From bb877a2135a0c40dc44a20b3e5edb4171e9d17e5 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 23 Aug 2016 17:44:39 +0100
Subject: [PATCH] JAL-2154 - only copy DBRef from contig to new CDS sequence
 which involve same mapped region

---
 src/jalview/analysis/AlignmentUtils.java |   71 ++++++++++++++++++++++--------
 1 file changed, 53 insertions(+), 18 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index d93f42f..ba9821c 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1708,23 +1708,6 @@ public class AlignmentUtils
           }
 
           /*
-           * copy protein's dbrefs to CDS sequence
-           * this enables Get Cross-References from CDS alignment
-           */
-          DBRefEntry[] proteinRefs = DBRefUtils.selectDbRefs(false,
-                  proteinProduct.getDBRefs());
-          if (proteinRefs != null)
-          {
-            for (DBRefEntry ref : proteinRefs)
-            {
-              DBRefEntry cdsToProteinRef = new DBRefEntry(ref);
-              cdsToProteinRef.setMap(new Mapping(proteinProduct,
-                      cdsToProteinMap));
-              cdsSeqDss.addDBRef(cdsToProteinRef);
-            }
-          }
-
-          /*
            * add another mapping from original 'from' range to CDS
            */
           AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
@@ -1885,7 +1868,7 @@ public class AlignmentUtils
         }
       }
     }
-
+    
     /*
      * assign 'from id' held in the mapping if set (e.g. EMBL protein_id),
      * else generate a sequence name
@@ -1895,10 +1878,62 @@ public class AlignmentUtils
     SequenceI newSeq = new Sequence(seqId, newSeqChars, 1, newPos);
     // newSeq.setDescription(mapFromId);
 
+    propagateDBRefsToCDS(newSeq, seq, mapping);
+
     return newSeq;
   }
 
   /**
+   * add any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to
+   * the given mapping.
+   * 
+   * @param cdsSeq
+   * @param contig
+   * @param mapping
+   * @return list of DBRefEntrys added.
+   */
+  public static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
+          SequenceI contig, Mapping mapping)
+  {
+
+    // gather direct refs from contig congrent with mapping
+    List<DBRefEntry> direct = new ArrayList<DBRefEntry>();
+    if (contig.getDBRefs() != null)
+    {
+      for (DBRefEntry dbr : contig.getDBRefs())
+      {
+        if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
+        {
+          MapList map = dbr.getMap().getMap();
+          // check if map is the CDS mapping
+          if (mapping.getMap().equals(map))
+          {
+            direct.add(dbr);
+          }
+        }
+      }
+    }
+
+    List<DBRefEntry> propagated = new ArrayList<DBRefEntry>();
+
+    // and generate appropriate mappings
+    for (DBRefEntry cdsref : direct)
+    {
+      Mapping cdsmap = cdsref.getMap();
+      MapList cdsposmap = new MapList(Arrays.asList(new int[][] { new int[]
+      { cdsSeq.getStart(), cdsSeq.getEnd() } }), cdsmap.getMap()
+              .getToRanges(), 3, 1);
+
+      DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
+              cdsref.getVersion(), cdsref.getAccessionId(), new Mapping(
+                      cdsmap.getTo(), cdsposmap));
+      cdsSeq.addDBRef(newref);
+      propagated.add(newref);
+    }
+    return propagated;
+  }
+
+  /**
    * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the
    * feature start/end ranges, optionally omitting specified feature types.
    * Returns the number of features copied.
-- 
1.7.10.2