public void GroupTest2()
{
// AACGTNA
// TACGNAT
// CCCTTAN
// CNTAAGG
// ATTAGCA
// ATAGCAT
var groupAlignment =
new GroupAlignment(
new[]
{
new Sequence(new[] { Nucleotide.A, Nucleotide.A, Nucleotide.C, Nucleotide.G, Nucleotide.T, Nucleotide.C, Nucleotide.A }),
new Sequence(new[] { Nucleotide.T, Nucleotide.A, Nucleotide.C, Nucleotide.G, Nucleotide.G, Nucleotide.A, Nucleotide.T }),
new Sequence(new[] { Nucleotide.C, Nucleotide.G, Nucleotide.C, Nucleotide.T, Nucleotide.T, Nucleotide.A, Nucleotide.C }),
new Sequence(new[] { Nucleotide.C, Nucleotide.C, Nucleotide.T, Nucleotide.A, Nucleotide.A, Nucleotide.G, Nucleotide.G }),
new Sequence(new[] { Nucleotide.A, Nucleotide.T, Nucleotide.T, Nucleotide.A, Nucleotide.G, Nucleotide.C, Nucleotide.A }),
new Sequence(new[] { Nucleotide.A, Nucleotide.T, Nucleotide.A, Nucleotide.G, Nucleotide.C, Nucleotide.A, Nucleotide.T })
},
true);
var estimator = new OperationDistanceEstimator(3, 2, 0, 1);
var groupAlgorithm = new GroupAlignmentAlgorithm(estimator);
groupAlgorithm.Condensate(groupAlignment);
}
public void FillAlignedSequencesWithDifferentCountTest()
{
// AACGCTAG
// ATCCTAG
var sequence1 =
new Sequence(
new[]
{
Nucleotide.A, Nucleotide.A, Nucleotide.C, Nucleotide.G, Nucleotide.C, Nucleotide.T,
Nucleotide.A, Nucleotide.G
},
1);
var sequence2 =
new Sequence(
new[]
{
Nucleotide.A, Nucleotide.T, Nucleotide.C, Nucleotide.C, Nucleotide.T, Nucleotide.A,
Nucleotide.G
},
2);
var estimator = new OperationDistanceEstimator(4, 2, 0, 1);
var multipleAlignment1 = new MultipleAlignment(1, new[] { sequence1 }, estimator);
var multipleAlignment2 = new MultipleAlignment(2, new[] { sequence2 }, estimator);
var newMultipleAlignment = new MultipleAlignment(3, multipleAlignment1, multipleAlignment2);
var algorithm = new MultipleAlignmentAlgorithm(estimator);
var groupAlgorithm = new GroupAlignmentAlgorithm(estimator);
algorithm.FillAlignedSequences(newMultipleAlignment, groupAlgorithm.GeneratePairAlignmentsMap(newMultipleAlignment));
}
public void GroupTest1()
{
// AACGTAG
// ATACTAC
// GACCTAC
// GTACTTG
// GTCGTTG
var groupAlignment =
new GroupAlignment(
new[]
{
new Sequence(new[] { Nucleotide.A, Nucleotide.A, Nucleotide.C, Nucleotide.G, Nucleotide.T, Nucleotide.A, Nucleotide.G }),
new Sequence(new[] { Nucleotide.A, Nucleotide.T, Nucleotide.A, Nucleotide.C, Nucleotide.T, Nucleotide.A, Nucleotide.C }),
new Sequence(new[] { Nucleotide.G, Nucleotide.A, Nucleotide.C, Nucleotide.C, Nucleotide.T, Nucleotide.A, Nucleotide.C }),
new Sequence(new[] { Nucleotide.G, Nucleotide.T, Nucleotide.A, Nucleotide.C, Nucleotide.T, Nucleotide.T, Nucleotide.G }),
new Sequence(new[] { Nucleotide.G, Nucleotide.T, Nucleotide.C, Nucleotide.G, Nucleotide.T, Nucleotide.T, Nucleotide.G })
},
true);
var estimator = new OperationDistanceEstimator(4, 2, 0, 1);
var groupAlgorithm = new GroupAlignmentAlgorithm(estimator);
groupAlgorithm.Condensate(groupAlignment);
}