*/
private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- public final static int DB_SOURCE = 1;
- public final static int DB_VERSION = 2;
- public final static int DB_ID = 4;
- public final static int DB_MAP = 8;
-
- public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
- public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID | DB_MAP;
-
- static
- {
- // TODO load these from a resource file?
- canonicalSourceNameLookup.put("uniprotkb/swiss-prot", DBRefSource.UNIPROT);
- canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
-
- // Ensembl values for dbname in xref REST service:
- canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
- canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
-
- canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
- canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
- // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
- // from ENA.
- canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
- canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
-
- // guarantee we always have lowercase entries for canonical string lookups
- for (String k : canonicalSourceNameLookup.keySet())
- {
- canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
- canonicalSourceNameLookup.get(k));
- }
- }
+ public final static int DB_SOURCE = 1;
+
+ public final static int DB_VERSION = 2;
+
+ public final static int DB_ID = 4;
+
+ public final static int DB_MAP = 8;
+
+ public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
+
+ public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID
+ | DB_MAP;
+
+ static
+ {
+ // TODO load these from a resource file?
+ canonicalSourceNameLookup.put("uniprotkb/swiss-prot",
+ DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
+
+ // Ensembl values for dbname in xref REST service:
+ canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
+
+ canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
+ canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+ // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+ // from ENA.
+ canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+ canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
+ // guarantee we always have lowercase entries for canonical string lookups
+ for (String k : canonicalSourceNameLookup.keySet())
+ {
+ canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
+ canonicalSourceNameLookup.get(k));
+ }
+ }
/**
* 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
+ * @param dbrefs
+ * DBRefEntry objects to search
+ * @param sources
+ * array of sources to select
* @return
*/
- public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs, String[] sources)
+ 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<String>();
- for (String src : sources)
- {
- srcs.add(src.toUpperCase(Locale.ROOT));
- }
-
- int nrefs = dbrefs.size();
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
- for (int ib = 0; ib < nrefs; ib++)
- {
- DBRefEntry dbr = dbrefs.get(ib);
- String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source.toUpperCase(Locale.ROOT)))
- {
- res.add(dbr);
- }
- }
- if (res.size() > 0)
- {
- // List<DBRefEntry> reply = new DBRefEntry[res.size()];
- return res;// .toArray(reply);
- }
- return null;
+ if (dbrefs == null || sources == null)
+ {
+ return dbrefs;
+ }
+
+ // BH TODO (what?)
+ HashSet<String> srcs = new HashSet<String>();
+ for (String src : sources)
+ {
+ srcs.add(src.toUpperCase(Locale.ROOT));
+ }
+
+ int nrefs = dbrefs.size();
+ List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ for (int ib = 0; ib < nrefs; ib++)
+ {
+ DBRefEntry dbr = dbrefs.get(ib);
+ String source = getCanonicalName(dbr.getSource());
+ if (srcs.contains(source.toUpperCase(Locale.ROOT)))
+ {
+ 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)
+ 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();
+ 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();
}
/**
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(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;
- }
-
- };
+ /**
+ * 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
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;
- }
- };
-
- /**
+ /**
+ * 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
*
return matches;
}
- /**
- * Returns true if either object is null, or they are equal
- *
- * @param o1
- * @param o2
- * @return
- */
- public static boolean nullOrEqual(Object o1, Object o2) {
- if (o1 == null || o2 == null) {
- return true;
- }
- return o1.equals(o2);
- }
-
- /**
