import java.util.*;
import java.io.*;
import java.lang.*;

public class Cryptoanalysis2 {

    public static void main(String[] args)
    {
        Manager manager = new Manager(8);
        manager.read("rnj.txt", "sample.txt");
        manager.run();
    }
}

class Manager{
    private double bias = 1;
    private String codefile;
    private int limit = 200;
    public int genNum =0;
    public int popSize = 30;
    public Genome[] mainpop = new Genome[popSize];
    private Tri master, code;
    
    public Manager(int g)
    {
        limit = g;
        initial();
    }
    public void initial()
    {
        for(int index=0; index < popSize; index++)
        {
            mainpop[index] = new Genome();
        }
    }
    public void read(String masterfile, String cipherfile)
    {
        codefile = cipherfile;
        master = new Tri(masterfile);
        code = new Tri(cipherfile);
        bias = master.maxRate /  code.maxRate;
    }
    public void run()
    {
        GA current = null;
       // while(genNum < limit)
        //{
            GA test = new GA(mainpop, popSize, genNum, master, code, bias);
            test.fitness();
            test.createNewPop();
            current = test;
            genNum++;
        //}
        current.translate(codefile);
    }
}
class GA{
    public Random generator = new Random();
    private int popSize;
    double[] fitness;
    public Util utility = new Util();
    public Genome top;
    private Genome[] population;
    public int generation;
    private Tri master, code;
    private double bias;
    public GA(Genome[] p, int size, int g, Tri m, Tri c, double b)
    {
        population = p;
        this.popSize = size;
        generation = g;
        master = m;
        code = c;
        bias = b;
    }     
     public void print()
     {
        for(int x =0; x < popSize; x++)
        {
            if(population[x] != null)
            {
                population[x].print();
                System.out.println();
            }
        }
     }
     
    public void createNewPop()
    {
       /* The selection process starts from randomly selecting a number in 
       the range of 0-1 and randomly selecting a pair of Genomes from the 
       current population. Look up the fitness value of each genome. 
       If the value exceed the random number, the genome is selected to be 
       a parent of new offspring, or else it is thrown away and the process 
       will select another genome.*/
        Genome[] tempPop = new Genome[popSize];
        Genome parentA,parentB;
        int selectedNum1,selectedNum2;
        Offspring offspring1 = new Offspring(); 
        Offspring offspring2 = new Offspring();

       
        //reproduce half time of population (in this case = 15)
        for(int index=0; index < popSize; index++)
        {
            double point = (Math.abs(generator.nextInt()) % (30 - 0)) + (int)Math.ceil(0);
            selectedNum1 = (Math.abs(generator.nextInt()) % (30 - 0)) ;
            selectedNum2 = (Math.abs(generator.nextInt()) % (30 - 0)) ;
            
            while(findRank(population[selectedNum1]) > point)
            {
                selectedNum1 = (Math.abs(generator.nextInt()) % (30 - 0));// select again bad rank
            }
            parentA = population[selectedNum1];
            while((findRank(population[selectedNum2])> point)||(selectedNum2 == selectedNum1))
            {
                selectedNum2 = (Math.abs(generator.nextInt()) % (30 - 0));// select again bad rank
            }
            parentB = population[selectedNum2];
            crossOver(parentA, parentB, offspring1, offspring2);
            
            //Mutate every 5 generations
            if((generation % 5) == 0)
            {
                offspring1.mutation();
                offspring2.mutation();
            }
            /*
            parentA.print();
            System.out.println();
            parentB.print();
            System.out.println();
            offspring1.print();
            System.out.println();
            offspring2.print();
            System.out.println();
            */
            tempPop[index] = offspring1;
            tempPop[index++] = offspring2;
        } 
        //copy genomes
        for(int index=0; index < popSize; index++)
        {
            population[index] = tempPop[index];
        }
    }
    
    public void crossOver(Genome x, Genome y, Offspring a, Offspring b)
    {
        int cop = (Math.abs(generator.nextInt()) % (13 - 0)) + (int)Math.ceil(0);

        for (int j =0; j <= cop; j++)
        {
                ((Genome) a).set[j] = x.set[j];
                ((Genome) b).set[j] = y.set[j];
        }

        for(int i= 0; i < y.set.length; i++)
        {
            int number = y.set[i];
            int cop1 = cop;
            for(int index = 0; index < cop1; index++)
            {
                if(number != a.set[index])
                {
                    cop1++;
                    a.set[cop1] = number;
                }
            }
        }
        
        for(int i=0; i < x.set.length; i++)
        {
            int number = x.set[i];
            int cop2 = cop;
            for(int index = 0; index < cop2; index++)
            {
                if(number != b.set[index])
                {
                    cop2++;
                    b.set[cop2] = number;
                }
            }
        }
        
