X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=993913136e2095b34f59a59c8935fd18b4ac46d0;hb=077fea81a02a33eefed6895bfa7cff993609dab8;hp=6be8dd5d36cc5ad47896c29f74cb2d29390af5f6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 6be8dd5..9939131 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -176,8 +176,11 @@ 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
-      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
-              .elementAt(i)).sequence, "pep");
+      // TODO: DNa/Pep switch
+      AlignSeq as = new AlignSeq(sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                      : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -1099,9 +1102,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String getPdbFile()
+  public String[] getPdbFile()
   {
-    return pdbentry.getFile();
+    return new String[]
+    { pdbentry.getFile() };
   }
 
   String lastMessage;