Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110

[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..5409d5b 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -198,6 +198,7 @@ public class EmblEntry
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
 
+
     /*
      * transform EMBL Database refs to canonical form
      */
@@ -210,13 +211,14 @@ 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 +246,11 @@ 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 +260,6 @@ 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
@@ -280,13 +283,13 @@ public class EmblEntry
         }
         else if (qname.equals("protein_id"))
         {
-          prid = q.getValues()[0];
+          prid = q.getValues()[0].trim();
         }
         else if (qname.equals("codon_start"))
         {
           try
           {
-            codonStart = Integer.parseInt(q.getValues()[0]);
+            codonStart = Integer.parseInt(q.getValues()[0].trim());
           } catch (NumberFormatException e)
           {
             System.err.println("Invalid codon_start in XML for "
@@ -296,7 +299,7 @@ public class EmblEntry
         else if (qname.equals("product"))
         {
           // sometimes name is returned e.g. for V00488
-          prname = q.getValues()[0];
+          prname = q.getValues()[0].trim();
         }
         else
         {