{
dss = dss.getDatasetSequence();
}
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+ DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
if (rfs != null)
{
for (DBRefEntry ref : rfs)
if (dataset != null)
{
// search for references to this sequence's direct references.
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
+ DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
List<SequenceI> rseqs = new ArrayList<SequenceI>();
CrossRef.searchDatasetXrefs(seq, !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());
+ DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs());
if (xrs != null)
{
for (DBRefEntry ref : xrs)
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.");
// FIXME should be dss not seq here?
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
+ DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
// less ambiguous would be a 'find primary dbRefEntry' method.
// filter for desired source xref here
found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
for (int rs = 0; rs < retrieved.length; rs++)
{
// TODO: examine each sequence for 'redundancy'
- DBRefEntry[] dbr = retrieved[rs].getDBRef();
+ DBRefEntry[] dbr = retrieved[rs].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);