JAL-1919 set default structure file format to mmCIF, refactored some StructureImportS...

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index d945699..1a58466 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -132,12 +132,12 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
-    String ext = StructureImportSettings.getCurrentDefaultFormat()
+    String ext = StructureImportSettings.getDefaultStructureFileFormat()
             .equalsIgnoreCase("mmcif") ? ".cif"
             : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
     file = ebi.fetchDataAsFile("pdb:" + id,
-            StructureImportSettings.getCurrentDefaultFormat().toLowerCase(),
+            StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
             ext)
             .getAbsolutePath();
     stopQuery();
@@ -150,7 +150,7 @@ public class Pdb extends EbiFileRetrievedProxy
 
       pdbAlignment = new FormatAdapter().readFile(file,
               jalview.io.AppletFormatAdapter.FILE,
-              StructureImportSettings.getCurrentDefaultFormat());
+              StructureImportSettings.getDefaultStructureFileFormat());
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();