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);
}