public void TestMatch2 () { Sequence seq = new Sequence( AlphabetType.DNA, "taaaccc" ); SeriesBest series = new SeriesBest(); Match match; series.Add( new Motif( "motif1", AlphabetType.DNA, "ta", 0.5 ) ); series.Add( new Gap( "gap", 1, 3, 1, new double[] { 1, 2, 1 }, 0.0 ) ); series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) ); match = seq.SearchBest( 1, seq.Length, series ); Assert.AreEqual( "taaacc", match.Letters() ); Assert.AreEqual( 1.00, match.Similarity, 1e-2 ); }
public void TestMatchStart() { Sequence seq = new Sequence(AlphabetType.DNA, "atgcatgc"); Series series = new SeriesBest("test", 1.0); series.Add(new Constraint("test", "START", +1)); series.Add(new Motif("motif", AlphabetType.DNA, "nnnn", 0.0)); Match match = series.Match(seq, 2); Assert.AreEqual("tgca", match.Letters()); match = series.Match(seq, 1); Assert.AreEqual(null, match); match = seq.SearchBest(0, 0, series); Assert.AreEqual("tgca", match.Letters()); }
public void TestPattern() { Series series1 = new SeriesBest("Series1", 1.0); series1.Add(new VoidPattern("VoidPattern1")); series1.Add(new VoidPattern("VoidPattern2")); Series series2 = new SeriesBest("Series2", 1.0); series2.Add(new VoidPattern("VoidPattern21")); series2.Add(series1); Definition definition = new Definition("test"); definition.Pattern = (series2); Assert.AreEqual("Series2", definition.Pattern.Name); Assert.AreEqual("VoidPattern21", definition.Patterns[1].Name); Assert.AreEqual("Series1", definition.Patterns[2].Name); Assert.AreEqual("VoidPattern1", definition.Patterns[3].Name); Assert.AreEqual("VoidPattern2", definition.Patterns[4].Name); }
public void TestMatchCenter() { Sequence seq = new Sequence(AlphabetType.DNA, "atgcatg"); Series series = new SeriesBest("test", 1.0); series.Add(new Constraint("test", "CENTER", -1)); series.Add(new Motif("motif", AlphabetType.DNA, "nnnn", 1.0)); Match match = series.Match(seq, 3); Assert.AreEqual("gcat", match.Letters()); match = series.Match(seq, 2); Assert.AreEqual(null, match); match = series.Match(seq, 4); Assert.AreEqual(null, match); match = seq.SearchBest(0, 0, series); Assert.AreEqual("gcat", match.Letters()); }
public void TestMatch1 () { Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" ); SeriesBest series = new SeriesBest(); Match match; series.Add( new Motif( "Motif1", AlphabetType.DNA, "aa", 0.5 ) ); match = seq.SearchBest( 1, seq.Length, series ); Assert.AreEqual( "aa", match.Letters() ); Assert.AreEqual( 2, match.Position() ); Assert.AreEqual( 1.00, match.Similarity, 1e-2 ); series.Add( new Gap( "Gap", 0, 2, 1 ) ); series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) ); match = seq.SearchBest( 1, seq.Length, series ); Assert.AreEqual( "aaacc", match.Letters() ); Assert.AreEqual( 2, match.Start ); Assert.AreEqual( 1.00, match.Similarity, 1e-2 ); }
/** Tests if the match method finds the best pattern */ public void TestMatch5 () { Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" ); SeriesBest series = new SeriesBest(); FeatureList matches; series.Add( new Motif( "motif1", AlphabetType.DNA, "aa", 0.5 ) ); series.Add( new Gap( "gap", 1, 3, 1 ) ); series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) ); matches = seq.Search( 1, seq.Length, series ); Assert.AreEqual( 2, matches.Count ); Assert.AreEqual( "taaacc", matches[ 0 ].Letters() ); Assert.AreEqual( 0.833, ( (Match) matches[ 0 ] ).Similarity, 1e-3 ); Assert.AreEqual( "aaacc", matches[ 1 ].Letters() ); Assert.AreEqual( 1.000, ( (Match) matches[ 1 ] ).Similarity, 1e-3 ); }