X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=2a510a25efda224b038ecc9cc470b9de91698558;hb=6e5d144752feac881f35390fffcebe8f4233d68d;hp=dc3d0eef52d3591a0bcdeafbf858ef2af27ec4ea;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index dc3d0ee..2a510a2 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -28,7 +28,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -60,6 +59,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
+  public JmolParser(boolean immediate, String inFile,
+          DataSourceType sourceType) throws IOException
+  {
+    super(immediate, inFile, sourceType);
+  }
+
   public JmolParser(String inFile, DataSourceType sourceType)
           throws IOException
   {
@@ -183,7 +188,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      xferSettings();
+      if (isParseImmediately())
+      {
+        // configure parsing settings from the static singleton
+        xferSettings();
+      }
 
       makeResidueList();
       makeCaBondList();
@@ -200,7 +209,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureImportSettings.isProcessSecondaryStructure())
+        // look at local setting for adding secondary tructure
+        if (predictSecondaryStructure)
         {
           createAnnotation(chainseq, chain, ms.at);
         }