source: cpp/frams/genetics/fB/fB_general.h @ 786

#ifndef _FB_GENERAL_H_
#define _FB_GENERAL_H_

#include <frams/util/sstring.h>

class fB_GenoHelpers
{
public:
        static int geneCount(SString geno)
        {
                int start = 0;
                int count = -1;
                do {
                        count++;
                        start = geno.indexOf("aa", start) + 1; // +1 is for progress, starting codons can overlap
                } while (start - 1 != -1);
                return count;
        }

        static SString getGene(int i, SString genotype, int &start, int &end)
        {
                start = 0;
                int count = -1;
                do {
                        count++;
                        start = genotype.indexOf("aa", start) + 1;
                } while (start - 1 != -1 && count != i);
                if (start - 1 == -1) // there is no gene with a given "i"
                {
                        start = -1;
                        end = -1;
                        return "";
                }
                end = start;
                end = genotype.indexOf("zz", end);
                if (end == -1) end = genotype.len();
                else end += 2;
                start -= 1;
                return genotype.substr(start, end - start);
        }

private:
        fB_GenoHelpers() {}
};

#endif // _FB_GENERAL_H_