static TDistance ComputeDistance(PairwiseAlignment alignment)
{
TDistance result = 0;
if (_alignmentType == AlignmentType.Nucleic)
{
switch (_distanceFunction)
{
case DistanceFunctionType.PercentIdentity:
result = (TDistance)(1.0f - alignment.PercentIdentity);
break;
case DistanceFunctionType.Kimura2:
result = (TDistance)(alignment.ComputeKimuraDistance());
break;
case DistanceFunctionType.JukesCantor:
result = (TDistance)(alignment.ComputeJukesCantorDistance());
break;
}
}
else
{
result = (TDistance)(1.0f - alignment.PercentSimilarity);
}
return(result);
}
static void WriteAlignment(StreamWriter writer, PairwiseAlignment alignment)
{
double kimeraDistance = alignment.ComputeKimuraDistance();
double jukesCantorDistance = alignment.ComputeJukesCantorDistance();
double percentIdentityDistance = alignment.PercentIdentity;
writer.WriteLine(">{0} Kimera: {1}, JukesCantor: {2}, PercentIdentity: {3}", alignment.Name1, kimeraDistance.ToString("F5"), jukesCantorDistance.ToString("F5"), alignment.PercentIdentity.ToString("F5"));
writer.WriteLine(alignment.Sequence1);
writer.WriteLine(">{0} Kimera: {1}, JukesCantor: {2}, PercentIdentity: {3}", alignment.Name2, kimeraDistance.ToString("F5"), jukesCantorDistance.ToString("F5"), alignment.PercentIdentity.ToString("F5"));
writer.WriteLine(alignment.Sequence2);
writer.WriteLine();
}