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

namespace UniqueMatches
{
    class Program
    {
        static void Main(string[] args)
        {
            Dictionary<string, string> existing_seqs = new Dictionary<string, string>();
            existing_seqs["A"] = "ACTGTGTGCTGGTCGTGACGAC";
            existing_seqs["Gene1 transcr1"] = "ACTGTGTGGATCGATCGATGGCCACAAATCA";
            existing_seqs["Gene2 transcr1"] = "AGGTCTGTGCCTGGGAAGCGCGTCGATCGATGCA";
            existing_seqs["Gene2 transcr2"] = "GCGCAGGTCTGTGCGCGGCCTGGGAATCGATCGATGCA";
            existing_seqs["Gene2 transcr2"] = "GCGCGGAACGTCGCGTCCCCGATCGATGCA";
            string target = "ACTGTGTGCTGGTCGTGACGACATGATCA"; // splice variant to detect

            bool found_a_probe = false;
            for (int L = 1; L < target.Length && !found_a_probe; L++)
            {
                for (int position = 0; position < target.Length - L && !found_a_probe; position++)
                {
                    string subseq = target.Substring(position, L);  // potential probe
                    Console.WriteLine("Will test potential probe " + subseq);
                    bool reject_seq = false;
                    foreach (KeyValuePair<string, string> current_pair in existing_seqs)
                    {
                        string existing_gene = current_pair.Key;
                        string matching_against_seq = current_pair.Value;
                        int matches_at_position = matching_against_seq.IndexOf(subseq);
                        if (matches_at_position >= 0)
                        {
                            reject_seq = true;
                            Console.WriteLine("Rejected seq " + subseq + " because of " + matching_against_seq);
                            break;
                        }
                    }
                    if (!reject_seq)
                    {
                        Console.WriteLine("Subsequence " + subseq + " is a possible probe");
                        found_a_probe = true;
                    }
                }
                if (!found_a_probe)
                {
                    Console.WriteLine("Could not find any subsequence that did not occur in any of the existing sequences");
                }
            }
            Console.ReadLine();
        }
    }
}