From e248608bb20e000c17ddc79390d9c1f1f0470e4f Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 21 Oct 2014 12:03:02 +0100
Subject: [PATCH] JAL-674 initial implementation - only need to extract PDB id
 from file, no SS transfer at this stage

---
 src/jalview/gui/AssociatePdbFileWithSeq.java |    6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 01f1cb0..ce75821 100644
--- 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;
-- 
1.7.10.2