public void TestConstructor () {
Definition container = new Definition();
container.Definitions.Add( new Definition( "Def", new Any( "Any", 1, 3, 1 ) ) );
Use use = new Use { Name = "Use" };
use.ReferTo( container, "Def" );
Assert.AreEqual( "Use", use.Name );
Assert.AreEqual( "Def", use.ReferencedDefinition.Name );
}
public void TestMatch ()
{
Definition def = new Definition();
def.Definitions.Add( new Definition("Def", new Motif("Motif", AlphabetType.DNA, "atg", 0.0)) );
Sequence seq = new Sequence(AlphabetType.DNA, "atgc");
Use use = new Use{ Name = "Use" };
use.ReferTo( def, "Def" );
Match match = use.Match(seq, 1);
Assert.AreEqual(use, match.MatchPattern);
Assert.AreEqual(1, match.Start);
Assert.AreEqual(3, match.Length);
Assert.AreEqual(1, match.Strand);
Assert.AreEqual(1.0, 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;
}