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);
}