/** test for case insensitivity of a match */
public void TestCaseInsensitivity()
{
RegularExp regx;
regx = new RegularExp("test", "act", true);
Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));
regx = new RegularExp("test", "act", true);
Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));
regx = new RegularExp("test", "ACT", true);
Assert.IsNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));
//---
regx = new RegularExp("test", "Act", true);
Assert.IsNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));
regx = new RegularExp("test", "Act", false);
Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "act"), 1));
regx = new RegularExp("test", "Act", false);
Assert.IsNotNull(regx.Match(new Sequence(AlphabetType.DNA, "ACT"), 1));
}
public void TestMatch()
{
Sequence seq = new Sequence(AlphabetType.DNA, "acctccgg");
RegularExp regx = new RegularExp("test","ctc.");
Match myMatch = regx.Match(seq, 1);
Assert.AreEqual(null, myMatch);
myMatch = regx.Match(seq, 3);
Assert.AreEqual(3, myMatch.Start);
Assert.AreEqual(4, myMatch.Length);
Assert.AreEqual(1, myMatch.Strand);
Assert.AreEqual(1.0, myMatch.Similarity, 1e-2);
regx = new RegularExp("test", "acc");
myMatch = regx.Match(seq, 1);
Assert.AreEqual(1, myMatch.Start);
regx = new RegularExp("test", "cgg");
myMatch = regx.Match(seq, 6);
Assert.AreEqual(8, myMatch.End);
//last test
//ISSUE: could be star problem
regx = new RegularExp("test", "c.*g");
FeatureList matches = seq.Search(0, 0, regx);
Assert.AreEqual(4, matches.Count);
Assert.AreEqual("cctccgg", matches[0].Letters());
Assert.AreEqual("ctccgg", matches[1].Letters());
Assert.AreEqual("ccgg", matches[2].Letters());
Assert.AreEqual("cgg", matches[3].Letters());
}
public void TestTest()
{
Sequence seq = new Sequence(AlphabetType.DNA, "acctccctcccgacgg");
RegularExp regx = new RegularExp("test","ctc.");
Match myMatch = regx.Match(seq, 3);
Assert.IsNotNull(myMatch);
FeatureList matches = seq.Search(0, 0, regx);
Assert.IsNotNull(matches);
}
/// <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;
}