+    {
+      // extract proteins.
+      product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
+              +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart
+              + prseq.length() - 1);
+      product.setDescription("Protein Product from " + sourceDb);
+      
+      if (!noPeptide)
+      {
+        // Protein is also added to vector of sequences returned
+        seqs.add(product);
+      }
+      // we have everything - create the mapping and perhaps the protein
+      // sequence
+      if (exon == null || exon.length == 0)
+      {
+        System.err
+                .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+                        + sourceDb + ":" + getAccession() + ")");
+        if (prseq.length() * 3 == dna.getSequence().length)
+        {
+          // this might occur for CDS sequences where no features are
+          // marked.
+          exon = new int[]
+          { dna.getStart(), dna.getEnd() };
+          map = new jalview.datamodel.Mapping(product, exon,
+                  new int[]
+                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+        }
+        if ((prseq.length() + 1) * 3 == dna.getSequence().length)
+        {
+          exon = new int[]
+          { dna.getStart(), dna.getEnd() - 3 };
+          map = new jalview.datamodel.Mapping(product, exon,
+                  new int[]
+                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+        }
+      }
+      else
+      {
+        if (isEmblCdna)
+        {
+          // TODO: Add a DbRef back to the parent EMBL sequence with the exon
+          // map
+
+          // make a new feature annotating the coding contig
+        }
+        else
+        {
+          map = new jalview.datamodel.Mapping(product, exon,
+                  new int[]
+                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          // reconstruct the EMBLCDS entry
+          DBRefEntry pcdnaref = new DBRefEntry();
+          pcdnaref.setAccessionId(prid);
+          pcdnaref.setSource(DBRefSource.EMBLCDS);
+          pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
+          jalview.util.MapList mp = new jalview.util.MapList(new int[]
+          { 1+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
+          pcdnaref.setMap(new Mapping(mp));
+          if (product!=null)
+            product.addDBRef(pcdnaref);
+          
+        }
+      }
+      // add cds feature to dna seq - this may include the stop codon
+      for (int xint = 0; exon != null && xint < exon.length; xint += 2)
+      {
+        SequenceFeature sf = new SequenceFeature();
+        sf.setBegin(exon[xint]);
+        sf.setEnd(exon[xint + 1]);
+        sf.setType(feature.getName());
+        sf.setFeatureGroup(sourceDb);
+        sf.setDescription("Exon " + (1 + xint) + " for protein '"
+                + prname + "' EMBLCDS:" + prid);
+        sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
+        sf.setValue(FeatureProperties.EXONPRODUCT, prname);
+        if (vals != null && vals.size() > 0)
+        {
+          Enumeration kv = vals.elements();
+          while (kv.hasMoreElements())
+          {
+            Object key = kv.nextElement();
+            if (key != null)
+              sf.setValue(key.toString(), vals.get(key));
+          }
+        }
+        dna.addSequenceFeature(sf);
+      }
+    }
+    // add dbRefs to sequence
+    if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+    {
+      for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+      {
+        DBRefEntry ref = (DBRefEntry) dbr.next();
+        ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
+                .getSource()));
+        // Hard code the kind of protein product accessions that EMBL cite
+        if (ref.getSource().equals(
+                jalview.datamodel.DBRefSource.UNIPROT))
+        {
+          ref.setMap(map);
+          /*if (map.getTo()!=null)
+          {
+            map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId());
+          }*/
+        }
+        if (product != null)
+        {
+          DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
+                  .getVersion(), ref.getAccessionId());
+          pref.setMap(null); // reference is direct
+          product.addDBRef(pref);
+          // Add converse mapping reference
+          if (map != null)
+          {
+            Mapping pmap = new Mapping(dna, map.getMap().getInverse());
+            pref = new DBRefEntry(sourceDb, getVersion(), this
+                    .getAccession());
+            pref.setMap(pmap);
+            if (map.getTo()!=null)
+            {
+              map.getTo().addDBRef(pref);
+            }
+          }
+        }
+        dna.addDBRef(ref);
+      }
+    }
+  }
 }
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index a9fe76e..0341ec3 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -78,7 +78,7 @@ public class EmblFeatureLocations {
               }
             }
         }
-    }
+    } else 
     if (locationType.equalsIgnoreCase("join")) {
         for (Enumeration le=locElements.elements();le.hasMoreElements();) {
           EmblFeatureLocElement loce = (EmblFeatureLocElement) le.nextElement();
@@ -92,10 +92,13 @@ public class EmblFeatureLocations {
           }
         }
         return se;
-    }
+    } else
     if (locationType!=null)
     {
-      jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
+      if (jalview.bin.Cache.log!=null)
+        jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
+      else
+        System.err.println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
     }
     // trim range if necessary.
     if (se!=null && sepos!=se.length)