- * match on all non-null fields in refa
- */
- // TODO unused - remove?
- public static DbRefComp matchNonNullonA = new DbRefComp()
- {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
- {
- if (refa.getSource() == null
- || DBRefUtils.getCanonicalName(refb.getSource()).equals(
- DBRefUtils.getCanonicalName(refa.getSource())))
- {
- if (refa.getVersion() == null
- || refb.getVersion().equals(refa.getVersion()))
- {
- if (refa.getAccessionId() == null
- || refb.getAccessionId().equals(refa.getAccessionId()))
- {
- if (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)
- {
- 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)
- {
- 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)
- {
- 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)
- {
- 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)
- {
- 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;
- }
- };
-
- /**
- * accession ID only must be identical.
- */
- public static DbRefComp matchId = new DbRefComp()
- {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
- {
- if (refa.getAccessionId() != null && refb.getAccessionId() != null
- && refb.getAccessionId().equals(refa.getAccessionId()))
- {
- return true;
- }
- return false;
- }
- };
-
- /**