public void MotifTestMatch () {
Sequence seq = new Sequence( AlphabetType.DNA, "aTtga" );
Motif motif = new Motif( "test", AlphabetType.DNA, "tgn", 0.0 );
Match match = motif.Match( seq, 3 );
Assert.AreEqual( 3, match.Start );
Assert.AreEqual( 3, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 1.0, match.Similarity, 1e-2 );
match = motif.Match( seq, 2 );
Assert.AreEqual( 2, match.Start );
Assert.AreEqual( 3, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 0.66, match.Similarity, 1e-2 );
}
public void MotifTestTwoMatches () {
Sequence seq = new Sequence( AlphabetType.DNA, "aTtgattgaca" );
Motif motif = new Motif( "test", AlphabetType.DNA, "attg", 0.0 );
Match match = motif.Match( seq, 1 );
Assert.AreEqual( 1, match.Start );
Assert.AreEqual( 4, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 1.0, match.Similarity, 1e-2 );
Assert.AreEqual( "attg", match.Letters() );
Match match2 = motif.Match( seq, 2 );
Assert.AreEqual( 2, match.Start );
Assert.AreEqual( 4, match.Length );
Assert.AreEqual( 1, match.Strand );
Assert.AreEqual( 0.25, match.Similarity, 1e-2 );
Assert.AreEqual( "ttga", match.Letters() );
}
public void MotifTestMatchSimiliarity ()
{
Sequence seq = new Sequence(AlphabetType.DNA, "aCtG", true);
Assert.AreEqual(2, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 1).Length);
Assert.AreEqual(3, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 3).Start);
Assert.AreEqual(0.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 1).Similarity);
Assert.AreEqual(0.5, (new Motif("test", AlphabetType.DNA, "cc", 0)).Match(seq, 1).Similarity, 1e-3);
Assert.AreEqual(1.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 2).Similarity, 1e-3);
Assert.AreEqual(0.0, (new Motif("test", AlphabetType.DNA, "ct", 0)).Match(seq, 3).Similarity, 1e-3);
Assert.AreEqual(1.0, (new Motif("test", AlphabetType.DNA, "ctga", 0)).Match(seq, 2).Similarity, 1e-3);
Motif seq1 = new Motif("test", AlphabetType.DNA, "cc", 0.6);
Assert.AreEqual(null, seq1.Match(seq, 1));
}
public void MotifTestMatchAlternatives ()
{
Sequence seq = new Sequence(AlphabetType.DNA, "atgc");
Motif motif = new Motif("test", AlphabetType.DNA,"[ga]tg[c]", 0.0);
Match match = motif.Match(seq, 1);
Assert.AreEqual(1.0, match.Similarity, 1e-2);
}