+ * 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)
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ 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(" "))
{
- if ((refa.getSource()==null || refb.getSource()==null)
- || refb.getSource().equals(refa.getSource()))
+ 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
+ {
+ jalview.bin.Console.errPrintln("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())))
{
- 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 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?)
- */
- public static DbRefComp matchDbAndIdAndEitherMap = 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, int mode)
{
- 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 && 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()
+ 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)
{
- 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)
- || (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;
+ }
+ };
+
+ /**
+ * 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
+ *
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence,
+ List
+ *
+ * Seq Type
+ * Primary DB
+ * Direct which will be promoted
+ *
+ *
+ * peptides
+ * Ensembl
+ * Uniprot
+ *
+ *
+ * peptides
+ * Ensembl
+ * Uniprot
+ *
+ *
+ * dna
+ * Ensembl
+ * ENA
+ *