import org.shogun.*;
import org.jblas.*;
import static org.shogun.EAlphabet.DNA;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

public class kernel_combined_modular {
	static {
		System.loadLibrary("modshogun");
	}

	public static void main(String argv[]) {
		modshogun.init_shogun_with_defaults();
		int cardinality = 2;
		int cache = 10;

		DoubleMatrix traindata_real = Load.load_numbers("../data/fm_train_real.dat");
		DoubleMatrix testdata_real = Load.load_numbers("../data/fm_test_real.dat");
		String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
		String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");

		RealFeatures subfeats_train = new RealFeatures(traindata_real);
		RealFeatures subfeats_test = new RealFeatures(testdata_real);

		CombinedKernel kernel= new CombinedKernel();
		CombinedFeatures feats_train = new CombinedFeatures();
		CombinedFeatures feats_test = new CombinedFeatures();

		GaussianKernel subkernel = new GaussianKernel(cache, 1.1);
		feats_train.append_feature_obj(subfeats_train);
		feats_test.append_feature_obj(subfeats_test);
		kernel.append_kernel(subkernel);

		StringCharFeatures subkfeats_train = new StringCharFeatures(fm_train_dna, DNA);
		StringCharFeatures subkfeats_test = new StringCharFeatures(fm_test_dna, DNA);
		int degree = 3;
		FixedDegreeStringKernel subkernel2= new FixedDegreeStringKernel(10, degree);
		feats_train.append_feature_obj(subkfeats_train);
		feats_test.append_feature_obj(subkfeats_test);
		kernel.append_kernel(subkernel2);

		subkfeats_train = new StringCharFeatures(fm_train_dna, DNA);
		subkfeats_test = new StringCharFeatures(fm_test_dna, DNA);
		LocalAlignmentStringKernel subkernel3 = new LocalAlignmentStringKernel(10);
		feats_train.append_feature_obj(subkfeats_train);
		feats_test.append_feature_obj(subkfeats_test);
		kernel.append_kernel(subkernel3);

		kernel.init(feats_train, feats_train);
		DoubleMatrix km_train=kernel.get_kernel_matrix();
		kernel.init(feats_train, feats_test);
		DoubleMatrix km_test=kernel.get_kernel_matrix();

		modshogun.exit_shogun();
	}
}