- * canonicalise source string before comparing. null is always wildcard
- *
- * @param o1 - null or source string to compare
- * @param o2 - null or source string to compare
- * @return true if either o1 or o2 are null, or o1 equals o2 under
- * DBRefUtils.getCanonicalName
- * (o1).equals(DBRefUtils.getCanonicalName(o2))
- */
- public static boolean nullOrEqualSource(String o1, String o2) {
- if (o1 == null || o2 == null) {
- return true;
- }
- return DBRefUtils.getCanonicalName(o1).equals(DBRefUtils.getCanonicalName(o2));
- }
-
- /**
- * Selects just the DNA or protein references from a set of references
- *
- * @param selectDna if true, select references to 'standard' DNA databases, else
- * to 'standard' peptide databases
- * @param refs a set of references to select from
- * @return
- */
- public static List<DBRefEntry> selectDbRefs(boolean selectDna, List<DBRefEntry> refs) {
- return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
- // could attempt to find other cross
- // refs here - ie PDB xrefs
- // (not dna, not protein seq)
- }
-
- /**
- * 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
- */
- public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
- if (dbRefs != null && source != null) {
- for (DBRefEntry dbref : dbRefs) {
- if (source.equalsIgnoreCase(dbref.getSource())) {
- matches.add(dbref);
- }
- }
- }
- return matches;
- }
-
- /**
- * promote direct database references to primary for nucleotide or protein
- * sequences if they have an appropriate primary ref
- * <table>
- * <tr>
- * <th>Seq Type</th>
- * <th>Primary DB</th>
- * <th>Direct which will be promoted</th>
- * </tr>
- * <tr align=center>
- * <td>peptides</td>
- * <td>Ensembl</td>
- * <td>Uniprot</td>
- * </tr>
- * <tr align=center>
- * <td>peptides</td>
- * <td>Ensembl</td>
- * <td>Uniprot</td>
- * </tr>
- * <tr align=center>
- * <td>dna</td>
- * <td>Ensembl</td>
- * <td>ENA</td>
- * </tr>
- * </table>
- *
- * @param sequence
- */
- public static void ensurePrimaries(SequenceI sequence, List<DBRefEntry> pr) {
- if (pr.size() == 0) {
- // nothing to do
- return;
- }
- int sstart = sequence.getStart();
- int send = sequence.getEnd();
- boolean isProtein = sequence.isProtein();
- BitSet bsSelect = new BitSet();
-
-// List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
-// {
-
-// List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
-// if (selfs == null || selfs.size() == 0)
-// {
-// // nothing to do
-// return;
-// }
-
- List<DBRefEntry> dbrefs = sequence.getDBRefs();
- bsSelect.set(0, dbrefs.size());
-
- if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
- return;
-
-// selfs.addAll(selfArray);
-// }
-
- // filter non-primary refs
- for (int ip = pr.size(); --ip >= 0;) {
- DBRefEntry p = pr.get(ip);
- for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) {
- if (dbrefs.get(i) == p)
- bsSelect.clear(i);
- }
-// while (selfs.contains(p))
-// {
-// selfs.remove(p);
-// }
- }
-// List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
-
- for (int ip = pr.size(), keys = 0; --ip >= 0 && keys != DBRefSource.PRIMARY_MASK;) {
- DBRefEntry p = pr.get(ip);
- if (isProtein) {
- switch (getCanonicalName(p.getSource())) {
- case DBRefSource.UNIPROT:
- keys |= DBRefSource.UNIPROT_MASK;
- break;
- case DBRefSource.ENSEMBL:
- keys |= DBRefSource.ENSEMBL_MASK;
- break;
- }
- } else {
- // TODO: promote transcript refs ??
- }
- if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
- return;
-// if (candidates != null)
- {
- for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))
-// for (int ic = 0, n = candidates.size(); ic < n; ic++)
- {
- DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
- if (cand.hasMap()) {
- Mapping map = cand.getMap();
- SequenceI cto = map.getTo();
- if (cto != null && cto != sequence) {
- // can't promote refs with mappings to other sequences
- continue;
- }
- MapList mlist = map.getMap();
- if (mlist.getFromLowest() != sstart && mlist.getFromHighest() != send) {
- // can't promote refs with mappings from a region of this sequence
- // - eg CDS
- continue;
- }
- }
- // and promote - not that version must be non-null here,
- // as p must have passed isPrimaryCandidate()
- cand.setVersion(p.getVersion() + " (promoted)");
- bsSelect.clear(ic);
- // selfs.remove(cand);
-// toPromote.add(cand);
- if (!cand.isPrimaryCandidate()) {
- System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence "
- + sequence.toString());
- }
- }
- }
- }
- }
+ /**
+ * Returns true if either object is null, or they are equal
