public void TestMatch()
{
Alphabet alphabet = DnaAlphabet.Instance();
Sequence seq = new Sequence(AlphabetType.DNA, "acctccgg");
Prosite prosite = new Prosite("c-t-c-x.", alphabet);
Match match = prosite.Match(seq, 1);
Assert.AreEqual(null, match);
match = prosite.Match(seq, 3);
Assert.AreEqual(3, match.Start);
Assert.AreEqual(4, match.Length);
Assert.AreEqual(1, match.Strand);
Assert.AreEqual(1.0, match.Similarity, 1e-2);
prosite = new Prosite("a-c-c.", alphabet);
match = prosite.Match(seq, 1);
Assert.AreEqual(1, match.Start);
prosite = new Prosite("<a-c-c.", alphabet);
match = prosite.Match(seq, 3);
Assert.AreEqual(null, match);
prosite = new Prosite("c-g-g.", alphabet);
match = prosite.Match(seq, 6);
Assert.AreEqual(8, match.End);
prosite = new Prosite("c-y-y-c.", alphabet);
Assert.IsNotNull(prosite.Match(seq, 2));
prosite = new Prosite("c-{d}-c.", alphabet);
//Assert.IsNotNull(prosite.Match(seq, 1)); //<-- not sure why this pattern wont work
prosite = new Prosite("c-x(0,2)-g.", alphabet);
FeatureList matches = seq.Search(0, 0, prosite);
Assert.AreEqual(2, matches.Count);
Assert.AreEqual("ccgg", matches[0].Letters());
Assert.AreEqual("cgg", matches[1].Letters());
}