    }
    
    public void fitness()
    {
        fitness = new double[popSize];
        top = population[0];
        for(int index=0; index < popSize; index++)
        {
            Genome current = population[index];
            current.gap = match(current);
            if (current.gap < top.gap)
                top = current;
            //return gap of each genome. the bigger its gap the worst its performance.
        }
        //insertion sort and save in fitness array.
        for(int l=0; l < popSize; l++)
        {
            fitness[l] = population[l].gap;
        }    
        for(int p=0; p < popSize; p++)
        {
             double key = fitness[p];
             int j;
            
             //shirt the larger gap to the right
            for(j = p; (j > 0) && (key < fitness[j-1]); j--)
                fitness[j] = fitness[j-1];
                
            fitness[j] = key;
        }
       /* for( int x=0; x< popSize; x++)
            System.out.println(fitness[x]);*/
        System.out.println("This genome has the highest fitness.");
        top.print();
        System.out.println();
    }
    
    public int findRank(Genome x)
    {
        int rank;
        int index =0;
        while(fitness[index] != x.gap)
        {
            index++;
        }
        rank = index;
        return rank;
    }

    public double match(Genome x)
    {
        double totalGap = 0;
        int digit1 =26,digit2 =26,digit3= 26;
        for (int a=0; a < 26; a++)
        {
           for (int b=0; b < 26; b++)
            {
                for (int c=0; c < 26; c++)
                {
                    if (code.Trigram[a][b][c]!= 0)
                    {
                        double currValue = (double) (code.Trigram[a][b][c] * bias) ;//frequency
                        //search
                        for(int d=0; d< 26; d++)
                        {
                            if (x.set[d] == a)
                                digit1 = d;
                            if (x.set[d] == b)
                                digit2 = d;
                            if (x.set[d] == c)
                                digit3 = d;
                        }
                        double value = compare(digit1, digit2, digit3);
                        
                        double gap = Math.abs(value - currValue);
                        totalGap = totalGap + gap;
                        //System.out.println("totalgap: "+ totalGap);
                        //System.out.println(getChar(a) + "-" + getChar(b) +"-" + getChar(c) + ": " +Trigram[a][b][c]);
                    }
                }
            }
        }
        return totalGap;
    }

    public double compare(int i, int j, int k)
    {
        double v = (double) master.Trigram[i][j][k];
        return v;
    }

    public void translate(String x)
    {
        String codefile = x;
        StringBuffer text = new StringBuffer();
        System.out.println("Here is the evolved code file.");
        try {
            FileReader fr = new FileReader (codefile);
            BufferedReader infile = new BufferedReader(fr);
            String line = infile.readLine();
            while (line != null)
            {
                for(int d=0; d < line.length(); d++)
                {	
                    line = line.toLowerCase();
                    char current = line.charAt(d);
                    int value = utility.changeChar(current);
                    if (value < 26)
                    {	
                        char mychar = utility.getChar(top.set[value]);
                        text.append(mychar);
                    }
                    else
                       text.append(line.charAt(d));
                }
            line = infile.readLine();
            }
            infile.close();
            System.out.print(text.toString());
            System.out.println();
        }
        catch (FileNotFoundException exception)
        {
                System.out.println("The file " + codefile + " was not found");
        }
        catch (IOException exception)
        {
                System.out.println(exception);
        }
    }
 }

class Genome
{
    public int[] set;
    public double gap = 0;
    Random generator = new Random();
    public Genome()
    {
        set = new int[26];
        //next = null;
        randomGenes();
    }
    
    public void print()
    {
        for (int i =0; i< set.length; i++)
        {
            //System.out.print(getChar(set[i]) + " ");
            System.out.print((set[i]) + " ");
        }
    }
    
    private void randomGenes()
    {
        int rangebeg = 0;
        int rangeend = 25;
        int [] temp = new int[set.length];
	for (int ra = 0; ra < temp.length; ra++)
	{
             temp[ra] = (int)(Math.floor(Math.random() *((rangeend - rangebeg)+1)) + (int)Math.ceil(rangebeg));
             
             //for uniqueness
		for (int rb =0; rb < ra; rb++)
		{
                    while (temp[ra] == temp[rb])
                    {
                        //use different method to make sure that even seed is the same, numbers are not indentical.
                        temp[ra] = (Math.abs(generator.nextInt()) % ((rangeend - rangebeg)+1)) + (int)Math.ceil(rangebeg);	
                        rb= 0;	
                    }
		}
	}
        for (int i = 0; i < set.length; i++)
	{
            set[i] = temp[i];
        }
    }
    
    public char getChar(int x)
    {
        char newchar = (char) (x + 'A');
        return newchar;
    }
    
    public int swapGeneChar(int x)
    {
        int a = set[x];
        return a;
    }
}
class Offspring extends Genome{

    public int[] set;
    public double gap = 0;
    Random generator = new Random();

    public Offspring()
    {
        set= new int[26];
    }
    
    public void mutation()
    {
         int rand1 = (Math.abs(generator.nextInt()) % (25+1 - 0)) + (int)Math.ceil(0);
         int rand2 = (Math.abs(generator.nextInt()) % (25+1 - 0)) + (int)Math.ceil(0);
         while (rand1 == rand2)
            rand2 = (Math.abs(generator.nextInt()) % (25+1 - 0)) + (int)Math.ceil(0);
        
