From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 21 Oct 2014 11:03:02 +0000 (+0100)
Subject: JAL-674 initial implementation - only need to extract PDB id from file, no SS transfe... 
X-Git-Tag: Jalview_2_9~169^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e248608bb20e000c17ddc79390d9c1f1f0470e4f;p=jalview.git

JAL-674 initial implementation - only need to extract PDB id from file, no SS transfer at this stage
---

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;