public void TestDistanceStartEnd()
{
Sequence seq = new Sequence(AlphabetType.DNA, "acgtactg");
Feature feature1 = new Feature("feature1", 2, 4, +1);
Feature feature2 = new Feature("feature2", 5, 7, +1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(5, feature1.DistanceStartEnd(feature2));
Assert.AreEqual(7, feature2.DistanceStartEnd(feature1));
}
public void TestDistanceDownStream()
{
Sequence seq = new Sequence( AlphabetType.DNA, "acgtactgactg", true );
Feature feature1;
Feature feature2;
feature1 = new Feature("feature1", 6, 8, +1);
feature2 = new Feature("feature2", 2, 3, +1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(5, feature1.DistanceDownstream(feature2));
Assert.AreEqual(2, feature2.DistanceDownstream(feature1));
//Reverse circular strand
feature1 = new Feature("feature1", 6, 8, -1);
feature2 = new Feature("feature2", 2, 3, -1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(5, feature2.DistanceDownstream(feature1));
Assert.AreEqual(2, feature1.DistanceDownstream(feature2));
//Circular mixed strand
feature1 = new Feature("feature1", 6, 8, +1);
feature2 = new Feature("feature2", 2, 3, -1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(5, feature2.DistanceDownstream(feature1));
Assert.AreEqual(5, feature1.DistanceDownstream(feature2));
seq = new Sequence(AlphabetType.DNA, "acgtactgactg", false);
//linear strand
feature1 = new Feature("feature1", 6, 8, +1);
feature2 = new Feature("feature2", 2, 3, +1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(4, feature1.DistanceDownstream(feature2));
Assert.AreEqual(2, feature2.DistanceDownstream(feature1));
//Linear mixed strand
feature1 = new Feature("feature1", 6, 8, +1);
feature2 = new Feature("feature2", 2, 3, -1);
feature1.SetSequence(seq);
feature2.SetSequence(seq);
Assert.AreEqual(4, feature1.DistanceDownstream(feature2));
Assert.AreEqual(1, feature2.DistanceDownstream(feature1));
}
public void TestIsInside()
{
Sequence seq = new Sequence(AlphabetType.DNA, "acgtgat");
Feature feature1 = new Feature("feature1", 2, 4, +1);
feature1.SetSequence(seq);
Assert.AreEqual(true, feature1.IsInside(seq, 2));
Assert.AreEqual(false, feature1.IsInside(seq, 1));
Assert.AreEqual(true, feature1.IsInside(seq, 4));
Assert.AreEqual(false, feature1.IsInside(seq, 5));
Sequence sub1 = new Sequence(seq, 2, 4, +1);
Assert.AreEqual(true, feature1.IsInside(sub1, 1));
Assert.AreEqual(false, feature1.IsInside(sub1, 0));
Assert.AreEqual(true, feature1.IsInside(sub1, 3));
Assert.AreEqual(false, feature1.IsInside(sub1, 4));
Sequence sub2 = new Sequence(sub1, 1, 3, +1);
Assert.AreEqual(true, feature1.IsInside(sub2, 1));
Assert.AreEqual(false, feature1.IsInside(sub2, 0));
Assert.AreEqual(true, feature1.IsInside(sub2, 3));
Assert.AreEqual(false, feature1.IsInside(sub2, 4));
sub2 = new Sequence(sub1, 1, 3, -1);
Assert.AreEqual(true, feature1.IsInside(sub2, 1));
Assert.AreEqual(false, feature1.IsInside(sub2, 0));
Assert.AreEqual(true, feature1.IsInside(sub2, 3));
Assert.AreEqual(false, feature1.IsInside(sub2, 4));
sub1 = new Sequence(seq, 2, 4, -1);
Assert.AreEqual(true, feature1.IsInside(sub1, 1));
Assert.AreEqual(false, feature1.IsInside(sub1, 0));
Assert.AreEqual(true, feature1.IsInside(sub1, 3));
Assert.AreEqual(false, feature1.IsInside(sub1, 4));
sub2 = new Sequence(sub1, 1, 3, +1);
Assert.AreEqual(true, feature1.IsInside(sub2, 1));
Assert.AreEqual(false, feature1.IsInside(sub2, 0));
Assert.AreEqual(true, feature1.IsInside(sub2, 3));
Assert.AreEqual(false, feature1.IsInside(sub2, 4));
sub2 = new Sequence(sub1, 1, 3, -1);
Assert.AreEqual(true, feature1.IsInside(sub2, 1));
Assert.AreEqual(false, feature1.IsInside(sub2, 0));
Assert.AreEqual(true, feature1.IsInside(sub2, 3));
Assert.AreEqual(false, feature1.IsInside(sub2, 4));
}
