updated mapping for EMBL_Services_V1.1.xsd and tested with basic CDS feature detection.

[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 0f4fc24..49d51ad 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -366,24 +366,24 @@ join(1..100,J00194.1:100..202)
             Qualifier q = (Qualifier) quals.next();
             if (q.getName().equals("translation")) 
             {
-              prseq=q.getValue();
+              prseq=q.getValues()[0];
             } 
             else
               if (q.getName().equals("protein_id")) 
               {
-                prid=q.getValue();
+                prid=q.getValues()[0];
               }
               else
                 if (q.getName().equals("codon_start"))
                 {
-                  prstart = Integer.parseInt(q.getValue());
+                  prstart = Integer.parseInt(q.getValues()[0]);
                 }
                 else 
                 if (q.getName().equals("product")){
-                  prname = q.getValue();
+                  prname = q.getValues()[0];
                 } else {
                   // throw anything else into the additional properties hash
-                  vals.put(q.getName(), q.getValue());
+                  vals.put(q.getName(), q.getValues().toString());
                 }
           }
         }