source: cpp/frams/genetics/fB/fB_general.h @ 912

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2018  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

#ifndef _FB_GENERAL_H_
#define _FB_GENERAL_H_

#include <frams/util/sstring.h>

class fB_GenoHelpers
{
public:
        static int geneCount(const SString& geno)
        {
                int start = 0;
                int prev = 0;
                int count = -1;
                do {
                        count++;
                        start = geno.indexOf("aa", start) + 1; // +1 is for progress, starting codons can overlap
                        int quotecount = 0;
                        for (int q = prev; q < start; q++) if (geno[q] == '\"') quotecount++;
                        prev = start;
                        if (quotecount % 2 != 0) count--; // 'aa' sequence is within quotes
                } while (start - 1 != -1);
                return count;
        }

        static SString getNonNestedGene(int i, const SString& genotype, int &start, int &end)
        {
                int count = -1;
                start = 0;
                int tmp = 0;
                SString result = "";
                do {
                        count++;
                        if (start < genotype.len())
                                result = getNextGene(start, genotype, tmp, start);
                        else
                                start = -1;
                } while (start != -1 && count < i);
                start = tmp;
                end = start;
                return result;
        }

        static int geneCountNoNested(const SString& geno)
        {
                int start = 0;
                int count = -1;
                int tmp = 0;
                do {
                        count++;
                        if (start < geno.len())
                                getNextGene(start, geno, tmp, start);
                        else
                                start = -1;
                } while (start != -1);
                return count;
        }

        static SString getGene(int i, const SString& genotype, int &start, int &end)
        {
                start = 0;
                int count = -1;
                do {
                        count++;
                        start = genotype.indexOf("aa", start) + 1;
                        int quotecount = 0;
                        for (int q = 0; q < start; q++) if (genotype[q] == '\"') quotecount++;
                        if (quotecount % 2 != 0) count--; // 'aa' sequence is within quotes
                } 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;
                int quotecount = 0;
                do {
                        quotecount = 0;
                        end = genotype.indexOf("zz", end);
                        if (end != -1)
                        {
                                for (int q = start; q < end; q++) if (genotype[q] == '\"') quotecount++;
                                if (quotecount % 2 != 0) end++;
                        }
                } while (quotecount % 2 != 0 && end != -1);

                if (end == -1) end = genotype.len();
                else end += 2;
                start -= 1;
                return genotype.substr(start, end - start);
        }

        static SString getNextGene(int searchbegin, const SString& genotype, int &start, int &end)
        {
                start = searchbegin;
                int count = -1;
                do {
                        count++;
                        start = genotype.indexOf("aa", start) + 1;
                        int quotecount = 0;
                        for (int q = 0; q < start; q++) if (genotype[q] == '\"') quotecount++;
                        if (quotecount % 2 != 0) count--; // 'aa' sequence is within quotes
                } while (start - 1 != -1 && count != 0);
                if (start - 1 == -1) // there is no gene with a given "i"
                {
                        start = -1;
                        end = -1;
                        return "";
                }
                end = start;
                int quotecount = 0;
                do {
                        quotecount = 0;
                        end = genotype.indexOf("zz", end);
                        if (end != -1)
                        {
                                for (int q = start; q < end; q++) if (genotype[q] == '\"') quotecount++;
                                if (quotecount % 2 != 0) end++;
                        }
                } while (quotecount % 2 != 0 && end != -1);

                if (end == -1) end = genotype.len();
                else end += 2;
                start -= 1;
                return genotype.substr(start, end - start);
        }
private:
        fB_GenoHelpers() {}
};

#endif // _FB_GENERAL_H_