JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 85cf48a..b0414af 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -30,6 +30,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
 import java.io.File;
@@ -63,13 +64,16 @@ public class FormatAdapter extends AppletFormatAdapter
 
   private void init()
   {
-    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    if (jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true))
     {
-      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+      annotFromStructure = jalview.bin.Cache.getDefault(
+              Preferences.ADD_TEMPFACT_ANN,
               true);
-      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+      localSecondaryStruct = jalview.bin.Cache.getDefault(
+              Preferences.ADD_SS_ANN,
               true);
-      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+      serviceSecondaryStruct = jalview.bin.Cache
+              .getDefault(Preferences.USE_RNAVIEW,
               true);
     }
     else