/*
 *                    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 junit.framework.TestCase;
import org.junit.*;

import java.util.ArrayList;
import java.util.List;


/**
 * Tests functionality of Site class.
 * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
 */
public class SiteTest extends TestCase {

	public static final String newline = System.getProperty("line.separator");

	private static Site catSite;
	private static Site bindingSite;

	private static List<Group> bindingSiteGroups;

	public SiteTest() {

		// sites CAT and AC1 from PDB entry 1a4w
		//SITE     1 CAT  3 HIS H  57  ASP H 102  SER H 195
		//SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460
		//SITE     2 AC1  6 HOH H 464  HOH H 497
		//groups for site CAT
		Chain chain = new ChainImpl();
		chain.setName("H");
		chain.setId("H");
		Group his57 = new AminoAcidImpl();
		//            his57.setPDBCode("57");
		his57.setResidueNumber("H", 57, ' ');
		his57.setPDBName("HIS");
		his57.setChain(chain);
		Group asp102 = new AminoAcidImpl();
		asp102.setResidueNumber("H", 102, ' ');
		asp102.setPDBName("ASP");
		asp102.setChain(chain);
		Group ser195 = new AminoAcidImpl();
		ser195.setResidueNumber("H", 195, ' ');
		ser195.setPDBName("SER");
		ser195.setChain(chain);
		List<Group> catSiteGroups = new ArrayList<Group>();
		catSiteGroups.add(his57);
		catSiteGroups.add(asp102);
		catSiteGroups.add(ser195);
		//make the catalytic site CAT
		catSite = new Site();
		catSite.setSiteID("CAT");
		catSite.setGroups(catSiteGroups);
		catSite.setEvCode("UNKNOWN");
		catSite.setDescription("ACTIVE SITE");
		//groups for site AC1
		Group arg221a = new AminoAcidImpl();
		arg221a.setResidueNumber("H", 221, 'A');
		arg221a.setPDBName("ARG");
		arg221a.setChain(chain);
		Group lys224 = new AminoAcidImpl();
		lys224.setResidueNumber("H", 224, ' ');
		lys224.setPDBName("LYS");
		lys224.setChain(chain);
		Group hoh403 = new HetatomImpl();
		hoh403.setResidueNumber("H", 403, ' ');
		hoh403.setPDBName("HOH");
		hoh403.setChain(chain);
		Group hoh460 = new HetatomImpl();
		hoh460.setResidueNumber("H", 460, ' ');
		hoh460.setPDBName("HOH");
		hoh460.setChain(chain);
		Group hoh464 = new HetatomImpl();
		hoh464.setResidueNumber("H", 464, ' ');
		hoh464.setPDBName("HOH");
		hoh464.setChain(chain);
		Group hoh497 = new HetatomImpl();
		hoh497.setResidueNumber("H", 497, ' ');
		hoh497.setPDBName("HOH");
		hoh497.setChain(chain);

		bindingSiteGroups = new ArrayList<Group>();

		bindingSiteGroups.add(arg221a);
		bindingSiteGroups.add(lys224);
		bindingSiteGroups.add(hoh403);
		bindingSiteGroups.add(hoh460);
		bindingSiteGroups.add(hoh464);
		bindingSiteGroups.add(hoh497);
		//make the binding site AC1
		bindingSite = new Site();
		bindingSite.setSiteID("AC1");
		bindingSite.setGroups(bindingSiteGroups);
		bindingSite.setEvCode("SOFTWARE");
		bindingSite.setDescription("BINDING SITE FOR RESIDUE NA H 541");


	}

	@BeforeClass
	public static void setUpClass() throws Exception {
	}

	@AfterClass
	public static void tearDownClass() throws Exception {
	}

	@Override
	@Before
	public void setUp() {
	}

	@Override
	@After
	public void tearDown() {
	}

	/**
	 * Test of toPDB method, of class Site.
	 */
	@Test
	public void testToPDB_0args() {
//        System.out.println("toPDB_0args");
		String expResult =  "SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460                    " + newline +
							"SITE     2 AC1  6 HOH H 464  HOH H 497                                          "+ newline;
		String result = bindingSite.toPDB();
//        System.out.println("Expected:");
//        System.out.println(expResult);
//        System.out.println("Got:");
//        System.out.println(result);
		assertEquals(expResult, result);
	}

	/**
	 * Test of toPDB method, of class Site.
	 */
	@Test
	public void testToPDB_StringBuffer() {
//        System.out.println("toPDB");
		StringBuffer buf = new StringBuffer("");
		String expResult =  "SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403  HOH H 460                    " + newline +
							"SITE     2 AC1  6 HOH H 464  HOH H 497                                          "+ newline;
		bindingSite.toPDB(buf);
		String result = buf.toString();
//        System.out.println("Expected:");
//        System.out.println(expResult);
//        System.out.println("Got:");
//        System.out.println(result);
		assertEquals(expResult, result);
	}


		/**
	 * Test of toPDB method, of class Site.
	 */
	@Test
	public void testRemark800ToPDB_0args() {
//        System.out.println("remark800toPDB_0args");
		String expResult =  "REMARK 800 SITE_IDENTIFIER: CAT                                                 " + newline +
							"REMARK 800 EVIDENCE_CODE: UNKNOWN                                               " + newline +
							"REMARK 800 SITE_DESCRIPTION: ACTIVE SITE                                        " + newline;
		String result = catSite.remark800toPDB();
//        System.out.println(result);
		assertEquals(expResult, result);
	}

	/**
	 * Test of toPDB method, of class Site.
	 */
	@Test
	public void testRemark800ToPDB_StringBuffer() {
//        System.out.println("remark800toPDB");
		StringBuffer buf = new StringBuffer("");
		String expResult =  "REMARK 800 SITE_IDENTIFIER: CAT                                                 " + newline +
							"REMARK 800 EVIDENCE_CODE: UNKNOWN                                               " + newline +
							"REMARK 800 SITE_DESCRIPTION: ACTIVE SITE                                        " + newline;
		catSite.remark800toPDB(buf);
		String result = buf.toString();
//        System.out.println(result);
		assertEquals(expResult, result);
	}



	/**
	 * Test of getSiteID method, of class Site.
	 */
	@Test
	public void testGetSiteID() {
//        System.out.println("getSiteID");
		String expResult = "CAT";
		String result = catSite.getSiteID();
		assertEquals(expResult, result);
	}

	/**
	 * Test of getGroups method, of class Site.
	 */
	@Test
	public void testGetGroups() {
//        System.out.println("getGroups");
		List<Group> expResult = bindingSiteGroups;
		List<Group> result = bindingSite.getGroups();
		assertEquals(expResult, result);
	}

	/**
	 * Test to see how the groups have been set in the Groups list
	 */
	@Test
	public void testGroup() {
		List<Group> result = bindingSite.getGroups();
		Group arg221 = result.get(0);
		ResidueNumber testResNum = new ResidueNumber("H", 221, 'A');
		assertEquals(testResNum, arg221.getResidueNumber());
		//test the chainId is also set
		assertEquals("H", arg221.getChainId());


		Group hoh403 = null;

		for (Group group : result) {
			if (group.getResidueNumber().getSeqNum() == 403) {
				hoh403 = group;
			}
		}

		ResidueNumber testResNum2 = new ResidueNumber("H", 403, ' ');
//        testResNum2.setChainId("H");
//        testResNum2.setSeqNum(403);
//        testResNum2.setInsCode("");
//        System.out.println(hoh403);
		assertEquals(testResNum2, hoh403.getResidueNumber());
		//test the chaiId is also set
		assertEquals("H", hoh403.getChainId());
	}
}
