JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test...

[jalview.git] / src / mc_view / PDBChain.java

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 70fda66..425bc18 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -229,11 +229,16 @@ public class PDBChain
    * @param seq
    * @param status
    *          The Status of the transferred annotation
-   * @param actualGroupId the group id for the features on the destination sequence (e.g. the official accession ID)
+   * 
+   * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
    */
   public void transferRESNUMFeatures(SequenceI seq,
-          String status)
+          String status, String altPDBID)
   {
+    if (altPDBID==null)
+    {
+      altPDBID = pdbid;
+    }
     SequenceI sq = seq;
     while (sq != null && sq.getDatasetSequence() != null)
     {
@@ -266,7 +271,7 @@ public class PDBChain
         int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping;
         SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
-                pdbid, feature.getScore());
+                altPDBID, feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""