Exemplo n.º 1
0
        public static void RNAMode(string measureType, string[] lines)
        {
            var uRNA = lines[1];
            var wRNA = lines[2];

            if (uRNA.Length % 3 != 0 || wRNA.Length % 3 != 0)
            {
                Console.WriteLine("Sekwencje RNA muszą byc podzielne przez 3.");
                return;
            }

            var matrix = new double[21, 21];

            for (var i = 3; i < lines.Length; i++)
            {
                var line = lines[i].Split(',');
                for (var j = 0; j < 21; j++)
                {
                    matrix[i - 3, j] = double.Parse(line[j]);
                }
            }

            var u = RNAToAcidsMapper.GetAcids(uRNA);
            var w = RNAToAcidsMapper.GetAcids(wRNA);

            if (measureType == "rd")
            {
                var(measure, d) = MatrixBuilder.GlobalForDistanceRNA(u, w, matrix);
                var optimalGlobalAlignment = GlobalAlignment.OptimalWithDistance(d, u, w);
                var newRnaU = RNAToAcidsMapper.GetRNA(optimalGlobalAlignment.uResult, uRNA);
                var newRnaW = RNAToAcidsMapper.GetRNA(optimalGlobalAlignment.wResult, wRNA);

                PrintResult("Global", "Distance", uRNA, newRnaU, wRNA, newRnaW, measure);
                PrintResult("Global", "Distance", u, optimalGlobalAlignment.uResult, w, optimalGlobalAlignment.wResult, measure);

                var similarityMatrix = ConvertDistanceToSimilarity(matrix);
                var(measureLocal, dLocal) = MatrixBuilder.LocalSimilarity(u, w, similarityMatrix);
                var(uResult, wResult)     = LocalAlignment.MaximalLocal(dLocal, u, w);
                PrintResult("Local", "Distance", u, uResult, w, wResult, measureLocal);
            }
            else
            {
                var(measure, d) = MatrixBuilder.GlobalForSimilarityRNA(u, w, matrix);
                var optimalGlobalAlignment = GlobalAlignment.OptimalWithSimilarity(d, u, w);
                var newRnaU = RNAToAcidsMapper.GetRNA(optimalGlobalAlignment.uResult, uRNA);
                var newRnaW = RNAToAcidsMapper.GetRNA(optimalGlobalAlignment.wResult, wRNA);
                PrintResult("Global", "Similarity", uRNA, newRnaU, wRNA, newRnaW, measure);
                PrintResult("Global", "Similarity", u, optimalGlobalAlignment.uResult, w, optimalGlobalAlignment.wResult, measure);

                var(measureLocal, dLocal) = MatrixBuilder.LocalSimilarityRNA(u, w, matrix);
                var(uResult, wResult)     = LocalAlignment.MaximalLocal(dLocal, u, w);
                var localRnaU = RNAToAcidsMapper.GetRNA(uResult, uRNA);
                var localRnaW = RNAToAcidsMapper.GetRNA(wResult, wRNA);

                PrintResult("Local", "Similarity", uRNA, localRnaU, wRNA, localRnaW, measureLocal);
            }
        }
Exemplo n.º 2
0
        public static void StandardMode(string measureType, string[] lines)
        {
            var u      = lines[1];
            var w      = lines[2];
            var matrix = new double[5, 5];

            for (var i = 3; i < lines.Length; i++)
            {
                var line = lines[i].Split(',');
                for (var j = 0; j < 5; j++)
                {
                    matrix[i - 3, j] = double.Parse(line[j]);
                }
            }


            if (measureType == "d")
            {
                var(measure, d) = MatrixBuilder.GlobalForDistance(u, w, matrix);
                var optimalGlobalAlignment = GlobalAlignment.OptimalWithDistance(d, u, w);
                PrintResult("Global", "Distance", u, optimalGlobalAlignment.uResult, w, optimalGlobalAlignment.wResult,
                            measure);

                var similarityMatrix = ConvertDistanceToSimilarity(matrix);
                //PrintMatrix(similarityMatrix);
                var(measureLocal, dLocal) = MatrixBuilder.LocalSimilarity(u, w, similarityMatrix);
                var(uResult, wResult)     = LocalAlignment.MaximalLocal(dLocal, u, w);
                PrintResult("Local", "Distance", u, uResult, w, wResult, measureLocal);
            }
            else
            {
                var(measure, d) = MatrixBuilder.GlobalForSimilarity(u, w, matrix);
                var optimalGlobalAlignment = GlobalAlignment.OptimalWithSimilarity(d, u, w);
                PrintResult("Global", "Similarity", u, optimalGlobalAlignment.uResult, w, optimalGlobalAlignment.wResult,
                            measure);

                var(measureLocal, dLocal) = MatrixBuilder.LocalSimilarity(u, w, matrix);
                var(uResult, wResult)     = LocalAlignment.MaximalLocal(dLocal, u, w);
                PrintResult("Local", "Similarity", u, uResult, w, wResult, measureLocal);
            }
        }