/*
* The MIT License
*
* Copyright (c) 2015 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.vcf.processor;
import com.google.common.collect.ComparisonChain;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.Iterators;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/**
* @author mccowan
*/
public class WidthLimitingDecoratorTest {
class Segment extends VcfFileSegment {
final int start, stop;
Segment(final int start, final int stop) {
this.start = start;
this.stop = stop;
}
@Override
public int start() {
return start;
}
@Override
public int stop() {
return stop;
}
@Override
public String contig() {
return "A";
}
@Override
public File vcf() {
return new File("B");
}
@Override
public String toString() {
return "Segment{" +
"start=" + start +
", stop=" + stop +
", vcf=" + vcf() +
", contig=" + contig() +
'}';
}
}
@Test
public void testForVcf() throws Exception {
final Segment entireThing = new Segment(1, 9942);
final ImmutableList<Segment> expectedSubThings = ImmutableList.of(
new Segment(1, 1000),
new Segment(1001, 2000),
new Segment(2001, 3000),
new Segment(3001, 4000),
new Segment(4001, 5000),
new Segment(5001, 6000),
new Segment(6001, 7000),
new Segment(7001, 8000),
new Segment(8001, 9000),
new Segment(9001, 9942)
);
final VcfFileSegmentGenerator.WidthLimitingDecorator strategy = VcfFileSegmentGenerator.WidthLimitingDecorator.wrapping(new VcfFileSegmentGenerator() {
@Override
public Iterable<VcfFileSegment> forVcf(final File vcf) {
return Collections.singleton((VcfFileSegment) entireThing);
}
}, 1000);
final List<VcfFileSegment> observed = new ArrayList<VcfFileSegment>();
Iterators.addAll(observed, strategy.forVcf(new File("B")).iterator());
final Iterator<VcfFileSegment> observedIterator = observed.iterator();
for (final VcfFileSegment e : expectedSubThings) {
Assert.assertTrue(observedIterator.hasNext());
final VcfFileSegment o = observedIterator.next();
Assert.assertEquals(ComparisonChain.start()
.compare(o.contig(), e.contig())
.compare(o.start(), e.start())
.compare(o.stop(), e.stop())
.compare(o.vcf(), e.vcf())
.result(), 0, String.format(String.format("observed=%s@%s:%s-%s expected=%s", o.vcf(), o.contig(), o.start(),
o.stop(), e.toString())));
}
}
}