();
+ if (refs == null || entry == null)
{
- if (comparator.matches(entry, ref[i]))
- {
- rfs.addElement(ref[i]);
- }
+ return rfs;
}
- // TODO Auto-generated method stub
- if (rfs.size()>0)
+ for (int i = 0; i < refs.length; i++)
{
- DBRefEntry[] rf = new DBRefEntry[rfs.size()];
- rfs.copyInto(rf);
- return rf;
+ if (comparator.matches(entry, refs[i]))
+ {
+ rfs.add(refs[i]);
+ }
}
- return null;
+ return rfs;
}
- public interface DbRefComp {
+
+ interface DbRefComp
+ {
public boolean matches(DBRefEntry refa, DBRefEntry refb);
}
+
/**
* 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)
{
- 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.getSource()==null || refb.getSource().equals(refa.getSource()))
+ if (refa.getMap() == null || (refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
- 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 true;
}
- return false;
}
- };
- /**
- * either field is null or field matches for all of source, version, accession id and map.
- */
- public static DbRefComp matchEitherNonNull = new DbRefComp()
+ }
+ }
+ 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)
{
- 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())))
{
- if ((refa.getSource()==null || refb.getSource()==null)
- || refb.getSource().equals(refa.getSource()))
- {
- 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)
- || (refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
- {
- return true;
- }
- }
- }
- }
- return false;
+ return true;
}
- };
- /**
- * accession ID and DB must be identical. Version is ignored. Map is either not defined or is a match (or is compatible?)
- */
- public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+ }
+ }
+ 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)
{
- 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 (refa.getSource()!=null && refb.getSource()!=null
- && refb.getSource().equals(refa.getSource()))
+ 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())))
{
- // 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)
- || (refa.getMap()!=null && refb.getMap()!=null && refb.getMap().equals(refa.getMap())))
- {
- return true;
- }
- }
- }
- return false;
+ return true;
+ }
}
- };
- /**
- * 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.
- */
- public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+ }
+ }
+ 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)
{
- 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)
{
- if (refa.getSource()!=null && refb.getSource()!=null
- && refb.getSource().equals(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)
- || (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;
+ return true;
}
- };
- /**
- * 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.
- */
- public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+ 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)
{
- 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)
{
- if (refa.getSource()!=null && refb.getSource()!=null
- && refb.getSource().equals(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;
+ return true;
}
- };
- /**
- * 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 equivalent to the maplist of map on b.
- */
- public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+ 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)
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ && refb.getAccessionId().equals(refa.getAccessionId()))
+ {
+ return true;
+ }
+ return false;
+ }
+ };
+
+ /**
+ * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
+ * database is PDB.
+ *
+ * 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)
{
- if (refa.getSource()!=null && refb.getSource()!=null
- && refb.getSource().equals(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;
+ chaincode = " ";
}
- };
- /**
- * used by file parsers to generate DBRefs from annotation within file (eg stockholm)
- * @param dbname
- * @param version
- * @param acn
- * @param seq where to anotate 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)
+ // 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);
+ }
+ }
+ if (ref != null)
+ {
+ seq.addDBRef(ref);
+ }
+ return ref;
+ }
+
+ /**
+ * 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)
{
- DBRefEntry ref = null;
- if (dbname!=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 DBRefEntry[] selectDbRefs(boolean selectDna,
+ 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 searchRefsForSource(DBRefEntry[] dbRefs,
+ String source)
+ {
+ List matches = new ArrayList();
+ if (dbRefs != null && source != null)
+ {
+ for (DBRefEntry dbref : dbRefs)
{
- String locsrc = jalview.util.DBRefUtils
- .getCanonicalName(dbname);
- if (locsrc.equals(jalview.datamodel.DBRefSource.PDB))
+ if (source.equalsIgnoreCase(dbref.getSource()))
{
- // check for chaincode and mapping
- // PFAM style stockhom PDB citation
- com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
- if (r.search(acn.trim()))
+ matches.add(dbref);
+ }
+ }
+ }
+ return matches;
+ }
+
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ *
+ *
+ * Seq Type |
+ * Primary DB |
+ * Direct which will be promoted |
+ *
+ *
+ * peptides |
+ * Ensembl |
+ * Uniprot |
+ *
+ *
+ * peptides |
+ * Ensembl |
+ * Uniprot |
+ *
+ *
+ * dna |
+ * Ensembl |
+ * ENA |
+ *
+ *
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence)
+ {
+ List pr = sequence.getPrimaryDBRefs();
+ if (pr.size() == 0)
+ {
+ // nothing to do
+ return;
+ }
+ List selfs = new ArrayList();
+ {
+ DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+ sequence.getDBRefs());
+ if (selfArray == null || selfArray.length == 0)
+ {
+ // nothing to do
+ return;
+ }
+ selfs.addAll(Arrays.asList(selfArray));
+ }
+
+ // filter non-primary refs
+ for (DBRefEntry p : pr)
+ {
+ while (selfs.contains(p))
+ {
+ selfs.remove(p);
+ }
+ }
+ List toPromote = new ArrayList();
+
+ for (DBRefEntry p : pr)
+ {
+ List promType = new ArrayList();
+ if (sequence.isProtein())
+ {
+ switch (getCanonicalName(p.getSource()))
+ {
+ case DBRefSource.UNIPROT:
+ // case DBRefSource.UNIPROTKB:
+ // case DBRefSource.UP_NAME:
+ // search for and promote ensembl
+ promType.add(DBRefSource.ENSEMBL);
+ break;
+ case DBRefSource.ENSEMBL:
+ // search for and promote Uniprot
+ promType.add(DBRefSource.UNIPROT);
+ break;
+ }
+ }
+ else
+ {
+ // TODO: promote transcript refs
+ }
+
+ // collate candidates and promote them
+ DBRefEntry[] candidates = selectRefs(selfs.toArray(new DBRefEntry[0]),
+ promType.toArray(new String[0]));
+ if (candidates != null)
+ {
+ for (DBRefEntry cand : candidates)
+ {
+ if (cand.hasMap())
{
- String pdbid = r.stringMatched(1);
- String chaincode = r.stringMatched(2);
- String mapstart = r.stringMatched(3);
- String mapend = r.stringMatched(4);
- if (chaincode.equals(" "))
+ if (cand.getMap().getTo() != null
+ && cand.getMap().getTo() != sequence)
+ {
+ // can't promote refs with mappings to other sequences
+ continue;
+ }
+ if (cand.getMap().getMap().getFromLowest() != sequence
+ .getStart()
+ && cand.getMap().getMap().getFromHighest() != sequence
+ .getEnd())
{
- chaincode = "_";
+ // can't promote refs with mappings from a region of this sequence
+ // - eg CDS
+ continue;
}
- // construct pdb ref.
- ref = new DBRefEntry(locsrc, version, pdbid+chaincode);
- PDBEntry pdbr = new PDBEntry();
- pdbr.setId(pdbid);
- seq.addPDBId(pdbr);
}
- } else {
- // default:
- ref = new DBRefEntry(locsrc, version, acn);
+ // and promote
+ cand.setVersion(p.getVersion() + " (promoted)");
+ selfs.remove(cand);
+ toPromote.add(cand);
+ if (!cand.isPrimaryCandidate())
+ {
+ System.out.println(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
+ }
}
}
- if (ref!=null)
- {
- seq.addDBRef(ref);
- }
- return ref;
}
-
-
+ }
+
}