Animal.cpp

#include "Animal.h"

int getEditDistance(string s1, string s2)
{
int n = s1.size();
    int m = s2.size();

    vector<int>prev(m+1, 0), curr(m+1, 0);

    for(int j =0; j<=m; j++)
    {
        prev[j] = j;
    }

    for(int i = 1; i <= n; i++)
    {
        curr[0] = i;
        for(int j = 1; j<= m; j++)
        {
            if(s1[i-1] == s2[j-1])
            {
                curr[j] = prev[j-1];
            }
            else
            {
                int mn = min(1 + prev[j], 1 + curr[j-1]);
                curr[j] = min(mn, 1 + prev[j-1]);
            }
        }
        prev = curr;
    }

    return prev[m];
}

double SimilarityPercentageOfTwoChromosomes(string s1, string s2)
{
    double max_length = max(s1.length(), s2.length());
    if (max_length > 0) {
        return ((max_length - getEditDistance(s1, s2)) / max_length) * 100;
    }
    return 1.0;

}


float Animal::SimilarityPercentageOfTwoAnimal(vector<Genome> chro1, vector<Genome> chro2)
{
    double sum1 = 0;
    for(int i = 0; i < chro1.size(); i++)
    {
        double MAX1 = 0;
        for(int j = 0; j < chro2.size(); j++)
        {
            double A = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA1(), chro2[j].getDNA1());
            double B = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA2(), chro2[j].getDNA2());
            double C = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA1(), chro2[j].getDNA2());
            double D = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA2(), chro2[j].getDNA1());
            double AB = (A + B) / 2;
            double CD = (C + D) / 2;
            double percentage_two_chro = max(AB, CD);
            if(percentage_two_chro > MAX1)
            {
                MAX1 = percentage_two_chro;
            }     
        }
        sum1 += MAX1;
    }
    double average_chro1_chro2 = sum1 / chro1.size();

    double sum2 = 0;
    for(int i = 0; i < chro2.size(); i++)
    {
        double MAX2 = 0;
        for(int j = 0; j < chro1.size(); j++)
        {
            double A = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA1(), chro2[j].getDNA1());
            double B = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA2(), chro2[j].getDNA2());
            double C = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA1(), chro2[j].getDNA2());
            double D = SimilarityPercentageOfTwoChromosomes(chro1[i].getDNA2(), chro2[j].getDNA1());
            double AB = (A + B) / 2;
            double CD = (C + D) / 2;
            double percentage_two_chro = max(AB, CD);
            if(percentage_two_chro > MAX2)
            {
                MAX2 = percentage_two_chro;
            }     
        }
        sum1 += MAX2;
    }
    double average_chro2_chro1 = sum2 / chro2.size();

    // mohasebe darsad genetici nahaei
    double final = ((average_chro1_chro2 + average_chro2_chro1));   
    return final; 

}

bool Animal::operator==(Animal& A)
{
    if(
        SimilarityPercentageOfTwoAnimal(chromosomes, A.chromosomes) >= 70 &&
        chromosomes.size() == A.chromosomes.size()
    )
    {
        return true;
    }
    return false;
}

Animal Animal::AsexualReproduction()

{
    // tedad chromosom ha 2 barabar mishavad:
    vector<Genome> n2Chromosomes = chromosomes;
    for(auto & i : chromosomes)
    {
        n2Chromosomes.push_back(i);
    }

    // sakhtane bache ba darsad tashabohe >= 70%:
    int count = ceil((0.7 * n2Chromosomes.size()));
    int _count = count;
    vector<Genome> childChromosomes;
    // sakht 70% az chromosom ha ke tekrari nabashand
        for(int i = 0; i < _count; i++)
        {
            int index = rand() % n2Chromosomes.size();
            bool flag = true;
            for(int i = 0; i < childChromosomes.size(); i++)
            {
                if(childChromosomes[i].getDNA1() == n2Chromosomes[index].getDNA1())
                {
                    flag = false;
                }
            }
            if(flag == true)
            {
                childChromosomes.push_back(n2Chromosomes[index]);
            }

        
        }
    //sakht baghie chromosom ha
    for(int i = 0; i < n2Chromosomes.size() - count; i++)
    {
        int index2 = rand() % (n2Chromosomes.size() - count);
        childChromosomes.push_back(n2Chromosomes[index2]);
    }

    Animal animal(childChromosomes);
    return animal;
}

Animal* Animal::operator+(Animal& A)
{
    AsexualReproduction();
    A.AsexualReproduction();

    // n zoj bashad
    if(chromosomes.size() % 2 == 0 || A.chromosomes.size() % 2 == 0)
    {
        vector<Genome> animalChild;
        Animal *child;
        // darsad tashabohe >= 70%
        while(true)
        {
            animalChild.clear();
            // nesfe chromosom ha az obj1:
            for(int i = 0; i < chromosomes.size() / 2; i++)
            {
                int ch1 = rand() % chromosomes.size();
                animalChild.push_back(chromosomes[ch1]);
            }
            // nesfe chromosom ha az obj2:
            for(int i = 0; i < A.chromosomes.size() / 2; i++)
            {
                int ch2 = rand() % A.chromosomes.size();
                animalChild.push_back(A.chromosomes[ch2]);
            }

            if(child->SimilarityPercentageOfTwoAnimal(chromosomes, A.chromosomes) >= 70)
            {
                break;
            }
        }

        return child;
    }
        else // n fard bashad
        {
            cout << "Child can't be created!" << endl;
            return NULL;
            
        }

    
}

void Animal::cell_death()
{
    for(auto & i : chromosomes)
    {
        // peivand kharab
        int x = 0;

        for (int j = 0; j < chromosomes.size(); j++)
        {
            for (int i = 0; i < chromosomes[j].getDNA1().size(); i++)
            {
                if (chromosomes[j].getDNA1()[i] == 'A' && chromosomes[j].getDNA2()[i] != 'T')
                    x++;
                else if (chromosomes[j].getDNA1()[i] == 'T' && chromosomes[j].getDNA2()[i] != 'A')
                    x++;
                else if (chromosomes[j].getDNA1()[i] == 'G' && chromosomes[j].getDNA2()[i] != 'C')
                    x++;
                else if (chromosomes[j].getDNA1()[i] == 'C' && chromosomes[j].getDNA2()[i] != 'G')
                    x++;
            }
        }
        // peivand AT , CG
        int AT = 0, CG = 0;
        for (int i = 0; i < chromosomes.size(); i++)
        {
            for (int j = 0; j < chromosomes[i].getDNA1().size(); j++)
            {
                if (chromosomes[i].getDNA1()[j] == 'A' && chromosomes[i].getDNA2()[j] == 'T' || chromosomes[i].getDNA1()[j] == 'T' && chromosomes[i].getDNA2()[j] == 'A')
                {
                    AT++;
                }
                if (chromosomes[i].getDNA1()[j] == 'C' && chromosomes[i].getDNA2()[j] == 'G' || chromosomes[i].getDNA1()[j] == 'G' && chromosomes[i].getDNA2()[j] == 'C')
                {
                    CG++;
                }
            }
        }

        vector<Genome>::iterator it;
        it = chromosomes.begin();

        // delete cell
        if (x > 5 || AT > 3 * CG)
        {  
            cout << "Cell died out!" << endl; 
            chromosomes.erase(it);
        }
    }
}