Merge branch 'develop' into efficiency/JAL-2034_JAL-1421

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index fb414f4..55bb03d 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,6 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
@@ -280,8 +281,10 @@ public class AppletFormatAdapter
       {
         // TODO obtain config value from preference settings.
         // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = !StructureImportSettings
-                .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+        boolean isParseWithJMOL = StructureImportSettings
+                .getDefaultPDBFileParser().equalsIgnoreCase(
+                        StructureImportSettings.StructureParser.JMOL_PARSER
+                                .toString());
         if (isParseWithJMOL)
         {
           StructureImportSettings.addSettings(annotFromStructure,
@@ -299,13 +302,15 @@ public class AppletFormatAdapter
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
         }
+        ((StructureFile) alignFile).setDbRefType(format);
       }
-      else if (format.equals("mmCIF"))
+      else if (format.equalsIgnoreCase("mmCIF"))
       {
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
       {
@@ -447,13 +452,15 @@ public class AppletFormatAdapter
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
+        ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
-      else if (format.equals("mmCIF"))
+      else if (format.equalsIgnoreCase("mmCIF"))
       {
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, source);
+        ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
       }
       else if (format.equals("STH"))
       {