/// <summary>
/// Generate a symmetric distance matrix from a set of aligned sequences.
/// </summary>
/// <param name="sequences">a set of aligned sequences</param>
public void GenerateDistanceMatrix(IList <ISequence> sequences)
{
if (sequences.Count <= 0)
{
throw new ArgumentException("empty sequence dataset");
}
// Construct a symmetric distance matrix
_distanceMatrix = new SymmetricDistanceMatrix(sequences.Count);
// Fill in values
Parallel.For(1, sequences.Count, PAMSAMMultipleSequenceAligner.parallelOption, row =>
{
for (int col = 0; col < row; ++col)
{
float distanceScore = KimuraDistanceScoreCalculator.CalculateDistanceScore(sequences[row], sequences[col]);
_distanceMatrix[row, col] = distanceScore;
_distanceMatrix[col, row] = distanceScore;
}
});
}
/// <summary>
/// Construct DistanceMatrix via Kimura method.
/// The two functions are defined in KimuraDistanceScoreCalculator class.
/// </summary>
public KimuraDistanceMatrixGenerator()
{
_kimuraDistanceScoreCalculator = new KimuraDistanceScoreCalculator();
}