public static void Main() {
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 0;
bool reverse = false;
bool use_sign = false;
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(EAlphabet.DNA);
charfeat.set_features(fm_train_dna);
StringUlongFeatures feats_train = new StringUlongFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse);
SortUlongString preproc = new SortUlongString();
preproc.init(feats_train);
feats_train.add_preprocessor(preproc);
feats_train.apply_preprocessor();
StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA);
charfeat_test.set_features(fm_test_dna);
StringUlongFeatures feats_test = new StringUlongFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse);
feats_test.add_preprocessor(preproc);
feats_test.apply_preprocessor();
CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
double[,] km_test = kernel.get_kernel_matrix();
modshogun.exit_shogun();
}
public static void Main() {
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 0;
bool reverse = false;
bool use_sign = false;
String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
double[] fm_test_real = Load.load_labels("../data/fm_test_real.dat");
StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA);
charfeat.set_features(fm_train_dna);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.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();
StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA);
charfeat_test.set_features(fm_test_dna);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse);
feats_test.add_preprocessor(preproc);
feats_test.apply_preprocessor();
HammingWordDistance distance = new HammingWordDistance(feats_train, feats_train, use_sign);
double[,] dm_train = distance.get_distance_matrix();
distance.init(feats_train, feats_test);
double[,] dm_test = distance.get_distance_matrix();
}
static void Main(string[] argv)
{
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 0;
bool reverse = false;
string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
DoubleMatrix fm_test_real = Load.load_numbers("../data/fm_test_real.dat");
StringCharFeatures charfeat = new StringCharFeatures(DNA);
charfeat.set_features(fm_train_dna);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.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();
StringCharFeatures charfeat_test = new StringCharFeatures(DNA);
charfeat_test.set_features(fm_test_dna);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse);
feats_test.add_preprocessor(preproc);
feats_test.apply_preprocessor();
ManhattanWordDistance distance = new ManhattanWordDistance(feats_train, feats_train);
DoubleMatrix dm_train = distance.get_distance_matrix();
distance.init(feats_train, feats_test);
DoubleMatrix dm_test = distance.get_distance_matrix();
modshogun.exit_shogun();
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 0;
bool reverse = false;
String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
double[,] fm_test_real = Load.load_numbers("../data/fm_test_real.dat");
StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA);
charfeat.set_features(fm_train_dna);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.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();
StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA);
charfeat_test.set_features(fm_test_dna);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat_test, order - 1, order, gap, reverse);
feats_test.add_preprocessor(preproc);
feats_test.apply_preprocessor();
ManhattanWordDistance distance = new ManhattanWordDistance(feats_train, feats_train);
double[,] dm_train = distance.get_distance_matrix();
distance.init(feats_train, feats_test);
double[,] dm_test = distance.get_distance_matrix();
foreach (double item in dm_train)
{
Console.Write(item);
}
foreach (double item in dm_test)
{
Console.Write(item);
}
modshogun.exit_shogun();
}
internal static ArrayList run(string[] strs)
{
modshogun.init_shogun_with_defaults();
StringCharFeatures f = new StringCharFeatures(strs, DNA);
f.obtain_by_sliding_window(5,1);
f.set_features(strs);
DynamicIntArray positions = new DynamicIntArray();
positions.append_element(0);
positions.append_element(6);
positions.append_element(16);
positions.append_element(25);
//f.obtain_by_position_list(8,positions);
ArrayList result = new ArrayList();
result.Add(f);
modshogun.exit_shogun();
return result;
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 0;
bool reverse = false;
bool use_sign = false;
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(EAlphabet.DNA);
charfeat.set_features(fm_train_dna);
StringUlongFeatures feats_train = new StringUlongFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order - 1, order, gap, reverse);
SortUlongString preproc = new SortUlongString();
preproc.init(feats_train);
feats_train.add_preprocessor(preproc);
feats_train.apply_preprocessor();
StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA);
charfeat_test.set_features(fm_test_dna);
StringUlongFeatures feats_test = new StringUlongFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat_test, order - 1, order, gap, reverse);
feats_test.add_preprocessor(preproc);
feats_test.apply_preprocessor();
CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
double[,] km_test = kernel.get_kernel_matrix();
modshogun.exit_shogun();
}
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();
}