using System;
using System.Collections.Generic;
using System.Text;

namespace nucl2aamap
{
    class Program
    {
        static string reverse(string inp)
        {
            string outp="";
            for (int i = inp.Length - 1; i >= 0; i--)
                outp += inp[i];
            return outp;
        }
        static string complement(string input)
        {
            string output="";
            for (int i = 0; i < input.Length; i++)
            {
                char c=input[i];
                switch (c)
                {
                    case 'A': output += "T"; break;
                    case 'T': output += "A"; break;
                    case 'C': output += "G"; break;
                    case 'G': output += "C"; break;
                }
            }
            return output;
        }
        static Dictionary<string,string> nucl2aamap;
        static string nucl2aa(string input)
        {
            string output="";
            int l = input.Length-3;
            for (int i = 0; i <= l; i += 3)
            {
                string codon = input.Substring(i, 3);
                string aa = nucl2aamap[codon];
                output += aa;
            }
            return output;
        }
        static void init()
        {
            seqs = new string[12];
            description = new string[12];
            nucl2aamap = new Dictionary<string, string>();
            nucl2aamap["TTT"] = "F";
            nucl2aamap["TTC"] = "F";
            nucl2aamap["TTA"] = "L";
            nucl2aamap["TTG"] = "L";
            nucl2aamap["CTT"] = "L";
            nucl2aamap["CTC"] = "L";
            nucl2aamap["CTA"] = "L";
            nucl2aamap["CTG"] = "L";
            nucl2aamap["ATT"] = "I";
            nucl2aamap["ATC"] = "I";
            nucl2aamap["ATA"] = "I";
            nucl2aamap["ATG"] = "M";
            nucl2aamap["GTT"] = "V";
            nucl2aamap["GTC"] = "V";
            nucl2aamap["GTA"] = "V";
            nucl2aamap["GTG"] = "V";
            nucl2aamap["TCT"] = "S";
            nucl2aamap["TCC"] = "S";
            nucl2aamap["TCA"] = "S";
            nucl2aamap["TCG"] = "S";
            nucl2aamap["CCT"] = "P";
            nucl2aamap["CCC"] = "P";
            nucl2aamap["CCA"] = "P";
            nucl2aamap["CCG"] = "P";
            nucl2aamap["ACT"] = "T";
            nucl2aamap["ACC"] = "T";
            nucl2aamap["ACA"] = "T";
            nucl2aamap["ACG"] = "T";
            nucl2aamap["GCT"] = "A";
            nucl2aamap["GCC"] = "A";
            nucl2aamap["GCA"] = "A";
            nucl2aamap["GCG"] = "A";
            nucl2aamap["TAT"] = "Y";
            nucl2aamap["TAC"] = "Y";
            nucl2aamap["TAA"] = "_";
            nucl2aamap["TAG"] = "_";
            nucl2aamap["CAT"] = "H";
            nucl2aamap["CAC"] = "H";
            nucl2aamap["CAA"] = "Q";
            nucl2aamap["CAG"] = "Q";
            nucl2aamap["AAT"] = "A";
            nucl2aamap["AAC"] = "A";
            nucl2aamap["AAA"] = "K";
            nucl2aamap["AAG"] = "K";
            nucl2aamap["GAT"] = "D";
            nucl2aamap["GAC"] = "D";
            nucl2aamap["GAA"] = "E";
            nucl2aamap["GAG"] = "E";
            nucl2aamap["TGT"] = "C";
            nucl2aamap["TGC"] = "C";
            nucl2aamap["TGA"] = "_";
            nucl2aamap["TGG"] = "W";
            nucl2aamap["CGT"] = "R";
            nucl2aamap["CGC"] = "R";
            nucl2aamap["CGA"] = "R";
            nucl2aamap["CGG"] = "R";
            nucl2aamap["AGT"] = "S";
            nucl2aamap["AGC"] = "S";
            nucl2aamap["AGA"] = "R";
            nucl2aamap["AGG"] = "R";
            nucl2aamap["GGT"] = "G";
            nucl2aamap["GGC"] = "G";
            nucl2aamap["GGA"] = "G";
            nucl2aamap["GGG"] = "G";
        }
        static string[] description;
        static string[] seqs;
        static void add_version(string desc, int pos, string seq)
        {
            description[pos]=desc+"std";
            description[pos+1]=desc+"rev";
            description[pos+2]=desc+"com";
            description[pos + 3] = desc + "rev,com";
            seqs[pos]=seq;
            seqs[pos+1]=reverse(seq);
            seqs[pos+2]=complement(seq);
            seqs[pos+3]=reverse(complement(seq));
        }
        static void Main(string[] args)
        {
            init();
            string seq = "ACTGGTCATGATC";
            add_version("0 ",0,seq);
            add_version("1 ",4,seq.Substring(1));
            add_version("2 ",8,seq.Substring(2));

            int lastbestpos = 0;
            string bestdescription = "";
            for (int i = 0; i < 12; i++)
            {
                string protein = nucl2aa(seqs[i]);
                int stoppos = protein.IndexOf("_");
                if (stoppos > lastbestpos)
                {
                    bestdescription = description[i];
                    lastbestpos = stoppos;
                }
    else if (stoppos==lastbestpos)
                {
                    bestdescription += description[i];
                }
                Console.WriteLine(description[i] + ": " + seqs[i] + " -> " + protein);
            }
            Console.WriteLine("Best match at " + bestdescription);
            Console.ReadKey();
        }
    }
}