+BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
+{
+ // when searching for a motif on a subsequence we should
+ // only search the subsequence ticket:199
+ string aaaa("AAAA");
+ string cccc("CCCC");
+ Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
+
+ // this shouldn't show up
+ s1.add_motif(cccc);
+ BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
+
+ s1.add_motif(aaaa);
+ BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
+
+ Sequence subseq1 = s1.subseq(4,5);
+ BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
+ subseq1.clear_motifs();
+ BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
+ // this is outside of our subsequence, and so shouldn't be found
+ subseq1.add_motif(aaaa);
+ BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
+
+ subseq1.add_motif(cccc);
+ BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
+ std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
+ BOOST_REQUIRE(motif_i != subseq1.motifs().end());
+ BOOST_CHECK_EQUAL(motif_i->begin, 1);
+ BOOST_CHECK_EQUAL(motif_i->end, 5);
+}
+