/*
 *                    PDB web 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.
 *
 *
 * Created on Jul 23, 2009
 * Created by ap3
 *
 */

package org.biojava.nbio.structure.test.align.fatcat;

import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.fatcat.FatCat;
import org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
import org.biojava.nbio.structure.align.xml.AFPChainXMLParser;

import java.io.IOException;

public class AFPChainSerialisationTest
extends TestCase
{



	/**
	 * @return the suite of tests being tested
	 */
	public static Test suite()
	{
		return new TestSuite( AFPChainSerialisationTest.class );
	}

	public AFPChainSerialisationTest(String testName){
		super(testName);
	}

//   public void testSerialization1P80_2IUF(){
//      String name1 = "1P80.D";
//      String name2 = "2IUF.E";
//
//      AtomCache cache =    TmpAtomCache.cache;
//      try {
//
//         Atom[] ca1 = cache.getAtoms(name1);
//         Atom[] ca2 = cache.getAtoms(name2);
//
//         testAlignment(name1,name2 ,ca1,ca2,false);
//         testAlignment(name1,name2,ca1,ca2,true);
//
//      } catch (Exception e){
//         e.printStackTrace();
//         fail(e.getMessage());
//      }
//
//   }

	public void testSerialization1a21_1hwg() throws IOException, StructureException{


		Structure s1 = getStructure("1a21", "A");
		Structure s2 = getStructure("1hwg","C");


		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s1);
		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s2);

		testAlignment("1a21.A","1hwg.C",ca1,ca2,false);
		testAlignment("1a21.A","1hwg.C",ca1,ca2,true);


	}


	// slow...
//   public void testSerialization1cdg_1tim(){
//
//      try {
//
//         Structure s1 = getStructure("1cdg", "A");
//         Structure s2 = getStructure("1tim","A");
//
//         Atom[] ca1 = StructureTools.getAtomCAArray(s1);
//         Atom[] ca2 = StructureTools.getAtomCAArray(s2);
//
//         testAlignment("1cdg.A","1tim.A",ca1,ca2,false);
//         testAlignment("1cdg.A","1tim.A",ca1,ca2,true);
//
//      } catch (Exception e) {
//         e.printStackTrace();
//         fail(e.getMessage());
//      }
//   }
//   public void testSerialization4hhb(){
//
//      try {
//
//         Structure s1 = getStructure("4hhb", "A");
//         Structure s2 = getStructure("4hhb", "B");
//
//         Atom[] ca1 = StructureTools.getAtomCAArray(s1);
//         Atom[] ca2 = StructureTools.getAtomCAArray(s2);
//
//         testAlignment("4hhb.A","4hhb.B",ca1,ca2,false);
//         testAlignment("4hhb.A","4hhb.B",ca1,ca2,true);
//
//      } catch (Exception e) {
//         e.printStackTrace();
//         fail(e.getMessage());
//      }
//   }


	private Structure getStructure(String pdbId, String chainId) throws IOException, StructureException{
		AtomCache cache = new AtomCache();
		Structure structure1 = cache.getStructure(pdbId);

		Chain c = structure1.getPolyChainByPDB(chainId);

		Structure s = new StructureImpl();
		s.addChain(c);

		return s;

	}

	private void testAlignment(String name1, String name2, Atom[] ca1, Atom[] ca2, boolean doRigid) throws StructureException,IOException{


		Atom[] ca3 = StructureTools.cloneAtomArray(ca2);


		AFPChain afpChain = doAlign(name1, name2, ca1,ca2,doRigid);



		String fatcat = afpChain.toFatcat(ca1, ca2);
		String xml 	  = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);


		//System.out.println(xml);
		AFPChain newChain = AFPChainXMLParser.fromXML (xml, ca1, ca3);

		// test blockNum and optLen arrays
		int blockNum = afpChain.getBlockNum();
		int[] optLen = afpChain.getOptLen();

		assertTrue("The nr of aligned blocks is not the same! " + blockNum + " " + newChain.getBlockNum() , blockNum == newChain.getBlockNum());



		for ( int i =0 ; i < blockNum ; i++){
			int newLenI = newChain.getOptLen()[i];
			assertTrue("The values in the optLen field don't match! pos:" + i + " orig:" + optLen[i] + " new:" +  newLenI,optLen[i] == newLenI);
		}

		// test the internal optAlign data structure:

		int[][][] optAln1 = afpChain.getOptAln();
		int[][][] optAln2 = newChain.getOptAln();

		for(int i = 0; i < blockNum; i ++)  {
			for(int j = 0; j < optLen[i]; j ++) {
				int p1 = optAln1[i][0][j];
				int p2 = optAln1[i][1][j];

				int n1 = optAln2[i][0][j];
				int n2 = optAln2[i][1][j];

				assertTrue(p1 == n1);
				assertTrue(p2 == n2);

