From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 7 May 2018 16:39:17 +0000 (+0100)
Subject: JAL-2321 add secondary structure & temp factor if not already present on mapped sequences
X-Git-Tag: Release_2_10_4~7^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a7a69103cb81f7e40803cbed0beb41d05707f641;p=jalview.git

JAL-2321 add secondary structure & temp factor if not already present on mapped sequences
---

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ad259fd..34ca6ba 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -398,8 +398,9 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {