- DBRefEntryI dnaRef = dnaDss.getSourceDBRef();
- if (dnaRef != null)
- {
- // assuming cds version same as dna ?!?
- DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(),
- dnaRef.getVersion(), cdsSeq.getName());
- proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
- .getInverse()));
- proteinProduct.addDBRef(proteinToCdsRef);
- }
+ // specific use case:
+ // Genomic contig ENSCHR:1, contains coding regions for ENSG01,
+ // ENSG02, ENSG03, with transcripts and products similarly named.
+ // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
+ // JBPNote: ?? can't actually create an example that demonstrates we
+ // need to
+ // synthesize an xref.
+ // TODO: merge conflicts from JAL-2154 branch and use PrimaryDBRefs()
+ // for (DBRefEntry primRef:dnaDss.getPrimaryDBRefs())
+ // {
+ // creates a complementary cross-reference to the source sequence's
+ // primary reference.
+
+ // // problem here is that the cross-reference is synthesized -
+ // cdsSeq.getName() may be like 'CDS|dnaaccession' or 'CDS|emblcdsacc'
+ // // assuming cds version same as dna ?!?
+ // DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(),
+ // dnaRef.getVersion(), cdsSeq.getName());
+ // proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
+ // .getInverse()));
+ // proteinProduct.addDBRef(proteinToCdsRef);
+ // }