}
/**
+ * 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
- * array of DBRef objects to search
+ * DBRefEntry objects to search
* @param sources
- * String[] array of source DBRef IDs to retrieve
+ * array of sources to select
* @return
*/
public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
};
/**
- * 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()
{
&& refb.getSource().equals(refa.getSource()))
{
// We dont care about version
- 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)
{
|| (refb.getMap().getMap() != null
&& refa.getMap().getMap() != null && (refb
.getMap().getMap().equals(refa.getMap().getMap()))))
- { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+ {
return true;
}
}
return (o1 == null ? o2.equals(o1) : o1.equals(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)
+ }
+
}