TestURLIdentifier.java

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure;

import static org.junit.Assert.*;

import java.io.IOException;
import java.net.URL;
import java.net.UnknownHostException;
import java.util.Arrays;

import org.biojava.nbio.structure.align.util.AtomCache;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class TestURLIdentifier {
	private static final Logger logger = LoggerFactory.getLogger(TestURLIdentifier.class);
	@Test
	public void testFileIdentifiers() throws StructureException, IOException {
		AtomCache cache = new AtomCache();

		URL url;
		Structure full, reduced;
		URLIdentifier id;

		url = getClass().getResource("/2pos.pdb");
		id = new URLIdentifier(url);

		full = id.loadStructure(cache);
		assertNotNull("PDB file didn't work",full);

		reduced = id.reduce(full);
		assertTrue(Arrays.deepEquals(StructureTools.getAllAtomArray(full),
				StructureTools.getAllAtomArray(reduced)));

		url = getClass().getResource("/4hhb.cif.gz");
		id = new URLIdentifier(url);

		full = id.loadStructure(cache);
		assertNotNull("CIF file didn't work",full);

		reduced = id.reduce(full);
		assertTrue(Arrays.deepEquals(StructureTools.getAllAtomArray(full),
				StructureTools.getAllAtomArray(reduced)));

	}

	@Test
	public void testURLParameters() throws StructureException, IOException {
		AtomCache cache = new AtomCache();

		URL url;
		Structure full, reduced;
		URLIdentifier id;

		String base = getClass().getResource("/2pos.pdb").getPath();

		url = new URL("file://" + base + "?format=PDB");
		id = new URLIdentifier(url);

		full = id.loadStructure(cache);
		assertNotNull(full);
		assertEquals("2POS",id.toCanonical().getPdbId());
//		assertEquals("2POS",full.getName()); // What should this get set to with identifiers?

		url = new URL("file://" + base + "?residues=A:1-5");
		id = new URLIdentifier(url);
		assertEquals("wrong canonical for residues=A:1-5","2POS.A_1-5",id.toCanonical().toString());

		full = id.loadStructure(cache);
		assertNotNull(full);
		reduced = id.reduce(full);
		assertEquals("wrong length for residues=A:1-5", 5, StructureTools.getRepresentativeAtomArray(reduced).length);

		url = new URL("file://" + base + "?chainId=A");
		id = new URLIdentifier(url);
		assertEquals("wrong canonical for chainId=A","2POS.A",id.toCanonical().toString());

		full = id.loadStructure(cache);
		assertNotNull(full);
		reduced = id.reduce(full);
		assertEquals("wrong length for chainName=A", 94, StructureTools.getRepresentativeAtomArray(reduced).length);

		try {
			url = new URL("http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
			id = new URLIdentifier(url);

			full = id.loadStructure(cache);
			assertNotNull(full);
			assertEquals("1B8G",id.toCanonical().getPdbId());
		} catch(UnknownHostException e) {
			logger.error("Unable to connect to rcsb.org");
			// still pass
		}
	}
}