import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
-import jalview.api.DBRefEntryI;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
* its dataset sequence to the dataset
*/
cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping);
+ // cdsSeq has a name constructed as CDS|<dbref>
+ // <dbref> will be either the accession for the coding sequence,
+ // marked in the /via/ dbref to the protein product accession
+ // or it will be the original nucleotide accession.
SequenceI cdsSeqDss = cdsSeq.createDatasetSequence();
cdsSeqs.add(cdsSeq);
if (!dataset.getSequences().contains(cdsSeqDss))
* same source and accession, so need a different accession for
* the CDS from the dna sequence
*/
- 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);
+ // }
/*
* transfer any features on dna that overlap the CDS