using System;
using L=Science.Biology.PopulationGenetics;

namespace ScienceTest.BiologyTest.PopulationGeneticsTest
{
	/// <summary>
	/// Caste System is considered.
	/// </summary>
	public class HierarchicalMatingWithBioGene
	{
		private string result;
		public string Result
		{
			get{return result;}
		}

		public HierarchicalMatingWithBioGene()
		{
		}

		public void Compute() 
		{
			L.Chromosome[] Ac = new L.Chromosome[22];
			Ac[0] = new L.Chromosome();
			Ac[1] = new L.Chromosome();
			Ac[2] = new L.Chromosome();
			Ac[3] = new L.Chromosome();
			Ac[4] = new L.Chromosome();
			
			// give one gene
			L.Gene g0 = new L.Gene();
			g0.NumberOfAllele = 3;
			g0.ChromosomeNumber = 6;
			g0.StartBase = 1000;
			g0.EndBase = 1000;
			g0.FindMutation();
		
			Ac[5] = new L.Chromosome(g0);

			Ac[6] = new L.Chromosome();
			Ac[7] = new L.Chromosome();
			Ac[8] = new L.Chromosome();
			Ac[9] = new L.Chromosome();
			Ac[10] = new L.Chromosome();
			Ac[11] = new L.Chromosome();
			Ac[12] = new L.Chromosome();
			Ac[13] = new L.Chromosome();
			Ac[14] = new L.Chromosome();
			Ac[15] = new L.Chromosome();
			Ac[16] = new L.Chromosome();
			Ac[17] = new L.Chromosome();
			Ac[18] = new L.Chromosome();
			Ac[19] = new L.Chromosome();
			Ac[20] = new L.Chromosome();
			Ac[21] = new L.Chromosome();  
            L.Chromosome X = new L.Chromosome();
			L.Chromosome Y = new L.Chromosome();
			L.Mitochondria mito = new L.Mitochondria();
		
			L.SocialGene[] sg = new L.SocialGene[1];
			sg[0] = new L.SocialGene();
			sg[0].NumberOfAllele = 5;

			double epsilon = 0.01; // input
			double delta = epsilon;      // input
			int times = 50; // input

			sg[0].From = 0;
			sg[0].To = 1;
			sg[0].ModifiedValue = epsilon/4.0;
			sg[0].SetMutation();

			sg[0].From = 1;
			sg[0].To = 2;
			sg[0].ModifiedValue = epsilon/3.0;
			sg[0].SetMutation(); 

			sg[0].From = 2;
			sg[0].To = 3;
			sg[0].ModifiedValue = epsilon/2.0;
			sg[0].SetMutation();   

			sg[0].From = 3;
			sg[0].To = 4;
			sg[0].ModifiedValue = epsilon;
			sg[0].SetMutation();    

			for(int f = 0; f < 5; f++)
				for(int m = 0; m < 5; m++)
					for(int b = 0; b < 5; b++)
					{
						sg[0].WhichFemale = f;
						sg[0].WhichMale = m;
						sg[0].WhichFemaleBaby = b;
						sg[0].WhichMaleBaby = b;
						if(m==b) sg[0].ModifiedValue = 1.0;
						else sg[0].ModifiedValue = 0.0;
						sg[0].SetReproductionXX();
						sg[0].SetReproductionXY();
					}
			

			L.ChromosomePair[] Cp = new L.ChromosomePair[22];
			for(int i = 0; i < 22; i++) Cp[i] = new L.ChromosomePair(Ac[i]);
			L.ChromosomePair XX = new L.ChromosomePair(X);

			L.GenotypeFemale fg = new L.GenotypeFemale(Cp,XX,mito,sg);
			L.GenotypeMale mg = new L.GenotypeMale(Cp,X,Y,mito,sg);

			L.PhenotypeFemale fph = new L.PhenotypeFemale(fg);
			L.PhenotypeMale mph = new L.PhenotypeMale(mg);

			for(int ph = 0; ph < fg.NumberOfAllele ; ph++)
			{
				fph.MapFrom = ph;
				fph.MapTo = ph % 5;
				fph.SetMap();
			}
			for(int ph = 0; ph < mg.NumberOfAllele ; ph++)
			{
				mph.MapFrom = ph;
				mph.MapTo = ph % 5;
				mph.SetMap();
			}

			L.Mating mating = new L.Mating();
            mating.HierarchicalMating(fph,mph); 

			L.Mutation mut = new L.Mutation(fg,mg);

			L.Reproduction reprod = new L.Reproduction(fg,mg); 
			
			L.Selection select = new L.Selection(fg,mg);

			select.WhichMale = 4;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 


			select.WhichMale = 9;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 

			select.WhichMale = 14;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 

			select.WhichMale = 19;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 

			select.WhichMale = 24;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 

			select.WhichMale = 29;
			select.ModifiedValue = delta;  
			select.SetDisadvantageXY(); 

			
			L.PopulationEquation eq 
				= new L.PopulationEquation(mating,mut,reprod,select);

			double[] initialPopulationXX = new double[30];
			double[] initialPopulationXY = new double[30];

			/*
			 * AA, AB, AC, BB, BC, CC : 0, 1, 2, 3, 4
			 */ 
			initialPopulationXX[0] = 1.0;  // AA : 0
			initialPopulationXY[0] = 1.0;
            initialPopulationXX[1] = 2.0; // 1.0;  // AA : 1
            initialPopulationXY[1] = 2.0; // 1.0;

            initialPopulationXX[17] = 3.0; // 1.0;  // BB : 2
            initialPopulationXY[17] = 3.0; // 1.0;
            initialPopulationXX[18] = 4.0; // 1.0;  // BB : 3
            initialPopulationXY[18] = 4.0; // 1.0;

            initialPopulationXX[29] = 5.0; // 1.0;  // CC : 4
            initialPopulationXY[29] = 5.0; // 1.0;
		
			eq.InitialAdultFemalePopulation = initialPopulationXX;
			eq.InitialAdultMalePopulation = initialPopulationXY;
			eq.SetInitialPopulation();

			for(int kt = 1; kt < 200; kt++)
			{
				eq.HowManyTimes  = times;
				eq.Compute();

			/*	foreach(double k in eq.BirthFemalePopulation)
					result += Convert.ToString(k)+"\r\n";
				result += "------\r\n";
				foreach(double k in eq.BirthMalePopulation)
					result += Convert.ToString(k)+"\r\n";
				result += "------\r\n"; 
				foreach(double k in eq.AdultFemalePopulation)
					result += Convert.ToString(k)+"\t";
				foreach(double k in eq.AdultMalePopulation)
					result += Convert.ToString(k)+"\t";
				result += "\r\n";
				foreach(double k in eq.ParentPopulation)
					result += Convert.ToString(k)+"\r\n";  

				result += eq.InfantMortality(); */
			}
            foreach (double k in eq.AdultFemalePopulation)
                result += Convert.ToString(k) + "\t";
            foreach (double k in eq.AdultMalePopulation)
                result += Convert.ToString(k) + "\t";
            result += "\r\n";
		}
	}
}