Merge commit

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 3c88083..fc57b27 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -425,9 +425,13 @@ public class EmblEntry
       { 1, dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
+      {
         for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
                 .addDBRef((DBRefEntry) i.next()))
+        {
           ;
+        }
+      }
     }
     try
     {
@@ -440,7 +444,9 @@ public class EmblEntry
           {
             for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                     .addDBRef((DBRefEntry) dbr.next()))
+            {
               ;
+            }
           }
         }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -456,7 +462,9 @@ public class EmblEntry
             {
               for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                       .addDBRef((DBRefEntry) dbr.next()))
+              {
                 ;
+              }
             }
           }
         }
@@ -582,8 +590,10 @@ public class EmblEntry
       }
     }
     Sequence product = null;
+    DBRefEntry protEMBLCDS = null;
     exon = adjustForPrStart(prstart, exon);
-
+    boolean noProteinDbref=true;
+    
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
@@ -659,8 +669,14 @@ public class EmblEntry
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
           if (product != null)
+          {
             product.addDBRef(pcdnaref);
-
+            protEMBLCDS = new DBRefEntry(pcdnaref);
+            protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+            product.addDBRef(protEMBLCDS);
+            
+          }     
+          
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -671,18 +687,20 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + (int) (xint / 2))
+        sf.setDescription("Exon " + (1 + xint / 2)
                 + " 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();
+          Enumeration kv = vals.keys();
           while (kv.hasMoreElements())
           {
             Object key = kv.nextElement();
             if (key != null)
+            {
               sf.setValue(key.toString(), vals.get(key));
+            }
           }
         }
         dna.addSequenceFeature(sf);
@@ -712,6 +730,7 @@ public class EmblEntry
                               + ref.getAccessionId());
             }
           }
+          noProteinDbref = false;
         }
         if (product != null)
         {
@@ -734,6 +753,33 @@ public class EmblEntry
         }
         dna.addDBRef(ref);
       }
+      if (noProteinDbref && product != null)
+      {
+        // add protein coding reference to dna sequence so xref matches
+        if (protEMBLCDS == null)
+        {
+          protEMBLCDS = new DBRefEntry();
+          protEMBLCDS.setAccessionId(prid);
+          protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+          protEMBLCDS.setVersion(getVersion());
+          protEMBLCDS
+                  .setMap(new Mapping(product, map.getMap().getInverse()));
+        }
+        product.addDBRef(protEMBLCDS);
+          
+        // Add converse mapping reference
+        if (map != null)
+        {
+          Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+                  .getInverse());
+          DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+          ncMap.setMap(pmap);
+          if (map.getTo() != null)
+          {
+            dna.addDBRef(ncMap);
+          }
+        }
+      }
     }
   }