JAL-2164 JAL-1919 disabled and removed PDB file parser configuration option, JmolPars...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 55bb03d..da7eb1d 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -279,29 +279,12 @@ 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"))