+ 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