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ public static boolean nullOrEqual(Object o1, Object o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return true;
+ }
+ return o1.equals(o2);
+ }
+
+ /**
+ * canonicalise source string before comparing. null is always wildcard
+ *
+ * @param o1
+ * - null or source string to compare
+ * @param o2
+ * - null or source string to compare
+ * @return true if either o1 or o2 are null, or o1 equals o2 under
+ * DBRefUtils.getCanonicalName
+ * (o1).equals(DBRefUtils.getCanonicalName(o2))
+ */
+ public static boolean nullOrEqualSource(String o1, String o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return true;
+ }
+ return DBRefUtils.getCanonicalName(o1)
+ .equals(DBRefUtils.getCanonicalName(o2));
+ }
+
+ /**
+ * Selects just the DNA or protein references from a set of references
+ *
+ * @param selectDna
+ * if true, select references to 'standard' DNA databases, else to
+ * 'standard' peptide databases
+ * @param refs
+ * a set of references to select from
+ * @return
+ */
+ public static List<DBRefEntry> selectDbRefs(boolean selectDna,
+ List<DBRefEntry> refs)
+ {
+ return selectRefs(refs,
+ selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
+ // could attempt to find other cross
+ // refs here - ie PDB xrefs
+ // (not dna, not protein seq)
+ }
+
+ /**
+ * 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
+ */
+ public static List<DBRefEntry> searchRefsForSource(
+ List<DBRefEntry> dbRefs, String source)
+ {
+ List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ if (dbRefs != null && source != null)
+ {
+ for (DBRefEntry dbref : dbRefs)
+ {
+ if (source.equalsIgnoreCase(dbref.getSource()))
+ {
+ matches.add(dbref);
+ }
+ }
+ }
+ return matches;
+ }
+
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ * <table>
+ * <tr>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>dna</td>
+ * <td>Ensembl</td>
+ * <td>ENA</td>
+ * </tr>
+ * </table>
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence,
+ List<DBRefEntry> pr)
+ {
+ if (pr.size() == 0)
+ {
+ // nothing to do
+ return;
+ }
+ int sstart = sequence.getStart();
+ int send = sequence.getEnd();
+ boolean isProtein = sequence.isProtein();
+ BitSet bsSelect = new BitSet();
+
+ // List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ // {
+
+ // List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
+ // if (selfs == null || selfs.size() == 0)
+ // {
+ // // nothing to do
+ // return;
+ // }
+
+ List<DBRefEntry> dbrefs = sequence.getDBRefs();
+ bsSelect.set(0, dbrefs.size());
+
+ if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK
+ : DBRefSource.DNA_CODING_MASK, bsSelect))
+ return;
+
+ // selfs.addAll(selfArray);
+ // }
+
+ // filter non-primary refs
+ for (int ip = pr.size(); --ip >= 0;)
+ {
+ DBRefEntry p = pr.get(ip);
+ for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect
+ .nextSetBit(i + 1))
+ {
+ if (dbrefs.get(i) == p)
+ bsSelect.clear(i);
+ }
+ // while (selfs.contains(p))
+ // {
+ // selfs.remove(p);
+ // }
+ }
+ // List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+ for (int ip = pr.size(), keys = 0; --ip >= 0
+ && keys != DBRefSource.PRIMARY_MASK;)
+ {
+ DBRefEntry p = pr.get(ip);
+ if (isProtein)
+ {
+ switch (getCanonicalName(p.getSource()))
+ {
+ case DBRefSource.UNIPROT:
+ keys |= DBRefSource.UNIPROT_MASK;
+ break;
+ case DBRefSource.ENSEMBL:
+ keys |= DBRefSource.ENSEMBL_MASK;
+ break;
+ }
+ }
+ else
+ {
+ // TODO: promote transcript refs ??
+ }
+ if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
+ return;
+ // if (candidates != null)
+ {
+ for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect
+ .nextSetBit(ic + 1))
+ // for (int ic = 0, n = candidates.size(); ic < n; ic++)
+ {
+ DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
+ if (cand.hasMap())
+ {
+ Mapping map = cand.getMap();
+ SequenceI cto = map.getTo();
+ if (cto != null && cto != sequence)
+ {
+ // can't promote refs with mappings to other sequences
+ continue;
+ }
+ MapList mlist = map.getMap();
+ if (mlist.getFromLowest() != sstart
+ && mlist.getFromHighest() != send)
+ {
+ // can't promote refs with mappings from a region of this sequence
+ // - eg CDS
+ continue;
+ }
+ }
+ // and promote - not that version must be non-null here,
+ // as p must have passed isPrimaryCandidate()
+ cand.setVersion(p.getVersion() + " (promoted)");
+ bsSelect.clear(ic);
+ // selfs.remove(cand);
+ // toPromote.add(cand);
+ if (!cand.isPrimaryCandidate())
+ {
+ System.out.println(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
+ }
+ }
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff