- // TODO: this is not a perfect implementation. We need to be able to add
- // individual references to each sequence in each family alignment that's
- // retrieved.
- startQuery();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
- for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
- {
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
- { // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
- }
- }
- stopQuery();
- return rcds;