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

[jalview.git] / src / MCview / AppletPDBCanvas.java

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 6be8dd5..cdad671 100755 (executable)
--- 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)