			}
		}

		String fatcat2 = newChain.toFatcat(ca1, ca3);
		//System.out.println("*** RESULT2 "+result2);

		assertEquals(fatcat,fatcat2);

		String xml2 = AFPChainXMLConverter.toXML(newChain, ca1, ca3);
		assertEquals(xml, xml2);

	}


	public AFPChain doAlign(String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException,IOException{
		FatCatParameters params = new FatCatParameters();

		FatCat fatCat = new FatCat();
		AFPChain afpChain;
		if ( doRigid)
			afpChain = fatCat.alignRigid(ca1,ca2,params);
		else
			afpChain = fatCat.alignFlexible(ca1,ca2,params);

		afpChain.setName1(name1);
		afpChain.setName2(name2);
		return afpChain;

	}

	public String[] align (String name1, String name2, Atom[] ca1, Atom[] ca2 , boolean doRigid) throws StructureException,IOException{

		AFPChain afpChain = doAlign(name1, name2, ca1, ca2, doRigid);
		// flexible original results:
		String fatcat = afpChain.toFatcat(ca1,ca2);
		//System.out.println(result1);


		String xml = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);

		String[] result = new String[2];
		result[0] = fatcat;
		result[1] = xml;
		return result;
	}


	public void testMulti() throws IOException, StructureException { 
		Atom[] ca1 = null;
		Atom[] ca2 = null;
		Atom[] ca3 = null;
		Atom[] ca4 = null;
		Atom[] ca5 = null;
		Atom[] ca6 = null;
		String[] result1 = null;
		String[] result2 = null;

		String name1 = "5pti.A";
		String name2 = "1znf.A";

		String name3 ="1hiv.A";
		String name4 ="1a4w.H";
		Structure s1 = getStructure("5pti","A");
		Structure s2 = getStructure("1znf","A");
		ca1 = StructureTools.getRepresentativeAtomArray(s1);
		ca2 = StructureTools.getRepresentativeAtomArray(s2);
		ca3 = StructureTools.cloneAtomArray(ca2);

		result1 = align(name1,name2,ca1, ca2,true);

		Structure s3 = getStructure("1hiv","A");
		Structure s4 = getStructure("1a4w","H");
		ca4 = StructureTools.getRepresentativeAtomArray(s3);
		ca5 = StructureTools.getRepresentativeAtomArray(s4);
		ca6 = StructureTools.cloneAtomArray(ca5);

		result2 = align(name3,name4,ca4, ca5,true);


		

		String xmlNew = "<multi>"+result1[1]+ result2[1] +"</multi>";
		//System.out.println(xmlNew);

		testSaxParser(xmlNew,name1,name2,result1,ca1,ca3,name3,name4,result2,ca4,ca6);


		//WARNING: THE ORDER CAN CHANGE: order of elements in XML is not necessarily the same!
		AFPChain[] chains = AFPChainXMLParser.parseMultiXML(xmlNew);

		assertTrue(chains.length == 2);

		// recreate the correct chains...
		AFPChain new1 = getAfpFor(name1,chains);
		AFPChain new2 = getAfpFor(name3,chains);

		assertNotNull(new1);
		assertNotNull(new2);

		assertTrue(new1.getName1().equals(name1));
		//System.out.println(new2.getName1() + " " + new2.getName2() + " "+ name3);
		assertTrue(new2.getName1().equals(name3));


		AFPChainXMLParser.rebuildAFPChain(new1, ca1, ca3);
		String fatcat1 = new1.toFatcat(ca1, ca3);
		assertEquals(fatcat1, result1[0]);
		String xmlnew1 = AFPChainXMLConverter.toXML(new1, ca1, ca3);
		assertTrue(xmlnew1.equals(result1[1]));

		AFPChainXMLParser.rebuildAFPChain(new2, ca4, ca6);
		String fatcat2 = new2.toFatcat(ca4, ca6);

		assertEquals(fatcat2,result2[0]);
		String xmlnew2 = AFPChainXMLConverter.toXML(new2, ca4, ca6);
		assertEquals(xmlnew2,result2[1]);
		


	}

	private void testSaxParser(String xmlNew, String name1, String name2,
			String[] result1, Atom[] ca1, Atom[] ca3, String name3,
			String name4, String[] result2, Atom[] ca4, Atom[] ca6) {




	}

	private AFPChain getAfpFor(String name1, AFPChain[] chains) {

		for ( AFPChain c : chains){
			//System.out.println("comparing with " + c.getName1());
			if (c.getName1().equals(name1))
				return c;
		}
		return null;
	}
}
