public void TestMatch() { Sequence seq = new Sequence(AlphabetType.DNA,"tttaagaacaagttt"); Motif motif = new Motif("motif", AlphabetType.DNA,"aag", 0.5); Iteration iteration; Match match; iteration = new Iteration("test",motif,1,3,0.0); match = iteration.Match(seq, 4); Assert.AreEqual(4, match.Start); Assert.AreEqual(9, match.Length); Assert.AreEqual(1, match.Strand); Assert.AreEqual("aagaacaag", match.Letters()); Assert.AreEqual(seq, match.BaseSequence); Assert.AreEqual(0.888, match.Similarity, 1e-3); iteration = new Iteration("test",motif,1,1,0.0); match = iteration.Match(seq, 4); Assert.AreEqual("aag", match.Letters()); Assert.AreEqual(1.0, match.Similarity, 1e-3); iteration = new Iteration("test",motif,1,2,0.0); match = iteration.Match(seq, 4); Assert.AreEqual("aagaac", match.Letters()); Assert.AreEqual(0.833, match.Similarity, 1e-3); iteration = new Iteration("test",motif,4,5,0.0); Assert.AreEqual(null, iteration.Match(seq, 4)); }
public void TestConstructor() { Motif motif = new Motif("motif", AlphabetType.DNA, "tgn", 0.0); Iteration iteration = new Iteration("test", motif, 3, 4, 0.0); Assert.AreEqual("test", iteration.Name); Assert.AreEqual(motif, iteration.Pattern); Assert.AreEqual(3, iteration.Minimum); Assert.AreEqual(4, iteration.Maximum); }
public void TestMatchVariablePattern() { Sequence seq = new Sequence(AlphabetType.DNA, "tttaagaacaagttt"); Gap gap = new Gap("gap", 1, 4, 1, new double[] { 0.0, 0.1, 1.0, 0.5 }, 0.0); Iteration iteration; Match match; iteration = new Iteration("test", gap, 1, 3, 0.0); match = iteration.Match(seq, 4); Assert.AreEqual("aagaacaag", match.Letters()); Assert.AreEqual(1.0, match.Similarity, 1e-3); }
/// <summary> /// /// Reads a pattern from a starting specified node. This method /// recursivly calls the reading methods of the different patterns. /// </summary> /// <param name="node">Node of the pattern the reading starts with.</param> /// <param name="definition">Pattern definition which pattern list will be extended /// with the pattern and all its sub-patterns read. /// </param> /// <returns>The read pattern or null if there is no pattern to read.</returns> /// <exception cref="System.SystemException">Thrown when unknown pattern was found</exception> public static IPattern ReadPattern (XmlNode node, Definition definition) { while (node != null && node.NodeType != XmlNodeType.Element) node = node.NextSibling; //Iterate thru the list of nodes until it is an element IPattern pattern = null; String mode = XMLHelper.GetAttrValueString(node, "mode"); switch (node.Name) { case "Any": pattern = new Any(); break; case "Alignment": pattern = new Alignment(); break; case "Composition" : pattern = new Composition(); break; case "Constraint": pattern = new Constraint(); break; case "Iteration": pattern = new Iteration(); break; case "Logic": pattern = new Logic(); break; case "Motif": pattern = new Motif(); break; case "PWM": pattern = new PWM(); break; case "Regex": pattern = new RegularExp(); break; case "Prosite": pattern = new Prosite(); break; case "Block": pattern = new Block(); break; case "Gap": pattern = new Gap(); break; case "Repeat": pattern = new Repeat(); break; case "Series": pattern = mode.Equals("ALL") ? pattern = new SeriesAll() : pattern = new SeriesBest(); break; case "Set": pattern = mode.Equals("ALL") ? pattern = new SetAll() : pattern = new SetBest(); break; case "Void": pattern = new VoidPattern(); break; case "Use": pattern = new Use(); break; throw new SystemException ("Unknown pattern found: " + node.Name); } pattern.ReadNode(node, definition); // read the node data and initialize the pattern definition.Patterns.Add (0, pattern); //Always adding the element to last index return pattern; }
public void TestMatchSubMatches() { Sequence seq = new Sequence(AlphabetType.DNA, "tttaagaacaagttt"); Motif motif = new Motif("motif", AlphabetType.DNA, "aag", 0.5); Iteration iteration = new Iteration("test", motif, 1, 3, 0.0); Match match = seq.SearchBest(0, 0, iteration); Assert.AreEqual("aag", match.Letters()); Assert.AreEqual(10, match.Start); Assert.AreEqual(1.0, match.Similarity); Assert.AreEqual("aag", match.SubMatches[0].Letters()); //sub match to properties? FeatureList matches = seq.Search(0, 0, iteration); Assert.AreEqual(3, matches.Count); Assert.AreEqual("aagaacaag", matches[0].Letters()); Assert.AreEqual(0.88, ((Match)matches[0]).Similarity, 1e-2); Assert.AreEqual("aacaag", matches[1].Letters()); Assert.AreEqual(0.83, ((Match)matches[1]).Similarity, 1e-2); Assert.AreEqual("aag", matches[2].Letters()); Assert.AreEqual(1.00, ((Match)matches[2]).Similarity, 1e-2); }