public void TestMatch()
        {
            Sequence seq = new Sequence(AlphabetType.DNA, "acctccgg");
            RegularExp regx = new RegularExp("test","ctc.");
            Match myMatch = regx.Match(seq, 1);

            Assert.AreEqual(null, myMatch);

            myMatch = regx.Match(seq, 3);
            Assert.AreEqual(3, myMatch.Start);
            Assert.AreEqual(4, myMatch.Length);
            Assert.AreEqual(1, myMatch.Strand);
            Assert.AreEqual(1.0, myMatch.Similarity, 1e-2);

            regx = new RegularExp("test", "acc");
            myMatch = regx.Match(seq, 1);
            Assert.AreEqual(1, myMatch.Start);

            regx = new RegularExp("test", "cgg");
            myMatch = regx.Match(seq, 6);
            Assert.AreEqual(8, myMatch.End);

            //last test
            
            //ISSUE: could be star problem
            regx = new RegularExp("test", "c.*g");
            FeatureList matches = seq.Search(0, 0, regx);
            Assert.AreEqual(4, matches.Count);
            Assert.AreEqual("cctccgg", matches[0].Letters());
            Assert.AreEqual("ctccgg", matches[1].Letters());
            Assert.AreEqual("ccgg", matches[2].Letters());
            Assert.AreEqual("cgg", matches[3].Letters());


        }
        /** test for case insensitivity of a match */
        public void TestCaseInsensitivity()
        {
            RegularExp regx;

            regx = new RegularExp("test", "act", true);
            Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));

            regx = new RegularExp("test", "act", true);
            Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));


            regx = new RegularExp("test", "ACT", true);
            Assert.IsNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));

            //---
            regx = new RegularExp("test", "Act", true);
            Assert.IsNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));

            regx = new RegularExp("test", "Act", false);
            Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));


            regx = new RegularExp("test", "Act", false);
            Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));
        }
        public void TestTest()
        {
            Sequence seq = new Sequence(AlphabetType.DNA, "acctccctcccgacgg");
            RegularExp regx = new RegularExp("test","ctc.");

            Match myMatch = regx.Match(seq, 3);

            Assert.IsNotNull(myMatch);

            FeatureList matches = seq.Search(0, 0, regx);
            Assert.IsNotNull(matches);
        }