X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=543d6802240037f8e121a081a19c059524b9ae86;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6be8dd5d36cc5ad47896c29f74cb2d29390af5f6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 6be8dd5..543d680 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 +176,9 @@ 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)
@@ -1099,9 +1100,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String getPdbFile()
+  public String[] getPdbFile()
   {
-    return pdbentry.getFile();
+    return new String[] { pdbentry.getFile() };
   }
 
   String lastMessage;