/** Tests the a match for an inverted repeat pattern */
public void TestMatchInverted()
{
Sequence seq = new Sequence(AlphabetType.DNA, "ttaccgtttgcaattt");
Repeat repeat = new Repeat("repeat", motif, Repeat.RepeatType.INVERTED, 0.5);
series.Add(repeat);
Match match = series.Match(seq, 3);
Assert.AreEqual(0.875, match.Similarity);
Assert.AreEqual("accgtttgcaa", match.Letters());
Assert.AreEqual("gcaa", match.SubMatches[2].Letters());
Assert.AreEqual(0.75, match.SubMatches[2].Similarity);
Assert.AreEqual(10, match.SubMatches[2].Start);
Assert.AreEqual(4, match.SubMatches[2].Length);
Assert.AreEqual(1, match.SubMatches[2].Strand);
match = seq.SearchBest(0, 0, series);
Assert.AreEqual("accgtttgcaa", match.Letters());
}
/// <summary>
/// The base constructor
/// </summary>
/// <param name="repeat">Reference of the repeat element</param>
public MatcherRepeat(Repeat repeat)
{
this.repeat = repeat;
}
/// <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;
}
/** Tests a weighted repeat */
public void TestMatchWeighted()
{
Sequence seq = new Sequence(AlphabetType.DNA, "ttaccgtttaacgttt");
Repeat repeat = new Repeat("repeat", motif, Repeat.RepeatType.DIRECT, 0.1);
series.Add(repeat);
repeat.Weight('a', 'a', 0.3);
repeat.Weight('c', 'a', 1.0);
repeat.Weight('g', 'g', 0.7);
Match match = series.Match(seq, 3);
Assert.AreEqual(0.75, match.Similarity);
Assert.AreEqual("accgtttaacg", match.Letters());
Assert.AreEqual("aacg", match.SubMatches[2].Letters());
Assert.AreEqual(0.5, match.SubMatches[2].Similarity, 1e-3);
match = seq.SearchBest(0, 0, series);
Assert.AreEqual("accgtttaacg", match.Letters());
}
/// <summary>
/// The default constructor that pass the Repeat element to its abstract
/// class.
/// </summary>
/// <param name="repeat"></param>
public MatcherInverted(Repeat repeat)
: base(repeat) { }
/// <summary>
/// Default constructor
/// </summary>
/// <param name="repeat"></param>
public MatcherDirect(Repeat repeat)
: base(repeat) { }
