- /**
- * 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<DBRefEntry>();
- 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<DBRefEntry>();
- 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;
- }
- };
-
- /**
+ /**
+ * 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(Locale.ROOT));
+ 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<DBRefEntry>();
+ 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<DBRefEntry>();
+ 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;
+ }
+
+ };
+
+ /**
+ * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
+ * database is PDB.
+ * <p>
+ * Used by file parsers to generate DBRefs from annotation within file (eg
+ * Stockholm)
+ *
+ * @param dbname
+ * @param version
+ * @param acn
+ * @param seq
+ * where to annotate with reference
+ * @return parsed version of entry that was added to seq (if any)
+ */
+ public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
+ String version, String acn)
+ {
+ DBRefEntry ref = null;
+ if (dbname != null)
+ {
+ String locsrc = DBRefUtils.getCanonicalName(dbname);
+ if (locsrc.equals(DBRefSource.PDB))
+ {
+ /*
+ * Check for PFAM style stockhom PDB accession id citation e.g.
+ * "1WRI A; 7-80;"
+ */
+ Regex r = new com.stevesoft.pat.Regex(
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
+ if (r.search(acn.trim()))
+ {
+ String pdbid = r.stringMatched(1);
+ String chaincode = r.stringMatched(2);
+ if (chaincode == null)
+ {
+ chaincode = " ";
+ }
+ // String mapstart = r.stringMatched(3);
+ // String mapend = r.stringMatched(4);
+ if (chaincode.equals(" "))
+ {
+ chaincode = "_";
+ }
+ // construct pdb ref.
+ ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
+ PDBEntry pdbr = new PDBEntry();
+ pdbr.setId(pdbid);
+ pdbr.setType(PDBEntry.Type.PDB);
+ pdbr.setChainCode(chaincode);
+ seq.addPDBId(pdbr);
+ }
+ else
+ {
+ System.err.println("Malformed PDB DR line:" + acn);
+ }
+ }
+ else
+ {
+ // default:
+ ref = new DBRefEntry(locsrc, version, acn.trim());
+ }
+ }
+ if (ref != null)
+ {
+ seq.addDBRef(ref);
+ }
+ return ref;
+ }
+
+ /**
+ * 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;
+ }
+ };
+
+ /**