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;
}