From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 26 Nov 2014 14:41:18 +0000 (+0000)
Subject: JAL-674 employ the provided DNA/Protein matrix string when mapping from sequence... 
X-Git-Tag: Jalview_2_9~121^2~7^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=0df5bf86b6dea4d148a6a8fdd1f4bdce4f475fa8;p=jalview.git

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e1c4dc5..691fdcd 100755
--- 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;