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 );
}
/** 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 );
}
