{
dss = dss.getDatasetSequence();
}
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+ DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
for (int r = 0; rfs != null && r < rfs.length; r++)
{
if (!refs.contains(rfs[r].getSource()))
{
// search for references to this sequence's direct references.
DBRefEntry[] lrfs = CrossRef
- .findXDbRefs(!dna, seqs[s].getDBRef());
+ .findXDbRefs(!dna, seqs[s].getDBRefs());
List<SequenceI> rseqs = new ArrayList<SequenceI>();
CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
null); // don't need to specify codon frame for mapping here
for (SequenceI rs : rseqs)
{
- DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef()); // not used??
+ DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs()); // not used??
for (int r = 0; rfs != null && r < rfs.length; r++)
{
if (!refs.contains(rfs[r].getSource()))
Vector cseqs = new Vector();
for (int s = 0; s < seqs.length; s++)
{
- DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
+ DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRefs());
for (int c = 0; c < cdna.length; c++)
{
if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
dss = dss.getDatasetSequence();
}
boolean found = false;
- DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
+ DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRefs());
if ((xrfs == null || xrfs.length == 0) && dataset != null)
{
System.out.println("Attempting to find ds Xrefs refs.");
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
+ DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRefs());
// less ambiguous would be a 'find primary dbRefEntry' method.
// filter for desired source xref here
found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
{
// TODO: examine each sequence for 'redundancy'
jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
- .getDBRef();
+ .getDBRefs();
if (dbr != null && dbr.length > 0)
{
for (int di = 0; di < dbr.length; di++)
}
// look for direct or indirect references in common
- DBRefEntry[] poss = nxt.getDBRef(), cands = null;
+ DBRefEntry[] poss = nxt.getDBRefs(), cands = null;
if (direct)
{
cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);