/*
* The MIT License
*
* Copyright (c) 2013 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 htsjdk.tribble.index;
import htsjdk.tribble.TestUtils;
import htsjdk.tribble.TribbleException;
import htsjdk.tribble.bed.BEDCodec;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.List;
/**
* User: jacob
* Date: 2012-Aug-23
*/
public class IndexFactoryTest {
final File sortedBedFile = new File(TestUtils.DATA_DIR + "bed/Unigene.sample.bed");
final File unsortedBedFile = new File(TestUtils.DATA_DIR + "bed/unsorted.bed");
final File discontinuousFile = new File(TestUtils.DATA_DIR + "bed/disconcontigs.bed");
final BEDCodec bedCodec = new BEDCodec();
@Test
public void testCreateLinearIndex() throws Exception {
Index index = IndexFactory.createLinearIndex(sortedBedFile, bedCodec);
String chr = "chr2";
Assert.assertTrue(index.getSequenceNames().contains(chr));
Assert.assertTrue(index.containsChromosome(chr));
Assert.assertEquals(1, index.getSequenceNames().size());
List<Block> blocks = index.getBlocks(chr, 1, 50);
Assert.assertEquals(1, blocks.size());
Block block = blocks.get(0);
Assert.assertEquals(78, block.getSize());
}
@Test(expectedExceptions = TribbleException.MalformedFeatureFile.class, dataProvider = "indexFactoryProvider")
public void testCreateIndexUnsorted(IndexFactory.IndexType type) throws Exception{
Index index = IndexFactory.createIndex(unsortedBedFile, bedCodec, type);
}
@Test(expectedExceptions = TribbleException.MalformedFeatureFile.class, dataProvider = "indexFactoryProvider")
public void testCreateIndexDiscontinuousContigs(IndexFactory.IndexType type) throws Exception{
Index index = IndexFactory.createIndex(discontinuousFile, bedCodec, type);
}
@DataProvider(name = "indexFactoryProvider")
public Object[][] getIndexFactoryTypes(){
return new Object[][] {
new Object[] { IndexFactory.IndexType.LINEAR },
new Object[] { IndexFactory.IndexType.INTERVAL_TREE }
};
}
}