From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 7 May 2018 16:43:56 +0000 (+0100)
Subject: JAL-2321 use configured values for structure derived annotation
X-Git-Tag: Release_2_10_4~7^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=df0734bbe3c42eb4e1d2e6471040888c85801ba5;p=jalview.git

JAL-2321 use configured values for structure derived annotation
---

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 34ca6ba..cd986c0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -399,7 +399,9 @@ public class StructureSelectionManager
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(false, pdbFile, sourceType);
-      pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
       pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)