public void TestAddGetPattern () { SetBest set = new SetBest(); Assert.AreEqual( 0, set.Count ); Motif motif = new Motif( "motif1", AlphabetType.DNA, "ACTG", 0.7 ); set.Add( motif ); Assert.AreEqual( 1, set.Count ); Assert.AreEqual( motif, set[0] ); }
/** Tests if the match method finds the best pattern */ public void TestMatch1 () { Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" ); SetBest set = new SetBest( "set1", 0.5 ); set.Add( new Motif( "motif1", AlphabetType.DNA, "taa", 0.0 ) ); set.Add( new Motif( "motif2", AlphabetType.DNA, "aacc", 0.0 ) ); FeatureList matches; matches = seq.Search( 1, seq.Length, set ); Assert.AreEqual( 3, matches.Count ); Assert.AreEqual( "taa", matches[ 0 ].Letters() ); Assert.AreEqual( 1.00, ( (Match) matches[ 0 ] ).Similarity, 1e-2 ); Assert.AreEqual( "aaac", matches[ 1 ].Letters() ); Assert.AreEqual( 0.75, ( (Match) matches[ 1 ] ).Similarity, 1e-2 ); Assert.AreEqual( "aacc", matches[ 2 ].Letters() ); Assert.AreEqual( 1.00, ( (Match) matches[ 2 ] ).Similarity, 1e-2 ); }
/** Tests the matching a pattern set against a sequence */ public void TestMatch () { Sequence seq = new Sequence( AlphabetType.DNA, "atgcatgc" ); SetBest set = new SetBest( "set1", 0.5 ); set.Add( new Motif( "motif1", AlphabetType.DNA, "tgca", 0.0 ) ); set.Add( new Motif( "", AlphabetType.DNA, "tgc", 0.0 ) ); Match match = set.Match( seq, 2 ); Assert.AreEqual( 2, match.Start ); Assert.AreEqual( 4, match.Length ); Assert.AreEqual( 1, match.Strand ); Assert.AreEqual( 1, match.Similarity, 1e-2 ); match = set.Match( seq, 1 ); Assert.AreEqual( null, match ); match = set.Match( seq, 6 ); Assert.AreEqual( 6, match.Start ); Assert.AreEqual( 3, match.Length ); Assert.AreEqual( 1, match.Similarity, 1e-2 ); }
/// <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; }