DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())