public final void setSequence(final String seq) {
try {
final String transformedSequence = FragmentRewriter.rewriteFragment(seq);
SequenceMatcherCompiler compiler = new SequenceMatcherCompiler();
matcher = compiler.compile(transformedSequence);
searcher = new BoyerMooreHorspoolSearcher(matcher);
} catch (ParseException ex) {
final String warning = String.format(SEQUENCE_PARSE_ERROR, seq, ex.getMessage());
getLog().warn(warning);
//throw new IllegalArgumentException(seq, ex);
isInvalidSubSequence = true;