public static void main(String argv[]) {
boolean reverse = false;
modshogun.init_shogun_with_defaults();
int order = 3;
int gap = 4;
String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, DNA);
StringWordFeatures feats = new StringWordFeatures(charfeat.get_alphabet());
feats.obtain_from_char(charfeat, order - 1, order, gap, reverse);
PositionalPWM ppwm = new PositionalPWM();
ppwm.set_sigma(5.0);
ppwm.set_mean(10.0);
DoubleMatrix pwm =
new DoubleMatrix(
new double[][] {
{0.0, 0.5, 0.1, 1.0}, {0.0, 0.5, 0.5, 0.0}, {1.0, 0.0, 0.4, 0.0}, {0.0, 0.0, 0.0, 0.0}
});
ppwm.set_pwm(logi(pwm));
ppwm.compute_w(20);
DoubleMatrix w = ppwm.get_w();
modshogun.exit_shogun();
}
