public void FillAlignedSequencesTest2()
{
// AACGCTAG
// ATCCTAGG
var sequence1 = new Sequence
{
Nucleotide.A,
Nucleotide.A,
Nucleotide.C,
Nucleotide.G,
Nucleotide.C,
Nucleotide.T,
Nucleotide.A,
Nucleotide.G
};
var sequence2 = new Sequence
{
Nucleotide.A,
Nucleotide.T,
Nucleotide.C,
Nucleotide.C,
Nucleotide.T,
Nucleotide.A,
Nucleotide.G,
Nucleotide.G
};
var pairAlignment = new PairAlignment(sequence1, sequence2);
var algorithm = new PairAlignmentAlgorithm(new OperationDistanceEstimator(4, 2, 0, 1));
algorithm.FillAlignedSequences(pairAlignment);
}
/// <summary>
/// The distance.
/// </summary>
/// <param name="pair">The pair sequence.</param>
/// <returns>The <see cref="int"/>.</returns>
public override double Distance(PairAlignment pair)
{
return pair.DynamicTable[new Index(pair.First.Count, pair.Second.Count)].Distance;
}
/// <summary>
/// The dynamic table fill.
/// </summary>
/// <param name="sequences">The group alignment.</param>
/// <returns>The dynamic table.</returns>
public Dictionary<Index, PairAlignment> GeneratePairAlignmentsMap(IEnumerable<Sequence> sequences)
{
var map = new Dictionary<Index, PairAlignment>();
var list = sequences.ToList();
foreach (var sequence in list)
{
// except the diagonal elements and filled cells (the table is been filling for symmetrical elements in one step)
foreach (var sequence2 in list.Where(a => a.Id != sequence.Id && !map.ContainsKey(new Index(sequence.Id.Value, a.Id.Value))))
{
var p = new PairAlignment(sequence, sequence2);
this.PairAlignmentAlgorithm.FillAlignedSequences(p);
map[new Index(sequence.Id.Value, sequence2.Id.Value)] = p;
map[new Index(sequence2.Id.Value, sequence.Id.Value)] = p;
}
}
return map;
}
/// <summary> /// Gets distance estimate for 2 sequences /// </summary> /// <param name="pair">The sequence pair.</param> /// <returns>Distance estimate</returns> public abstract double Distance(PairAlignment pair);
