JAL-2113 tidy up canonicalisation of Uniprot xrefs in EMBL data

[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 ac0d339..43581da 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -210,13 +210,14 @@ public class EmblEntry
       }
     }
 
+    SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
     try
     {
       for (EmblFeature feature : features)
       {
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
         {
-          parseCodingFeature(feature, sourceDb, dna, peptides);
+          parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
         }
       }
     } catch (Exception e)
@@ -244,9 +245,11 @@ public class EmblEntry
    *          parent dna sequence for this record
    * @param peptides
    *          list of protein product sequences for Embl entry
+   * @param matcher
+   *          helper to match xrefs in already retrieved sequences
    */
   void parseCodingFeature(EmblFeature feature, String sourceDb,
-          SequenceI dna, List<SequenceI> peptides)
+          SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
 
@@ -256,7 +259,6 @@ public class EmblEntry
     String prname = "";
     String prid = null;
     Map<String, String> vals = new Hashtable<String, String>();
-    SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
 
     /*
      * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS