- SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
- : retrievedSequence.getDatasetSequence();
- importCrossRefSeq(cf, dss, retrievedDss);
- rseqs.add(retrievedDss);
- if (dataset.findIndex(retrievedDss) == -1)
+ SequenceI retrievedDss = retrievedSequence
+ .getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
+ addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+ retrievedDss);
+ }
+ // JBPNote: What assumptions are made for dbref structures on
+ // retrieved sequences ?
+ // addedXref will be true means importCrossRefSeq found
+ // sequences with dbrefs with mappings to sequences congruent with dss
+
+ if (!addedXref)
+ {
+ // try again, after looking for matching IDs
+ // shouldn't need to do this unless the dbref mechanism has broken.
+ updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
+ for (SequenceI retrievedSequence : retrieved)