/*
* 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.alignment.batch;
import com.milaboratory.core.alignment.AffineGapAlignmentScoring;
import com.milaboratory.core.sequence.NucleotideSequence;
import org.junit.Assert;
import org.junit.Test;
public class SimpleBatchAlignerTest {
@Test
public void test1() {
NucleotideSequence ref1 = new NucleotideSequence("ATAAGAGACACATAGGTCTGGC"),
ref2 = new NucleotideSequence("ATTAGAGACACATAGGTCTAGC"),
ref3 = new NucleotideSequence("ATGAGAGACACATAGGTCTTGC"),
ref4 = new NucleotideSequence("ATCAGAGACACTTAGGTCTCGC"),
ref5 = new NucleotideSequence("ATCAGAAATAAAAATAACTGGC");
NucleotideSequence query = new NucleotideSequence("ATCAGAGACACATAGGTCTGGC");
SimpleBatchAlignerParameters<NucleotideSequence> batchAlignerParameters = new SimpleBatchAlignerParameters<>(5,
0.5f, 0f, true, AffineGapAlignmentScoring.getNucleotideBLASTScoring());
SimpleBatchAligner<NucleotideSequence, Integer> simpleBatchAligner = new SimpleBatchAligner<>(batchAlignerParameters);
simpleBatchAligner.addReference(ref1, 0);
simpleBatchAligner.addReference(ref2, 1);
simpleBatchAligner.addReference(ref3, 2);
simpleBatchAligner.addReference(ref4, 3);
simpleBatchAligner.addReference(ref5, 4);
AlignmentResult<AlignmentHit<NucleotideSequence, Integer>> result = simpleBatchAligner.align(query);
System.out.println(result);
Assert.assertEquals((Integer) 0, result.getHits().get(0).getRecordPayload());
Assert.assertEquals(4, result.getHits().size());
}
}