+ * 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)
{
- if ((refa.getSource() == null || refb.getSource() == null)
- || refb.getSource().equals(refa.getSource()))
+ String locsrc = DBRefUtils.getCanonicalName(dbname);
+ if (locsrc.equals(DBRefSource.PDB))
{
- if ((refa.getVersion() == null || refb.getVersion() == null)
- || refb.getVersion().equals(refa.getVersion()))
+ /*
+ * 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()))
{
- if ((refa.getAccessionId() == null || refb.getAccessionId() == null)
- || refb.getAccessionId().equals(refa.getAccessionId()))
+ String pdbid = r.stringMatched(1);
+ String chaincode = r.stringMatched(2);
+ if (chaincode == null)
{
- if ((refa.getMap() == null || refb.getMap() == null)
- || (refb.getMap() != null && refb.getMap().equals(
- refa.getMap())))
- {
- return true;
- }
+ 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
+ {
+ jalview.bin.Console.errPrintln("Malformed PDB DR line:" + acn);
}
}
- return false;
+ 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()
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
{
if (refa.getSource() != null && refb.getSource() != null
- && refb.getSource().equals(refa.getSource()))
+ && 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
+ // 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())))
+ || (refa.getMap() != null && refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
return true;
}
@@ -284,30 +458,33 @@ public class DBRefUtils
* 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()
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
{
if (refa.getSource() != null && refb.getSource() != null
- && refb.getSource().equals(refa.getSource()))
+ && 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)
|| (refa.getMap() != null && refb.getMap() != null))
- if ((refb.getMap().getMap() == null && refa.getMap().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())))
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap().getInverse()
+ .equals(refa.getMap().getMap())))
{
return true;
}
+ }
}
}
return false;
@@ -319,12 +496,15 @@ public class DBRefUtils
* 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()
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
{
if (refa.getSource() != null && refb.getSource() != null
- && refb.getSource().equals(refa.getSource()))
+ && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource())))
{
// We dont care about version
// if ((refa.getVersion()==null || refb.getVersion()==null)
@@ -337,12 +517,13 @@ public class DBRefUtils
{
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()))))
+ 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;
}
@@ -353,37 +534,35 @@ public class DBRefUtils
};
/**
- * 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.
+ * 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()
{
- public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
{
- // System.err.println("Comparing A: "+refa.getSrcAccString()+(refa.hasMap()?" has map.":"."));
- // System.err.println("Comparing B: "+refb.getSrcAccString()+(refb.hasMap()?" has map.":"."));
if (refa.getSource() != null && refb.getSource() != null
- && refb.getSource().equals(refa.getSource()))
+ && 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.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() != null
- && refa.getMap().getMap() != null && (refb
- .getMap().getMap().equals(refa.getMap().getMap()))))
- { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+ && refa.getMap().getMap() != null
+ && (refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
+ {
return true;
}
}
@@ -393,57 +572,255 @@ public class DBRefUtils
};
/**
- * used by file parsers to generate DBRefs from annotation within file (eg
- * stockholm)
+ * Returns the (possibly empty) list of those supplied dbrefs which have the
+ * specified source database, with a case-insensitive match of source name
*
- * @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)
+ * @param dbRefs
+ * @param source
+ * @return
*/
- public static DBRefEntry parseToDbRef(SequenceI seq, String dbname,
- String version, String acn)
+ 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
+ *