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 a0e1234..5409d5b 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -21,6 +21,7 @@
 package jalview.datamodel.xdb.embl;
 
 import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
@@ -34,6 +35,7 @@ import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
+import java.text.ParseException;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
@@ -195,33 +197,28 @@ public class EmblEntry
     // dbref
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
             new int[] { 1, dna.getLength() }, 1, 1));
-    // TODO: transform EMBL Database refs to canonical form
+
+
+    /*
+     * transform EMBL Database refs to canonical form
+     */
     if (dbRefs != null)
     {
       for (DBRefEntry dbref : dbRefs)
       {
+        dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
         dna.addDBRef(dbref);
       }
     }
 
+    SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
     try
     {
       for (EmblFeature feature : features)
       {
-        if (feature.dbRefs != null)
-        {
-          for (DBRefEntry dbref : feature.dbRefs)
-          {
-            /*
-             * convert UniProtKB/Swiss-Prot to UNIPROT
-             */
-            dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
-            dna.addDBRef(dbref);
-          }
-        }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
         {
-          parseCodingFeature(feature, sourceDb, dna, peptides);
+          parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
         }
       }
     } catch (Exception e)
@@ -249,9 +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);
 
@@ -261,7 +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
@@ -285,13 +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 "
@@ -301,7 +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
         {
@@ -423,13 +421,17 @@ public class EmblEntry
     }
 
     /*
-     * add mappings for Uniprot xrefs
+     * add dbRefs to sequence, and mappings for Uniprot xrefs
      */
     if (feature.dbRefs != null)
     {
       boolean mappingUsed = false;
       for (DBRefEntry ref : feature.dbRefs)
       {
+        /*
+         * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+         */
+        ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
         if (ref.getSource().equals(DBRefSource.UNIPROT))
         {
           String proteinSeqName = DBRefSource.UNIPROT + "|"
@@ -485,6 +487,7 @@ public class EmblEntry
             }
           }
         }
+        dna.addDBRef(ref);
       }
       if (noProteinDbref && product != null)
       {
@@ -566,7 +569,7 @@ public class EmblEntry
   }
 
   /**
-   * Returns the CDS positions as a list of [start, end, start, end...]
+   * Returns the CDS positions as a single array of [start, end, start, end...]
    * positions. If on the reverse strand, these will be in descending order.
    * 
    * @param feature
@@ -578,8 +581,18 @@ public class EmblEntry
     {
       return new int[] {};
     }
-    List<int[]> ranges = DnaUtils.parseLocation(feature.location);
-    return ranges == null ? new int[] {} : listToArray(ranges);
+
+    try
+    {
+      List<int[]> ranges = DnaUtils.parseLocation(feature.location);
+      return listToArray(ranges);
+    } catch (ParseException e)
+    {
+      Cache.log.warn(String.format(
+              "Not parsing inexact CDS location %s in ENA %s",
+              feature.location, this.accession));
+      return new int[] {};
+    }
   }
 
   /**