JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable...

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 1a639f1..42a8ead 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -280,7 +280,8 @@ public class AppletFormatAdapter
       {
         // TODO obtain config value from preference settings.
         // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = false;
+        boolean isParseWithJMOL = !StructureViewSettings
+                .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
         if (isParseWithJMOL)
         {
           StructureViewSettings.addSettings(annotFromStructure,
@@ -291,6 +292,8 @@ public class AppletFormatAdapter
         }
         else
         {
+          StructureViewSettings.addSettings(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct);
           StructureViewSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,