Example #1
0
File: Tigr.cs Project: gumik/SCTIGR
		private void Assembly()
		{
			profile.AddSequence(sequences[0], 0);
			
			var lastSegment = 0;
			var firstSegment = 0;
			
			AssemblyInit(sequences[0]);
			
			int change = 0; // 0 - there was align, 1 - there wasn't align on last, 2 - there wasn't align at all
			while (true)
			{
				int seq;
				
				if (change == 0)
				{
					seq = lastSegment;
				}
				else if (change == 1)
				{
					seq = firstSegment;
				}
				else 
				{
					break;
				}
				
				var list = GetProbablyBest(seq);
				if (list.Count == 0)
				{
					if (change == 0)
					{
						seq = firstSegment;
						list = GetProbablyBest(seq);
						if (list.Count == 0)
						{
							break;
						}
					}
					else
					{
						break;
					}
				}
				
				var wasAlign = false;
				foreach (var probSeq in list)
				{
					var sm = new SmithWaterman(profile, sequences[probSeq]);
					sm.Calculate();
					var alignment = sm.GetBest();
					AssemblyCandidate(sequences[probSeq], alignment.First.Value.Item1 - alignment.First.Value.Item2);
					
					if (IsGoodAlignment(sequences[probSeq], alignment))
					{						
						var side = AddSequence(sequences[probSeq], alignment);
						
						if ((side & 1) != 0)
						{
							firstSegment = probSeq;
						}
						else if ((side & 2) != 0)
						{
							lastSegment = probSeq;
							change = 0;
						}
						
						RemoveSeq(probSeq);
						//AssemblyGoodAlignmentAdded(profile);
						AssemblyGoodAlignment();
						wasAlign = true;
						break;
					}
				}
				
				if (!wasAlign)
				{
					change++;
				}
			}
			
			AssemblyEnd();
		}
Example #2
0
File: Test.cs Project: gumik/SCTIGR
        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));
            }
        }