public static void Main() { modshogun.init_shogun_with_defaults(); bool reverse = false; int order = 3; int gap = 0; string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, EAlphabet.DNA); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order - 1, order, gap, reverse); charfeat = new StringCharFeatures(fm_test_dna, EAlphabet.DNA); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat, order - 1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); CommWordStringKernel kernel = new CommWordStringKernel(feats_train, feats_train, false); double[,] km_train = kernel.get_kernel_matrix(); kernel.init(feats_train, feats_test); double[,] km_test = kernel.get_kernel_matrix(); }
public static void Main() { modshogun.init_shogun_with_defaults(); bool reverse = false; int order = 3; int gap = 0; string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, EAlphabet.DNA); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse); charfeat = new StringCharFeatures(fm_test_dna, EAlphabet.DNA); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); CommWordStringKernel kernel = new CommWordStringKernel(feats_train, feats_train, false); double[,] km_train = kernel.get_kernel_matrix(); kernel.init(feats_train, feats_test); double[,] km_test = kernel.get_kernel_matrix(); modshogun.exit_shogun(); }
internal static ArrayList run(IList para) { bool reverse = false; modshogun.init_shogun_with_defaults(); int order = (int)((int?)para[0]); int gap = (int)((int?)para[1]); string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, DNA); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse); charfeat = new StringCharFeatures(fm_test_dna, DNA); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); CommWordStringKernel kernel = new CommWordStringKernel(feats_train, feats_train, false); DoubleMatrix km_train = kernel.get_kernel_matrix(); kernel.init(feats_train, feats_test); DoubleMatrix km_test = kernel.get_kernel_matrix(); ArrayList result = new ArrayList(); result.Add(km_train); result.Add(km_test); result.Add(kernel); modshogun.exit_shogun(); return result; }
static void Main(string[] argv) { modshogun.init_shogun_with_defaults(); int num = 10; int order = 7; int gap = 0; bool reverse = false; string[] POS = new string[141]; for (int i = 0; i < 60; i++) { POS[i] = repeat("ACGT", 10); } for (int i = 61; i < 82; i++) { POS[i] = repeat("TTGT", 10); } for (int i = 83; i < 141; i++) { POS[i] = repeat("ACGT", 10); } string[] NEG = new string[141]; for (int i = 0; i < 60; i++) { NEG[i] = repeat("ACGT", 10); } for (int i = 61; i < 82; i++) { NEG[i] = repeat("TTGT", 10); } for (int i = 83; i < 141; i++) { NEG[i] = repeat("ACGT", 10); } string[] POSNEG = new string[282]; for (int i = 0; i < 141; i++) { POSNEG[i] = POS[i]; POSNEG[i + 141] = NEG[i]; } for(int i = 0; i < 10; i++) { Alphabet alpha = new Alphabet(DNA); StringCharFeatures traindat = new StringCharFeatures(alpha); traindat.set_features(POSNEG); StringWordFeatures trainudat = new StringWordFeatures(traindat.get_alphabet()); trainudat.obtain_from_char(traindat, order-1, order, gap, reverse); SortWordString pre = new SortWordString(); pre.init(trainudat); trainudat.add_preprocessor(pre); trainudat.apply_preprocessor(); CommWordStringKernel spec = new CommWordStringKernel(10, false); spec.set_normalizer(new IdentityKernelNormalizer()); spec.init(trainudat, trainudat); DoubleMatrix K = spec.get_kernel_matrix(); } modshogun.exit_shogun(); }
internal static HandleRef getCPtr(CommWordStringKernel obj) { return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr; }
internal static HandleRef getCPtr(CommWordStringKernel obj) { return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr); }