*/
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;
*/
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;
*/
private boolean isResidueObserved(Residue residue)
{
- Set<String> annotations = getResidueAnnotaitons(residue,
+ Set<String> annotations = getResidueAnnotations(residue,
ResidueDetailType.ANNOTATION);
if (annotations == null || annotations.isEmpty())
{
* @param type
* @return
*/
- private Set<String> getResidueAnnotaitons(Residue residue,
+ private Set<String> getResidueAnnotations(Residue residue,
ResidueDetailType type)
{
HashSet<String> foundAnnotations = new HashSet<>();