/** Tests the adding of symbols to the composition */ public void TestAdd() { Composition composition = new Composition( "Composition", AlphabetType.DNA, 1, 3, 1, Composition.MatchMode.ALL, 0.0 ); composition.Add('a', 1.0); composition.Add('c', 3.0); composition.Add('t', 4.0); composition.Add('g', 2.0); composition.DefaultWeight = (3.5); Assert.AreEqual(4.0, composition.MaxWeight); Assert.AreEqual(1.0, composition.MinWeight); Assert.AreEqual(1.0, composition.Weight('a')); Assert.AreEqual(3.0, composition.Weight('c')); Assert.AreEqual(4.0, composition.Weight('t')); Assert.AreEqual(2.0, composition.Weight('g')); Assert.AreEqual(3.5, composition.Weight('u')); }
/** Test the setter for the default weight */ public void TestDefaultWeight() { Composition composition = new Composition( "Composition", AlphabetType.DNA, 1, 3, 1, Composition.MatchMode.ALL, 0.0 ); composition.DefaultWeight = (7.0); Assert.AreEqual(7.0, composition.MaxWeight); Assert.AreEqual(7.0, composition.MinWeight); composition.Add('c', 3.0); Assert.AreEqual(7.0, composition.MaxWeight); Assert.AreEqual(3.0, composition.MinWeight); }
public void TestMatchBest() { Sequence seq = new Sequence(AlphabetType.DNA, "actcctctg"); Composition composition = new Composition("Composition", AlphabetType.DNA, 3, 8, 1.7, Composition.MatchMode.BEST, 0.0); composition.Add('a', 1.0); composition.Add('c', 2.0); composition.Add('t', 3.0); composition.DefaultWeight = (1.0); Match match = composition.Match(seq, 1); Assert.AreEqual(1, match.Start); Assert.AreEqual(8, match.End); Assert.AreEqual("actcctct", match.Letters()); Assert.AreEqual(0.75, match.Similarity, 1e-2); match = seq.SearchBest(0, 0, composition); Assert.AreEqual(6, match.Start); Assert.AreEqual("tct", match.Letters()); Assert.AreEqual(0.88, match.Similarity, 1e-2); }
/** Test for match method from pattern interface */ public void TestMatchAll() { Sequence seq = new Sequence(AlphabetType.DNA, "act"); Composition composition = new Composition( "Composition", AlphabetType.DNA, 2, 3, 1, Composition.MatchMode.ALL, 0.0 ); composition.Add('a', 1.0); composition.Add('c', 2.0); composition.DefaultWeight = (3.0); Match match = composition.Match(seq, 1); Assert.AreEqual(2, match.Length); Assert.AreEqual(1, match.Start); Assert.AreEqual(2, match.End); Assert.AreEqual("ac", match.Letters()); Assert.AreEqual(0.5, match.Similarity, 1e-2); match = seq.SearchBest(0, 0, composition); Assert.AreEqual(2, match.Start); Assert.AreEqual("ct", match.Letters()); Assert.AreEqual(0.83, match.Similarity, 1e-2); FeatureList matches = seq.Search(0, 0, composition); Assert.AreEqual(3, matches.Count); Assert.AreEqual("ac", matches[0].Letters()); Assert.AreEqual("act", matches[1].Letters()); Assert.AreEqual("ct", matches[2].Letters()); }