Merge branch 'develop' into features/JAL-2113_emblXml1.2

JAL-2113 JAL-1919 mmcif/pdb configurable retrieval from EBI/PDBe - verfied as working

diff --combined src/jalview/ws/dbsources/Pdb.java
index 0d590b0,b2063c1..c87a111
--- 1/src/jalview/ws/dbsources/Pdb.java
--- 2/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@@ -1,3 -1,3 +1,4 @@@
++
  /*
   * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   * Copyright (C) $$Year-Rel$$ The Jalview Authors
@@@ -53,7 -53,7 +54,7 @@@ public class Pdb extends EbiFileRetriev
  
    public static final String FEATURE_RES_NUM = "RESNUM";
  
-   private static String currentDefaultFomart = DBRefSource.PDB;
+   private static String currentDefaultFormat = DBRefSource.PDB;
  
    /*
     * (non-Javadoc)
@@@ -132,11 -132,11 +133,11 @@@
        stopQuery();
        return null;
      }
-     String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+     String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
              : ".xml";
      EBIFetchClient ebi = new EBIFetchClient();
      file = ebi.fetchDataAsFile("pdb:" + id,
-             getCurrentDefaultFomart().toLowerCase(), ext)
 -            getCurrentDefaultFormat().toLowerCase(), "raw", ext)
++            getCurrentDefaultFormat().toLowerCase(), ext)
              .getAbsolutePath();
      stopQuery();
      if (file == null)
@@@ -148,7 -148,7 +149,7 @@@
  
        pdbAlignment = new FormatAdapter().readFile(file,
                jalview.io.AppletFormatAdapter.FILE,
-               getCurrentDefaultFomart());
+               getCurrentDefaultFormat());
        if (pdbAlignment != null)
        {
          List<SequenceI> toremove = new ArrayList<SequenceI>();
@@@ -263,14 -263,14 +264,14 @@@
      return 0;
    }
  
-   public static String getCurrentDefaultFomart()
+   public static String getCurrentDefaultFormat()
    {
-     return currentDefaultFomart;
+     return currentDefaultFormat;
    }
  
-   public static void setCurrentDefaultFomart(String currentDefaultFomart)
+   public static void setCurrentDefaultFormat(String currentDefaultFomart)
    {
-     Pdb.currentDefaultFomart = currentDefaultFomart;
+     Pdb.currentDefaultFormat = currentDefaultFomart;
    }
  
    /**