/**
* Add search results for regions in other sequences that translate or are
- * translated from a particular position in seq
+ * translated from a particular position in seq (which may be an aligned or
+ * dataset sequence)
*
* @param seq
* @param index
SearchResultsI results)
{
SequenceI ds = seq.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = seq;
+ }
for (SequenceToSequenceMapping ssm : mappings)
{
ssm.markMappedRegion(ds, index, results);
}
/**
- * Returns the first mapping found which is between the given sequence and
- * another, is a triplet mapping (3:1 or 1:3), and covers the full extent of
- * both sequences involved.
+ * Returns the first mapping found which is between the given dataset sequence
+ * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
+ * of both sequences involved
*
* @param seq
* @return