/// <summary>
/// Construct a calculator with selected distance function
///
/// A distance function is assigned to the class and it is
/// read-only for a given set of input sequences.
/// </summary>
/// <param name="kmerLength">positive integer kmer length</param>
/// <param name="moleculeType">molecule type: DNA, RNA or Protein</param>
/// <param name="DistanceFunctionName">DistanceFunctionTypes member</param>
public KmerDistanceScoreCalculator(int kmerLength, MoleculeType moleculeType, DistanceFunctionTypes DistanceFunctionName)
{
if (kmerLength <= 0)
{
throw new ArgumentException("Kmer length needs to be positive");
}
_kmerLength = kmerLength;
switch (moleculeType)
{
case (MoleculeType.DNA):
_numberOfPossibleKmers = (int)Math.Pow(15, _kmerLength);
break;
case (MoleculeType.RNA):
_numberOfPossibleKmers = (int)Math.Pow(15, _kmerLength);
break;
case (MoleculeType.Protein):
_numberOfPossibleKmers = (int)Math.Pow(25, _kmerLength);
break;
default:
throw new Exception("Invalid molecular type");
}
switch (DistanceFunctionName)
{
case (DistanceFunctionTypes.EuclideanDistance):
_distanceFunction = new DistanceFunctionSelector(EuclideanDistance);
break;
case (DistanceFunctionTypes.CoVariance):
_distanceFunction = new DistanceFunctionSelector(CoVariance);
break;
case (DistanceFunctionTypes.PearsonCorrelation):
_distanceFunction = new DistanceFunctionSelector(PearsonCorrelation);
break;
case (DistanceFunctionTypes.ModifiedMUSCLE):
_distanceFunction = new DistanceFunctionSelector(ModifiedMUSCLE);
break;
default:
throw new ArgumentException("Similarity Function Name is not in the list...");
}
}
/// <summary>
/// Construct a calculator with selected distance function
///
/// A distance function is assigned to the class and it is
/// read-only for a given set of input sequences.
/// </summary>
/// <param name="kmerLength">positive integer kmer length</param>
/// <param name="alphabetType">molecule type: DNA, RNA or Protein</param>
/// <param name="DistanceFunctionName">DistanceFunctionTypes member</param>
public KmerDistanceScoreCalculator(int kmerLength, IAlphabet alphabetType, DistanceFunctionTypes DistanceFunctionName)
{
if (kmerLength <= 0)
{
throw new ArgumentException("Kmer length needs to be positive");
}
_kmerLength = kmerLength;
if (alphabetType is DnaAlphabet)
{
_numberOfPossibleKmers = (int)Math.Pow(15, _kmerLength);
}
else if (alphabetType is RnaAlphabet)
{
_numberOfPossibleKmers = (int)Math.Pow(15, _kmerLength);
}
else if (alphabetType is ProteinAlphabet)
{
_numberOfPossibleKmers = (int)Math.Pow(25, _kmerLength);
}
else
{
throw new Exception("Invalid molecular type");
}
switch (DistanceFunctionName)
{
case (DistanceFunctionTypes.EuclideanDistance):
_distanceFunction = new DistanceFunctionSelector(EuclideanDistance);
break;
case (DistanceFunctionTypes.CoVariance):
_distanceFunction = new DistanceFunctionSelector(CoVariance);
break;
case (DistanceFunctionTypes.PearsonCorrelation):
_distanceFunction = new DistanceFunctionSelector(PearsonCorrelation);
break;
case (DistanceFunctionTypes.ModifiedMUSCLE):
_distanceFunction = new DistanceFunctionSelector(ModifiedMUSCLE);
break;
default:
throw new ArgumentException("Similarity Function Name is not in the list...");
}
}
