X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=df5353c318c9f003d26519b058c2da21adc73998;hb=4dad2ddfc361c0f408b8e2320e7186f985f3bb2d;hp=416773d9035986e9b59ee92537fa3f415a616332;hpb=68c26e8852772be21fdb5b091fa9083d8cdb6eec;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 416773d..df5353c 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -38,6 +38,26 @@ import jalview.datamodel.SequenceI;
 public class FormatAdapter extends AppletFormatAdapter
 {
 
+  public FormatAdapter()
+  {
+    super();
+    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    {
+      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+              true);
+      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+            true);
+    serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+            true);
+    }
+    else
+    {
+      // disable all PDB annotation options
+      annotFromStructure = false;
+      localSecondaryStruct = false;
+      serviceSecondaryStruct = false;
+    }
+  }
   public String formatSequences(String format, SequenceI[] seqs,
           String[] omitHiddenColumns)
   {