com.milaboratory.core.motif.MotifUtilsTest.java Source code

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Here is the source code for com.milaboratory.core.motif.MotifUtilsTest.java

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/*
 * Copyright 2015 MiLaboratory.com
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.milaboratory.core.motif;

import com.milaboratory.core.sequence.NucleotideSequence;
import junit.framework.Assert;
import org.apache.commons.math3.random.RandomGenerator;
import org.apache.commons.math3.random.Well19937c;
import org.junit.Test;

import static com.milaboratory.test.TestUtil.its;
import static com.milaboratory.test.TestUtil.randomSequence;

public class MotifUtilsTest {
    @Test
    public void test1() throws Exception {
        RandomGenerator rg = new Well19937c();
        for (int i = 0; i < its(1000, 10000); ++i) {
            int length = 10 + rg.nextInt(30);
            NucleotideSequence seq1 = randomSequence(NucleotideSequence.ALPHABET, length, length);
            NucleotideSequence seq2 = randomSequence(NucleotideSequence.ALPHABET, length, length);
            Motif<NucleotideSequence> motif = MotifUtils.twoSequenceMotif(seq1, 0, seq2, 0, length);
            Assert.assertTrue(motif.matches(seq1, 0));
            Assert.assertTrue(motif.matches(seq2, 0));
        }
    }
}