X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;fp=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=552f00edc24cbc8fea60631a5ce93f6369dc71e0;hp=da7eb1da92673dad8d17848ba8fadaaaa760b99a;hb=ce6f02a53c98e51cb96533d40db5f94d1bfea00a;hpb=057fedb7eada7cd6b023503bfa2db948209d9356

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index da7eb1d..552f00e 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;
 
@@ -277,22 +278,11 @@ public class AppletFormatAdapter
         alignFile = new JPredFile(inFile, type);
         ((JPredFile) alignFile).removeNonSequences();
       }
-      else if (format.equals("PDB"))
-      {
-
-          StructureImportSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
-        ((StructureFile) alignFile).setDbRefType(format);
-      }
-      else if (format.equalsIgnoreCase("mmCIF"))
+      else if (format.equals("PDB") || format.equalsIgnoreCase("mmCIF"))
       {
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        alignFile = new JmolParser(inFile, type);
         ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
@@ -426,8 +416,7 @@ 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 +430,7 @@ 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"))