public void TestConvertPosition () {
Sequence seq = new Sequence( AlphabetType.DNA, "actgat" );
Sequence sub1 = new Sequence( seq, 2, 4, +1 );
Assert.AreEqual( 2, seq.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( seq, 2 ) );
Sequence sub2 = new Sequence( sub1, 1, 3, +1 );
Assert.AreEqual( 2, seq.Position( sub2, 1 ) );
Assert.AreEqual( 1, sub1.Position( seq, 2 ) );
Assert.AreEqual( 1, sub1.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( sub2, 1 ) );
sub2 = new Sequence( sub1, 1, 3, -1 );
Assert.AreEqual( 4, seq.Position( sub2, 1 ) );
Assert.AreEqual( 1, sub2.Position( seq, 4 ) );
Assert.AreEqual( 3, sub2.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( sub2, 3 ) );
sub1 = new Sequence( seq, 2, 4, -1 );
Assert.AreEqual( 4, seq.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( seq, 4 ) );
sub2 = new Sequence( sub1, 1, 3, +1 );
Assert.AreEqual( 2, seq.Position( sub2, 1 ) );
Assert.AreEqual( 1, sub2.Position( seq, 2 ) );
Assert.AreEqual( 3, sub2.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( sub2, 3 ) );
sub2 = new Sequence( sub1, 1, 3, -1 );
Assert.AreEqual( 4, seq.Position( sub2, 1 ) );
Assert.AreEqual( 1, sub2.Position( seq, 4 ) );
Assert.AreEqual( 1, sub2.Position( sub1, 1 ) );
Assert.AreEqual( 1, sub1.Position( sub2, 1 ) );
}
/// <summary>
/// Implementation of the <see cref="QUT.Bio.BioPatML.Patterns.IPattern">pattern interface</see>.
/// </summary>
/// <param name="sequence">Sequence to compare with.</param>
/// <param name="position">Matching position.</param>
/// <returns>The result.</returns>
public override Match Match(Sequence sequence, int position)
{
int absAlignPos = AlignPosition();
int absPos = sequence.Position() + position - 1;
Increment = absAlignPos - absPos;
Matched.Set(sequence, position + Increment, 0, sequence.Strand, 1.0);
return Matched;
}
public void TestPosition () {
Sequence seq = new Sequence( AlphabetType.DNA, "actg" );
Assert.AreEqual( 1, seq.Position() );
}