patch for JAL-556 - more robust mapping of sequence to structure sequence with correc...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 478706a..483f1a4 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -133,8 +133,10 @@ public class StructureSelectionManager
 
       for (int i = 0; i < pdb.chains.size(); i++)
       {
+        
+        // TODO: correctly determine sequence type for mixed na/peptide structures
         AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
-                .elementAt(i)).sequence, AlignSeq.PEP);
+                .elementAt(i)).sequence, ((PDBChain)pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
         as.calcScoreMatrix();
         as.traceAlignment();
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));