/** Tests the weigthed matching */
public void TestMatchWeighted () {
Gap gap = new Gap( "test", 1, 4, 1, new double[] { 0.5, 0.5, 0.5 }, 0.0 );
Sequence seq = new Sequence( AlphabetType.DNA, "actga" );
Match match = gap.Match( seq, 1 );
Assert.AreEqual( "a", match.Letters() );
Assert.AreEqual( 1.0, match.Similarity, 1e-1 );
}
public void Setup()
{
series = new SeriesBest("series", 0.0);
motif = new Motif("motif", AlphabetType.DNA, "accg", 1.0);
gap = new Gap("gap", 3, 3);
gap.Impact = 0.0;
series.Add(motif);
series.Add(gap);
}
public void TestMatchVariablePattern()
{
Sequence seq = new Sequence(AlphabetType.DNA, "tttaagaacaagttt");
Gap gap = new Gap("gap", 1, 4, 1, new double[] { 0.0, 0.1, 1.0, 0.5 }, 0.0);
Iteration iteration;
Match match;
iteration = new Iteration("test", gap, 1, 3, 0.0);
match = iteration.Match(seq, 4);
Assert.AreEqual("aagaacaag", match.Letters());
Assert.AreEqual(1.0, match.Similarity, 1e-3);
}
public void TestMatch () {
Gap gap = new Gap( "test", 0, 3, 1 );
Sequence seq = new Sequence( AlphabetType.DNA, "act" );
FeatureList matches = seq.Search( 0, 0, gap );
Assert.AreEqual( 9, matches.Count );
Assert.AreEqual( "", matches[ 0 ].Letters() );
Assert.AreEqual( "a", matches[ 1 ].Letters() );
Assert.AreEqual( "ac", matches[ 2 ].Letters() );
Assert.AreEqual( "act", matches[ 3 ].Letters() );
Assert.AreEqual( "", matches[ 4 ].Letters() );
Assert.AreEqual( "c", matches[ 5 ].Letters() );
Assert.AreEqual( "ct", matches[ 6 ].Letters() );
Assert.AreEqual( "", matches[ 7 ].Letters() );
Assert.AreEqual( "t", matches[ 8 ].Letters() );
}
/** Tests the weigthed matching */
public void TestMatchWeighted1 () {
Gap gap = new Gap( "test", 1, 4, 1, new double[] { 1, 5, 10 }, 0.0 );
Sequence seq = new Sequence( AlphabetType.DNA, "actga" );
Match match = gap.Match( seq, 1 );
Assert.AreEqual( "a", match.Letters() );
Assert.AreEqual( 0.1, match.Similarity, 1e-1 );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "ac", match.Letters() );
Assert.AreEqual( 0.5, match.Similarity, 1e-1 );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "act", match.Letters() );
Assert.AreEqual( 1.0, match.Similarity, 1e-1 );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "actg", match.Letters() );
Assert.AreEqual( 1.0, match.Similarity, 1e-1 );
Assert.AreEqual( 1, gap.Increment );
}
/** Tests the matching with increment. */
public void TestMatchIncrement () {
Gap gap = new Gap( "test", 1, 8, 1.7 );
Sequence seq = new Sequence( AlphabetType.DNA, "actgactg" );
Match match = gap.Match( seq, 1 );
Assert.AreEqual( "a", match.Letters() );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "act", match.Letters() );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "actg", match.Letters() );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "actgac", match.Letters() );
Assert.AreEqual( 0, gap.Increment );
match = gap.Match( seq, 1 );
Assert.AreEqual( "actgactg", match.Letters() );
Assert.AreEqual( 1, gap.Increment );
}
/** Tests the weigthed matching */
public void TestMatchWeighted2 () {
Gap gap = new Gap( "test", 1, 4, 1, new double[] { 1, 5, 10 }, 0.0 );
Sequence seq = new Sequence( AlphabetType.DNA, "act" );
FeatureList matches = seq.Search( 0, 0, gap );
Assert.AreEqual( 6, matches.Count );
Assert.AreEqual( "a", matches[ 0 ].Letters() );
Assert.AreEqual( 0.1, ( (Match) matches[ 0 ] ).Similarity, 1e-1 );
Assert.AreEqual( "ac", matches[ 1 ].Letters() );
Assert.AreEqual( 0.5, ( (Match) matches[ 1 ] ).Similarity, 1e-1 );
Assert.AreEqual( "act", matches[ 2 ].Letters() );
Assert.AreEqual( 1.0, ( (Match) matches[ 2 ] ).Similarity, 1e-1 );
Assert.AreEqual( "c", matches[ 3 ].Letters() );
Assert.AreEqual( 0.1, ( (Match) matches[ 3 ] ).Similarity, 1e-1 );
Assert.AreEqual( "ct", matches[ 4 ].Letters() );
Assert.AreEqual( 0.5, ( (Match) matches[ 4 ] ).Similarity, 1e-1 );
Assert.AreEqual( "t", matches[ 5 ].Letters() );
Assert.AreEqual( 0.1, ( (Match) matches[ 5 ] ).Similarity, 1e-1 );
}
/// <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;
}