X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=9695891e566bad7f332692a2cf64e68d476e2110;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=da7eb1da92673dad8d17848ba8fadaaaa760b99a;hpb=13bc8a3fb89b083922d9fa9dad5050e6aaa1f661;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index da7eb1d..9695891 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
@@ -279,20 +280,34 @@ 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(inFile, type);
+        }
+        else
+        {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+          StructureImportSettings.setShowSeqFeatures(true);
+          alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
+        }
         ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equalsIgnoreCase("mmCIF"))
       {
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
         ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
@@ -426,8 +441,7 @@ public class AppletFormatAdapter
         {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
@@ -441,8 +455,7 @@ public class AppletFormatAdapter
       {
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, source);
+        alignFile = new JmolParser(source);
         ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
       }
       else if (format.equals("STH"))