        int temp = set[rand1];
        set[rand1] = set[rand2];
        set[rand2] = temp;
    }
    
    public char getChar(int x)
    {
        char newchar = (char) (x + 'A');
        return newchar;
    }
}
class Tri{

    public String file;
    public int[][][] Trigram = new int[26][26][26];
    public int Int2=0,Int1=0,Int=0;
    public int Total=0;	//counts # of alphabetic chars in file
    public int max=0;      //highest=largest single trigram count
    public double maxRate = 0;
    public Util utility = new Util();

public Tri(String filename){
    file = filename;
    //initialize trigram array
    for (int A=0; A < 26; A++)
    {
        for (int B=0; B < 26; B++)
        {
            for (int C=0; C < 26; C++)
                Trigram[A][B][C]=0;
        }
    }
    //read file
    System.out.println("Processing " + file + " ...");
    try {
            FileReader fr = new FileReader (file);
            BufferedReader infile = new BufferedReader(fr);
            int readint = infile.read();
            
            while (readint != -1)
            {
                char input = (char) readint;
                Character temp = new Character(input);
                char read = temp.toLowerCase(input);
                //System.out.println(read + " " + changeChar(read));
                Int = utility.changeChar(read);
                if((Int >= 0) && (Int < 26))
                {
                    Total++; 
                    if( Total > 2 )
                    {
                        Trigram[Int2][Int1][Int] = Trigram[Int2][Int1][Int] + 1;
                        if(Trigram[Int2][Int1][Int] > max)
                            max = Trigram[Int2][Int1][Int];
                    }
                    Int2 = Int1;
                    Int1 = Int;
                }
                readint = infile.read();
            }
            infile.close();        
        }
        catch (FileNotFoundException exception)
        {
            System.out.println("The file " + file + " was not found");
        }
        catch (IOException exception)
        {
            System.out.println(exception);
        }
        System.out.println("Total alphabetic characters:  " + Total);
        System.out.println("Max number of trigrams: " + max);
        maxRate = (double) max/Total;

        //print trigram array
       /*for (int a=0; a < 26; a++)
        {
           for (int b=0; b < 26; b++)
            {
                for (int c=0; c < 26; c++)
                    System.out.println(getChar(a) + "-" + getChar(b) +"-" + getChar(c) + ": " +Trigram[a][b][c]);
            }
        }*/
    }
}
class Util{
    public Util(){};
    public int changeChar(char c){
        switch(c)
        {
            case 'a':
                return 0;
            case 'b':
                return 1;
            case 'c':
                return 2;
            case 'd':
                return 3;
            case 'e':
                return 4;
            case 'f':
                return 5;
            case 'g':
                return 6;
            case 'h':
                return 7;
            case 'i':
                return 8;
            case 'j':
                return 9;
            case 'k':
                return 10;
            case 'l':
                return 11;
            case 'm':
                return 12;
            case 'n':
                return 13;
            case 'o':
                return 14;
            case 'p':
                return 15;
            case 'q':
                return 16;
            case 'r':
                return 17;
            case 's':
                return 18;
            case 't':
                return 19;
            case 'u':
                return 20;
            case 'v':
                return 21;
            case 'w':
                return 22;
            case 'x':
                return 23;
            case 'y':
                return 24;
            case 'z':
                return 25;
            case ' ':
            case '.':
            case ',':
            case '!':
            case '?':
            case ';':
            case ':':
            case '*':
            case '=':
            case '+':
            case '-':
            case '/':
                return 26;
            default:
                return 26;
      }
}   
    public char getChar(int i){
        char value;
        if ( i == 0)
            value ='a';
        else if ( i == 1)
            value ='b';
        else if ( i == 2)
            value ='c'; 
        else if ( i == 3)
            value ='d'; 
        else if ( i == 4)
            value ='e';                
        else if ( i == 5)
            value ='f'; 
        else if ( i == 6)
            value ='g';
        else if ( i == 7)
            value ='h'; 
        else if ( i == 8)
            value ='i'; 
        else if ( i == 9)
            value ='j'; 
        else if ( i == 10)
            value ='k'; 
        else if ( i == 11)
            value ='l'; 
        else if ( i == 12)
            value ='m'; 
        else if ( i == 13)
            value ='n'; 
        else if ( i == 14)
            value ='o'; 
        else if ( i == 15)
            value ='p'; 
        else if ( i == 16)
            value ='q'; 
        else if ( i == 17)
            value ='r'; 
        else if ( i == 18)
            value ='s'; 
        else if ( i == 19)
            value ='t'; 
        else if ( i == 20)
            value ='u'; 
        else if ( i == 21)
            value ='v'; 
        else if ( i == 22)
            value ='w'; 
        else if ( i == 23)
            value ='x'; 
        else if ( i == 24)
            value ='y'; 
        else if ( i == 25)
            value ='z';
        else
            value = '!';
        return value;
   }

}