JAL-674 employ the provided DNA/Protein matrix string when mapping from sequence...

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e1c4dc5..691fdcd 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -361,8 +361,8 @@ public class PDBfile extends jalview.io.AlignFile
           AlignmentI al, String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
-            .replaceMatchingSeqsWith(seqs, annotations, prot, al,
-                    AlignSeq.PEP, false);
+            .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+                    false);
     for (PDBChain ch : chains)
     {
       int p = 0;