Beispiel #1
0
		public Tigr(int merLength, int maxOverhang, int minOverlap, float minSimilarity, string[] sequences)
		{
			this.sequences = sequences;
			this.merLength = merLength;
			this.maxOverhang = maxOverhang;
			this.minOverlap = minOverlap;
			this.minSimilarity = minSimilarity;
			profile = new Profile();
		}
Beispiel #2
0
        public SmithWaterman(Profile profile, string sequence)
        {
            MatchScore = 2;
            MismatchScore = -1;
            InsertionScore = -2;
            DeletionScore = -2;

            this.profile = profile;
            this.sequence = sequence;
        }
Beispiel #3
0
 public static void AssemblyGoodAlignmentAdded(Profile profile)
 {
     Console.WriteLine(string.Format("AssemblyGoodAlignmentAdded: \n{0}", profile));
     for (var c = 0; c < profile.Length; ++c)
     {
         Console.Write(profile[c]);
     }
     Console.WriteLine();
     //Console.ReadKey();
 }
Beispiel #4
0
        public static void SM()
        {
            var sequence = "AC TGTTTT";
            var profile = new Profile();
            profile.AddSequence("GGGGACTG", 0);

            var sm = new SmithWaterman(profile, sequence);
            sm.InsertionScore = -2;
            sm.DeletionScore = -2;
            sm.MismatchScore = -1;
            sm.MatchScore = 2;
            sm.Calculate();
            sm.PrintResult();
            var seq = sm.GetBest();

            foreach (var i in seq)
            {
                Console.Write(string.Format("({0},{1}) ", i.Item1, i.Item2));
            }
        }
Beispiel #5
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        public static void ProfileTest()
        {
            var profile = new Profile();

            while (true)
            {
                var sequence = Console.ReadLine();
                var begin = int.Parse(Console.ReadLine());

                profile.AddSequence(sequence, begin);
                Console.WriteLine(profile);
            }
        }