private void DownloadAlignmentIfNeccessary(ref MultiSequenceAlignment msa, string suffix, IAlphabet alphabet = null)
{
if (msa == null)
{
var alignmentString = this.GetStringFromURLRequest(suffix).Result;
var parser = new FastAParser {
Alphabet = alphabet
};
var seqs = parser.Parse(new MemoryStream(Encoding.Unicode.GetBytes(alignmentString)));
msa = new MultiSequenceAlignment(seqs.ToList());
}
}
/// <summary>
/// Get the Blosum90 alignment score.
/// </summary>
/// <returns></returns>
public double GetUnmaskedBlosum90AlignmentScore()
{
var blosum = new Bio.SimilarityMatrices.SimilarityMatrix(SimilarityMatrices.SimilarityMatrix.StandardSimilarityMatrix.Blosum90);
return(MultiSequenceAlignment.MultipleAlignmentScoreFunction(this.UnmaskedAminoAcidAlignment.Sequences.ToList(), blosum, -5, -2));
}
