// mappings are made (but content matches retrieved set)
boolean updateRefFrame = sequence.getDBRef() == null
|| sequence.getDBRef().length == 0;
+ // TODO:
// verify sequence against the entry sequence
String nonGapped = AlignSeq.extractGaps("-. ",
// unknownSequences.remove(sequence);
int absEnd = absStart + nonGapped.length();
absStart += 1;
+ if (!trimDatasetSeqs) {
+ // insert full length sequence from record
+ sequence.setSequence(entry.getSequenceAsString());
+ sequence.setStart(entry.getStart());
+ }
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
- sequence.setStart(absStart);
- sequence.setEnd(absEnd);
+ if (trimDatasetSeqs) {
+ // just fix start/end
+ sequence.setStart(absStart);
+ sequence.setEnd(absEnd);
+ }
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)
{