public void TestSetGet () {
Sequence seq = new Sequence( AlphabetType.DNA, "atcg" );
Match m = new Match( null );
m.Set( seq, 3, 4, +1, 0.75 );
Assert.AreEqual( seq, m.BaseSequence );
Assert.AreEqual( 3, m.Start );
Assert.AreEqual( 4, m.Length );
Assert.AreEqual( 1, m.Strand );
Assert.AreEqual( 0.75, m.Similarity, 1e-3 );
Assert.AreEqual( 1, m.CalcMismatches() );
Assert.AreEqual( 3, m.Matches );
}
public void TestSetMatch () {
Sequence seq = new Sequence( AlphabetType.DNA, "atcg" );
Match m1 = new Match( null );
Match m2 = new Match( null );
m1.Set( seq, 3, 2, +1, 0.5 );
m2.Set( m1 );
Assert.AreEqual( seq, m2.BaseSequence );
Assert.AreEqual( 3, m2.Start );
Assert.AreEqual( 2, m2.Length );
Assert.AreEqual( 1, m2.Strand );
Assert.AreEqual( 0.5, m2.Similarity, 1e-3 );
Assert.AreEqual( "cg", m2.Letters() );
}
/// <summary>
/// Creates a deep copy of the given match object.
/// </summary>
/// <param name="match">Match object to copy.</param>
/// <returns>Returns a deep copy.</returns>
public Match Clone(Match match)
{
Match newMatch = new Match(null);
newMatch.Set(match);
newMatch.SubMatchedList = null;
for (int i = 0; i < match.SubMatchNumber; i++)
newMatch.Add(Clone(match.GetSubMatch(i)));
return (newMatch);
}