+ * Returns those DBRefEntry objects whose source identifier (once converted to
+ * Jalview's canonical form) is in the list of sources to search for. Returns
+ * null if no matches found.
+ *
+ * @param dbrefs DBRefEntry objects to search
+ * @param sources array of sources to select
+ * @return
+ */
+ public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs, String[] sources)
+ {
+ if (dbrefs == null || sources == null)
+ {
+ return dbrefs;
+ }
+
+ // BH TODO (what?)
+ HashSet<String> srcs = new HashSet<>();
+ for (String src : sources)
+ {
+ srcs.add(src.toUpperCase());
+ }
+
+ int nrefs = dbrefs.size();
+ List<DBRefEntry> res = new ArrayList<>();
+ for (int ib = 0; ib < nrefs; ib++)
+ {
+ DBRefEntry dbr = dbrefs.get(ib);
+ String source = getCanonicalName(dbr.getSource());
+ if (srcs.contains(source.toUpperCase()))
+ {
+ res.add(dbr);
+ }
+ }
+ if (res.size() > 0)
+ {
+ // List<DBRefEntry> reply = new DBRefEntry[res.size()];
+ return res;// .toArray(reply);
+ }
+ return null;
+ }
+
+ private static boolean selectRefsBS(List<DBRefEntry> dbrefs, int sourceKeys, BitSet bsSelect)
+ {
+ if (dbrefs == null || sourceKeys == 0)
+ {
+ return false;
+ }
+ for (int i = 0, n = dbrefs.size(); i < n; i++)
+ {
+ DBRefEntry dbr = dbrefs.get(i);
+ if ((dbr.getSourceKey() & sourceKeys) != 0)
+ {
+ bsSelect.clear(i);
+ }
+ }
+ return !bsSelect.isEmpty();
+ }
+
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry, according to the given comparator.
+ *
+ * @param refs
+ * an array of database references to search
+ * @param entry
+ * an entry to compare against
+ * @param comparator
+ * @return
+ */
+ static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
+ DbRefComp comparator)
+ {
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || entry == null)
+ {
+ return rfs;
+ }
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (comparator.matches(entry, refs[i]))
+ {
+ rfs.add(refs[i]);
+ }
+ }
+ return rfs;
+ }
+
+ /**
+ * look up source in an internal list of database reference sources and return
+ * the canonical jalview name for the source, or the original string if it has
+ * no canonical form.
+ *
+ * @param source
+ * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or
+ * original source
+ */
+ public static String getCanonicalName(String source)
+ {
+ if (source == null)
+ {
+ return null;
+ }
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
+ return canonical == null ? source : canonical;
+ }
+
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry. Currently uses a comparator which matches if
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param ref Set of references to search
+ * @param entry pattern to match
+ * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref, DBRefEntry entry, int mode) {
+ return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
+ }
+
+ /**
+ * Returns a list of those references that match the given accession id
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param refs Set of references to search
+ * @param accId accession id to match
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || accId == null) {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++) {
+ DBRefEntry e = refs.get(i);
+ if (accId.equals(e.getAccessionId())) {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+// return searchRefs(refs, new DBRefEntry("", "", accId), matchId, SEARCH_MODE_FULL);
+ }
+
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry, according to the given comparator.
+ *
+ * @param refs an array of database references to search
+ * @param entry an entry to compare against
+ * @param comparator
+ * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION
+ * optional
+ * @return
+ */
+ static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
+ List<DBRefEntry> rfs = new ArrayList<>();
+ if (refs == null || entry == null) {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++) {
+ DBRefEntry e = refs.get(i);
+ if (comparator.matches(entry, e, SEARCH_MODE_FULL)) {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+ }
+
+ interface DbRefComp {
+ default public boolean matches(DBRefEntry refa, DBRefEntry refb) {
+ return matches(refa, refb, SEARCH_MODE_FULL);
+ };
+
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
+ }
+
+ /**
+ * match on all non-null fields in refa
+ */
+ // TODO unused - remove? would be broken by equating "" with null
+ public static DbRefComp matchNonNullonA = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if ((mode & DB_SOURCE) != 0 &&
+ (refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource())))) {
+ if ((mode & DB_VERSION) != 0 &&
+ (refa.getVersion() == null || refb.getVersion().equals(refa.getVersion()))) {
+ if ((mode & DB_ID) != 0 &&
+ (refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId()))) {
+ if ((mode & DB_MAP) != 0 &&
+ (refa.getMap() == null || (refb.getMap() != null && refb.getMap().equals(refa.getMap())))) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * either field is null or field matches for all of source, version, accession
+ * id and map.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchEitherNonNull = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (nullOrEqualSource(refa.getSource(), refb.getSource())
+ && nullOrEqual(refa.getVersion(), refb.getVersion())
+ && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
+ && nullOrEqual(refa.getMap(), refb.getMap())) {
+ return true;
+ }
+ return false;
+ }
+
+ };
+
+ /**
+ * accession ID and DB must be identical. Version is ignored. Map is either not
+ * defined or is a match (or is compatible?)
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
+ // We dont care about version
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ // FIXME should be && not || here?
+ || refb.getAccessionId().equals(refa.getAccessionId())) {
+ if ((refa.getMap() == null || refb.getMap() == null) || (refa.getMap() != null
+ && refb.getMap() != null && refb.getMap().equals(refa.getMap()))) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical. Version is ignored. No map on either
+ * or map but no maplist on either or maplist of map on a is the complement of
+ * maplist of map on b.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
+ // We dont care about version
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ || refb.getAccessionId().equals(refa.getAccessionId())) {
+ if ((refa.getMap() == null && refb.getMap() == null)
+ || (refa.getMap() != null && refb.getMap() != null)) {
+ if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
+ && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap()))) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical. Version is ignored. No map on both or
+ * or map but no maplist on either or maplist of map on a is equivalent to the
+ * maplist of map on b.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
+ // We dont care about version
+ // if ((refa.getVersion()==null || refb.getVersion()==null)
+ // || refb.getVersion().equals(refa.getVersion()))
+ // {
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ || refb.getAccessionId().equals(refa.getAccessionId())) {
+ if (refa.getMap() == null && refb.getMap() == null) {
+ return true;
+ }
+ if (refa.getMap() != null && refb.getMap() != null
+ && ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
+ && refb.getMap().getMap().equals(refa.getMap().getMap())))) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical, or null on a. Version is ignored. No
+ * map on either or map but no maplist on either or maplist of map on a is
+ * equivalent to the maplist of map on b.
+ */
+ public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
+ .equals(DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ if (refa.getAccessionId() == null || refa.getAccessionId().equals(refb.getAccessionId()))
+ {
+ if (refa.getMap() == null || refb.getMap() == null)
+ {
+ return true;
+ }
+ if ((refa.getMap() != null && refb.getMap() != null)
+ && (refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
+ && (refb.getMap().getMap().equals(refa.getMap().getMap()))))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * Returns the (possibly empty) list of those supplied dbrefs which have the
+ * specified source database, with a case-insensitive match of source name
+ *
+ * @param dbRefs
+ * @param source
+ * @return