- product.addDBRef(pcdnaref);
- protEMBLCDS = new DBRefEntry(pcdnaref);
- protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- product.addDBRef(protEMBLCDS);
+ /*
+ * make xref with mapping from protein to EMBL dna
+ */
+ DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+ getSequenceVersion(), proteinId, new Mapping(
+ dnaToProteinMapping.getMap().getInverse()));
+ product.addDBRef(proteinToEmblRef);
+
+ /*
+ * make xref from protein to EMBLCDS; we assume here that the
+ * CDS sequence version is same as dna sequence (?!)
+ */
+ MapList proteinToCdsMapList = new MapList(new int[] { 1,
+ translationLength }, new int[] { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * translationLength }, 1, 3);
+ DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
+ DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
+ new Mapping(proteinToCdsMapList));
+ product.addDBRef(proteinToEmblCdsRef);
+
+ /*
+ * make 'direct' xref from protein to EMBLCDSPROTEIN
+ */
+ proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
+ proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+ proteinToEmblProteinRef.setMap(null);
+ product.addDBRef(proteinToEmblProteinRef);