JAL-674 initial implementation - only need to extract PDB id from file, no SS transfe...

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 01f1cb0..ce75821 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -44,10 +44,12 @@ public class AssociatePdbFileWithSeq
           SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
+    MCview.PDBfile pdbfile = null;
     try
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
-
+      // TODO JAL-674 extract secondary structure and transfer it to associated
+      // sequence
+      pdbfile = new MCview.PDBfile(false, false, choice, protocol);
       if (pdbfile.id == null)
       {
         String reply = null;