Revert "JAL-2164 JAL-1919 disabled and removed PDB file parser configuration option...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index da7eb1d..55bb03d 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -279,12 +279,29 @@ public class AppletFormatAdapter
       }
       else if (format.equals("PDB"))
       {
-
+        // TODO obtain config value from preference settings.
+        // Set value to 'true' to test PDB processing with Jmol: JAL-1213
+        boolean isParseWithJMOL = StructureImportSettings
+                .getDefaultPDBFileParser().equalsIgnoreCase(
+                        StructureImportSettings.StructureParser.JMOL_PARSER
+                                .toString());
+        if (isParseWithJMOL)
+        {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
           alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
+        }
+        else
+        {
+          StructureImportSettings.addSettings(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct);
+          StructureImportSettings.setShowSeqFeatures(true);
+          alignFile = new MCview.PDBfile(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct, inFile,
+                  type);
+        }
         ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equalsIgnoreCase("mmCIF"))