/*
 *                    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.secstruc;

import java.io.IOException;
import java.util.Arrays;
import java.util.List;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.junit.Test;

import static org.junit.Assert.*;

/**
 * Test all the options for writting and fetching DSSP file formats. Also
 * compare that files match the prediction (assumed to be correct).
 *
 * @author Aleix Lafita
 *
 */
public class TestDSSPParser {

	@Test
	public void testDSSPParser() throws IOException, StructureException {

		// List of names to test the DSSP prediction
		List<String> names = Arrays.asList("5pti");

		for (String name : names) {

			AtomCache cache = new AtomCache();
			Structure s = cache.getStructure(name);

			// Test loading from file
			List<SecStrucState> file = DSSPParser.parseFile(
					"src/test/resources/" + name + ".dssp", s, false);

			// Test fetching from PDB
			List<SecStrucState> pdb = DSSPParser.fetch(name, s, false);

			// Test predicting, writting and parsing back
			SecStrucCalc sec = new SecStrucCalc();
			List<SecStrucState> pred = sec.calculate(s, false);

			List<SecStrucState> parseBack = DSSPParser.parseString(
					sec.toString(), s, false);

			assertTrue(
					"SS assignment lengths do not match",
					file.size() == pdb.size()
							&& pred.size() == parseBack.size()
							&& pred.size() == file.size());

			for (int i = 0; i < file.size(); i++) {
				assertEquals("SS assignment position " + (i + 1)
						+ " does not match", file.get(i), pdb.get(i));
				assertEquals("SS assignment position " + (i + 1)
						+ " does not match", pred.get(i), parseBack.get(i));
				assertEquals("SS assignment position " + (i + 1)
						+ " does not match", file.get(i), pred.get(i));
			}
		}
	}
}