public PatternIdentifier()
{
_apm = new ApproximatePatternMatchingCalculator();
_patternConverter = new PatternConverter();
_ngen = new NeighborhoodGenerator();
_rc = new ReverseComplement();
}
public string Solve(string dna, int k, double[,] profile)
{
PatternConverter patternConverter = new PatternConverter();
var kmers = ExtractKmers(dna, k).ToList();
double maxProbability = 0;
int maxIndex = -1;
for (var row = 0; row < kmers.Count; row++)
{
string kmer = kmers[row];
double product = 1;
for (int index = 0; index < kmer.Length; index++)
{
product *= profile[patternConverter.SymbolToNumber(kmer[index]), index];
}
if (maxProbability < product)
{
maxProbability = product;
maxIndex = row;
}
}
return kmers[maxIndex];
}
public FrequencyCalculator()
{
converter = new PatternConverter();
}
public ClumpFinder()
{
_calculator = new FrequencyCalculator();
_converter = new PatternConverter();
}