/** 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 );
}
/** 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 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 );
}
