private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ protected static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
- private final static String NEWLINE = System.lineSeparator();
+ protected final static String NEWLINE = System.lineSeparator();
private String curSourceDBRef;
@Override
public HashSet<String> getAllMappingAccession()
{
- HashSet<String> accessions = new HashSet<String>();
+ HashSet<String> accessions = new HashSet<>();
List<Entity> entities = siftsEntry.getEntity();
for (Entity entity : entities)
{
entity = getEntityById(entityId);
String originalSeq = AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seq.getSequenceAsString());
- HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ HashMap<Integer, int[]> mapping = new HashMap<>();
DBRefEntryI sourceDBRef;
sourceDBRef = getValidSourceDBRef(seq);
// TODO ensure sequence start/end is in the same coordinate system and
seqCoordSys = CoordinateSys.PDB;
}
- HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
+ HashSet<String> dbRefAccessionIdsString = new HashSet<>();
for (DBRefEntry dbref : seq.getDBRefs())
{
dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
- TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
+ TreeMap<Integer, String> resNumMap = new TreeMap<>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
}
if (!isObserved)
{
- ++pdbeNonObservedCount;
+ ++pdbeNonObservedCount; // TODO this value is never used
}
- if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
+ if (seqCoordSys == CoordinateSys.PDB) // FIXME: is seqCoordSys ever PDBe
// ???
{
// if the sequence has a primary reference to the PDB, then we are
private Set<String> getResidueAnnotaitons(Residue residue,
ResidueDetailType type)
{
- HashSet<String> foundAnnotations = new HashSet<String>();
+ HashSet<String> foundAnnotations = new HashSet<>();
List<ResidueDetail> resDetails = residue.getResidueDetail();
for (ResidueDetail resDetail : resDetails)
{
public int resCount;
+ protected SiftsEntitySortPojo()
+ {
+ }
+
@Override
public int compareTo(SiftsEntitySortPojo o)
{
{
return pdbeNonObserved;
}
+
public SequenceI getSeq()
{
return seq;