public void TestMatch2 () {
Sequence seq = new Sequence( AlphabetType.DNA, "taaaccc" );
SeriesBest series = new SeriesBest();
Match match;
series.Add( new Motif( "motif1", AlphabetType.DNA, "ta", 0.5 ) );
series.Add( new Gap( "gap", 1, 3, 1, new double[] { 1, 2, 1 }, 0.0 ) );
series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) );
match = seq.SearchBest( 1, seq.Length, series );
Assert.AreEqual( "taaacc", match.Letters() );
Assert.AreEqual( 1.00, match.Similarity, 1e-2 );
}
public void TestMatchStart()
{
Sequence seq = new Sequence(AlphabetType.DNA, "atgcatgc");
Series series = new SeriesBest("test", 1.0);
series.Add(new Constraint("test", "START", +1));
series.Add(new Motif("motif", AlphabetType.DNA, "nnnn", 0.0));
Match match = series.Match(seq, 2);
Assert.AreEqual("tgca", match.Letters());
match = series.Match(seq, 1);
Assert.AreEqual(null, match);
match = seq.SearchBest(0, 0, series);
Assert.AreEqual("tgca", match.Letters());
}
public void TestPattern()
{
Series series1 = new SeriesBest("Series1", 1.0);
series1.Add(new VoidPattern("VoidPattern1"));
series1.Add(new VoidPattern("VoidPattern2"));
Series series2 = new SeriesBest("Series2", 1.0);
series2.Add(new VoidPattern("VoidPattern21"));
series2.Add(series1);
Definition definition = new Definition("test");
definition.Pattern = (series2);
Assert.AreEqual("Series2", definition.Pattern.Name);
Assert.AreEqual("VoidPattern21", definition.Patterns[1].Name);
Assert.AreEqual("Series1", definition.Patterns[2].Name);
Assert.AreEqual("VoidPattern1", definition.Patterns[3].Name);
Assert.AreEqual("VoidPattern2", definition.Patterns[4].Name);
}
public void TestMatchCenter()
{
Sequence seq = new Sequence(AlphabetType.DNA, "atgcatg");
Series series = new SeriesBest("test", 1.0);
series.Add(new Constraint("test", "CENTER", -1));
series.Add(new Motif("motif", AlphabetType.DNA, "nnnn", 1.0));
Match match = series.Match(seq, 3);
Assert.AreEqual("gcat", match.Letters());
match = series.Match(seq, 2);
Assert.AreEqual(null, match);
match = series.Match(seq, 4);
Assert.AreEqual(null, match);
match = seq.SearchBest(0, 0, series);
Assert.AreEqual("gcat", match.Letters());
}
public void TestMatch1 () {
Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" );
SeriesBest series = new SeriesBest();
Match match;
series.Add( new Motif( "Motif1", AlphabetType.DNA, "aa", 0.5 ) );
match = seq.SearchBest( 1, seq.Length, series );
Assert.AreEqual( "aa", match.Letters() );
Assert.AreEqual( 2, match.Position() );
Assert.AreEqual( 1.00, match.Similarity, 1e-2 );
series.Add( new Gap( "Gap", 0, 2, 1 ) );
series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) );
match = seq.SearchBest( 1, seq.Length, series );
Assert.AreEqual( "aaacc", match.Letters() );
Assert.AreEqual( 2, match.Start );
Assert.AreEqual( 1.00, 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;
}
/** Tests if the match method finds the best pattern */
public void TestMatch5 () {
Sequence seq = new Sequence( AlphabetType.DNA, "taaacc" );
SeriesBest series = new SeriesBest();
FeatureList matches;
series.Add( new Motif( "motif1", AlphabetType.DNA, "aa", 0.5 ) );
series.Add( new Gap( "gap", 1, 3, 1 ) );
series.Add( new Motif( "motif2", AlphabetType.DNA, "cc", 0.5 ) );
matches = seq.Search( 1, seq.Length, series );
Assert.AreEqual( 2, matches.Count );
Assert.AreEqual( "taaacc", matches[ 0 ].Letters() );
Assert.AreEqual( 0.833, ( (Match) matches[ 0 ] ).Similarity, 1e-3 );
Assert.AreEqual( "aaacc", matches[ 1 ].Letters() );
Assert.AreEqual( 1.000, ( (Match) matches[ 1 ] ).Similarity, 1e-3 );
}
