X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;fp=src%2FMCview%2FAppletPDBCanvas.java;h=cdad6713c5230ed580fdbd8292f375c3a0139484;hb=5f4142b92b29077571a78d891c0483a30579812e;hp=6be8dd5d36cc5ad47896c29f74cb2d29390af5f6;hpb=fe5f751c21190cad65c44f0ec892e99f8efcbb62;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 6be8dd5..cdad671 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -176,8 +176,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
+      // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
-              .elementAt(i)).sequence, "pep");
+              .elementAt(i)).sequence, ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)