X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=b45d0072ce2c11e63735cb7d5268dcebfd3d0dcd;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=eb7bd997e910b4d7a5db901f2631e493bdb19f98;hpb=208f2c3de82e3327c4f930ab7d04f5b812ccd277;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index eb7bd99..b45d007 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -82,6 +82,22 @@ public class SiftsClient implements SiftsClientI
    */
   private static File mockSiftsFile;
 
+  private static final int BUFFER_SIZE = 4096;
+
+  public static final int UNASSIGNED = Integer.MIN_VALUE;
+
+  private static final int PDB_RES_POS = 0;
+
+  private static final int PDB_ATOM_POS = 1;
+
+  private static final int PDBE_POS = 2;
+
+  private static final String NOT_OBSERVED = "Not_Observed";
+
+  protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+
+  protected final static String NEWLINE = System.lineSeparator();
+
   private Entry siftsEntry;
 
   private StructureFile pdb;
@@ -100,22 +116,6 @@ public class SiftsClient implements SiftsClientI
    */
   private jalview.datamodel.Mapping seqFromPdbMapping;
 
-  private static final int BUFFER_SIZE = 4096;
-
-  public static final int UNASSIGNED = Integer.MIN_VALUE;
-
-  private static final int PDB_RES_POS = 0;
-
-  private static final int PDB_ATOM_POS = 1;
-
-  private static final int PDBE_POS = 2;
-
-  private static final String NOT_OBSERVED = "Not_Observed";
-
-  protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
-
-  protected final static String NEWLINE = System.lineSeparator();
-
   private String curSourceDBRef;
 
   private HashSet<String> curDBRefAccessionIdsString;
@@ -824,7 +824,7 @@ public class SiftsClient implements SiftsClientI
    */
   private boolean isResidueObserved(Residue residue)
   {
-    Set<String> annotations = getResidueAnnotaitons(residue,
+    Set<String> annotations = getResidueAnnotations(residue,
             ResidueDetailType.ANNOTATION);
     if (annotations == null || annotations.isEmpty())
     {
@@ -847,7 +847,7 @@ public class SiftsClient implements SiftsClientI
    * @param type
    * @return
    */
-  private Set<String> getResidueAnnotaitons(Residue residue,
+  private Set<String> getResidueAnnotations(Residue residue,
           ResidueDetailType type)
   {
     HashSet<String> foundAnnotations = new HashSet<>();