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);
}