X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=56b132508ce5ad76c91fef93ce9885864fb02443;hb=c14d9e8c9ff59de1857d4834ee70e80abf623415;hp=67d70595c9cb50ab9d52df716a94705248567057;hpb=10083e0731425dedd9c2e4f3677dbdee2db8bc33;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 67d7059..56b1325 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -187,12 +187,12 @@ public class EmblEntry
    */
   public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
   {
-    SequenceI dna = new Sequence(sourceDb + "|" + accession,
-            sequence.getSequence());
+    SequenceI dna = makeSequence(sourceDb);
     dna.setDescription(description);
     DBRefEntry retrievedref = new DBRefEntry(sourceDb,
             getSequenceVersion(), accession);
     dna.addDBRef(retrievedref);
+    dna.setSourceDBRef(retrievedref);
     // add map to indicate the sequence is a valid coordinate frame for the
     // dbref
     retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
@@ -235,6 +235,17 @@ public class EmblEntry
   }
 
   /**
+   * @param sourceDb
+   * @return
+   */
+  SequenceI makeSequence(String sourceDb)
+  {
+    SequenceI dna = new Sequence(sourceDb + "|" + accession,
+            sequence.getSequence());
+    return dna;
+  }
+
+  /**
    * Extracts coding region and product from a CDS feature and properly decorate
    * it with annotations.
    * 
@@ -322,13 +333,15 @@ public class EmblEntry
     Mapping dnaToProteinMapping = null;
     if (translation != null && proteinName != null && proteinId != null)
     {
+      int translationLength = translation.length();
+
       /*
        * look for product in peptides list, if not found, add it
        */
       product = matcher.findIdMatch(proteinId);
       if (product == null)
       {
-        product = new Sequence(proteinId, translation, 1, translation.length());
+        product = new Sequence(proteinId, translation, 1, translationLength);
         product.setDescription(((proteinName.length() == 0) ? "Protein Product from "
                 + sourceDb
                 : proteinName));
@@ -340,30 +353,32 @@ public class EmblEntry
       // sequence
       if (exons == null || exons.length == 0)
       {
+        /*
+         * workaround until we handle dna location for CDS sequence
+         * e.g. location="X53828.1:60..1058" correctly
+         */
         System.err
                 .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
                         + sourceDb + ":" + getAccession() + ")");
-        if (translation.length() * 3 == (1 - codonStart + dna.getSequence().length))
+        if (translationLength * 3 == (1 - codonStart + dna.getSequence().length))
         {
           System.err
                   .println("Not allowing for additional stop codon at end of cDNA fragment... !");
-          // this might occur for CDS sequences where no features are
-          // marked.
+          // this might occur for CDS sequences where no features are marked
           exons = new int[] { dna.getStart() + (codonStart - 1),
               dna.getEnd() };
           dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
-              translation.length() },
-                  3, 1);
+              translationLength }, 3, 1);
         }
-        if ((translation.length() + 1) * 3 == (1 - codonStart + dna.getSequence().length))
+        if ((translationLength + 1) * 3 == (1 - codonStart + dna
+                .getSequence().length))
         {
           System.err
                   .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
           exons = new int[] { dna.getStart() + (codonStart - 1),
               dna.getEnd() - 3 };
           dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
-              translation.length() },
-                  3, 1);
+              translationLength }, 3, 1);
         }
       }
       else
@@ -382,28 +397,37 @@ public class EmblEntry
         else
         {
           // final product length truncation check
-          int[] cdsRanges = adjustForProteinLength(translation.length(), exons);
-          dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] { 1,
-              translation.length() }, 3, 1);
+          int[] cdsRanges = adjustForProteinLength(translationLength, exons);
+          dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] {
+              1, translationLength }, 3, 1);
           if (product != null)
           {
             /*
+             * make xref with mapping from protein to EMBL dna
+             */
+            DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+                    getSequenceVersion(), proteinId, new Mapping(
+                            dnaToProteinMapping.getMap().getInverse()));
+            product.addDBRef(proteinToEmblRef);
+
+            /*
              * make xref from protein to EMBLCDS; we assume here that the 
              * CDS sequence version is same as dna sequence (?!)
              */
             MapList proteinToCdsMapList = new MapList(new int[] { 1,
-                translation.length() }, new int[] { 1 + (codonStart - 1),
-                (codonStart - 1) + 3 * translation.length() }, 1, 3);
+                translationLength }, new int[] { 1 + (codonStart - 1),
+                (codonStart - 1) + 3 * translationLength }, 1, 3);
             DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
                     DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
                     new Mapping(proteinToCdsMapList));
             product.addDBRef(proteinToEmblCdsRef);
 
             /*
-             * make xref from protein to EMBLCDSPROTEIN
+             * make 'direct' xref from protein to EMBLCDSPROTEIN
              */
             proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
             proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+            proteinToEmblProteinRef.setMap(null);
             product.addDBRef(proteinToEmblProteinRef);
           }
         }
@@ -414,8 +438,8 @@ public class EmblEntry
        */
       for (int xint = 0; exons != null && xint < exons.length; xint += 2)
       {
-        SequenceFeature sf = makeCdsFeature(exons, xint, proteinName, proteinId, vals,
-                codonStart);
+        SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
+                proteinId, vals, codonStart);
         sf.setType(feature.getName()); // "CDS"
         sf.setEnaLocation(feature.getLocation());
         sf.setFeatureGroup(sourceDb);
@@ -437,7 +461,7 @@ public class EmblEntry
          */
         String source = DBRefUtils.getCanonicalName(ref.getSource());
         ref.setSource(source);
-        DBRefEntry proteinToDnaRef = new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+        DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(), ref.getVersion(), ref
                 .getAccessionId());
         if (source.equals(DBRefSource.UNIPROT))
         {
@@ -469,7 +493,9 @@ public class EmblEntry
               peptides.add(proteinSeq);
             }
             dnaToProteinMapping.setTo(proteinSeq);
-            proteinSeq.addDBRef(proteinToDnaRef);
+            dnaToProteinMapping.setMappedFromId(proteinId);
+            proteinSeq.addDBRef(proteinDbRef);
+            proteinSeq.setSourceDBRef(proteinDbRef);
             ref.setMap(dnaToProteinMapping);
           }
           hasUniprotDbref = true;
@@ -479,7 +505,7 @@ public class EmblEntry
           /*
            * copy feature dbref to our protein product
            */
-          DBRefEntry pref = proteinToDnaRef;
+          DBRefEntry pref = proteinDbRef;
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
@@ -514,6 +540,7 @@ public class EmblEntry
                 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
       }
       product.addDBRef(proteinToEmblProteinRef);
+      product.setSourceDBRef(proteinToEmblProteinRef);
 
       if (dnaToProteinMapping != null
               && dnaToProteinMapping.getTo() != null)
@@ -521,6 +548,7 @@ public class EmblEntry
         DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
                 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
         dnaToEmblProteinRef.setMap(dnaToProteinMapping);
+        dnaToProteinMapping.setMappedFromId(proteinId);
         dna.addDBRef(dnaToEmblProteinRef);
       }
     }