/* Copyright (C) 2009-2010 Syed Asad Rahman <asad@ebi.ac.uk>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.smsd.algorithm.vflib;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

import java.io.InputStream;

import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.smsd.interfaces.AbstractSubGraphTest;
import org.openscience.cdk.smsd.tools.MolHandler;

/**
 * @author Syed Asad Rahman &lt;asad@ebi.ac.uk&gt;
 *
 * @cdk.module test-smsd
 * @cdk.require java1.6+
 */
public class VFlibTurboHandlerTest extends AbstractSubGraphTest {

    public VFlibTurboHandlerTest() {}

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

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

    @Before
    @Override
    public void setUp() {}

    @After
    @Override
    public void tearDown() {}

    /**
     * Test of isSubgraph method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    @Override
    public void testIsSubgraph() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        assertTrue(smsd1.isSubgraph(true));
    }

    /**
     * Test of set method, of class VFlibSubStructureHandler.
     * @throws Exception
     */
    @Test
    public void testSet_IAtomContainer_IAtomContainer() throws Exception {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        assertTrue(smsd1.isSubgraph(true));
    }

    /**
     * Test of set method, of class VFlibSubStructureHandler.
     * @throws CDKException
     */
    @Test
    public void testSet_String_String() throws CDKException {
        String molfile = "data/mdl/decalin.mol";
        String queryfile = "data/mdl/decalin.mol";
        IAtomContainer query = new AtomContainer();
        IAtomContainer target = new AtomContainer();

        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(molfile);
        MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
        reader.read(query);
        ins = this.getClass().getClassLoader().getResourceAsStream(queryfile);
        reader = new MDLV2000Reader(ins, Mode.STRICT);
        reader.read(target);

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(query, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        assertTrue(smsd1.isSubgraph(true));
    }

    /**
     * Test of set method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    public void testSet_MolHandler_MolHandler() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());

        IAtomContainer target1 = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");
        MolHandler source = new MolHandler(queryac, true, true);
        MolHandler target = new MolHandler(target1, true, true);
        VFlibSubStructureHandler instance = new VFlibSubStructureHandler();
        instance.set(source, target);
        assertTrue(instance.isSubgraph(true));
    }

    /**
     * Test of getAllAtomMapping method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    public void testGetAllAtomMapping() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        smsd1.isSubgraph(true);

        assertEquals(4, smsd1.getAllAtomMapping().size());
    }

    /**
     * Test of getAllMapping method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    public void testGetAllMapping() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        smsd1.isSubgraph(true);

        assertEquals(4, smsd1.getAllMapping().size());
    }

    /**
     * Test of getFirstAtomMapping method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    public void testGetFirstAtomMapping() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        smsd1.isSubgraph(true);

        assertEquals(7, smsd1.getFirstAtomMapping().size());
    }

    /**
     * Test of getFirstMapping method, of class VFlibSubStructureHandler.
     * @throws InvalidSmilesException
     */
    @Test
    public void testGetFirstMapping() throws InvalidSmilesException {
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
        IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");

        VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
        MolHandler mol1 = new MolHandler(queryac, true, true);
        MolHandler mol2 = new MolHandler(target, true, true);
        smsd1.set(mol1, mol2);
        smsd1.isSubgraph(true);

        assertEquals(7, smsd1.getFirstMapping().size());
    }
}
