/* Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) project
 *
 * 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.
 *
 * 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.graph.invariant;

import java.io.InputStream;

import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.templates.TestMoleculeFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Checks the functionality of the MorganNumberTools.
 *
 * @cdk.module test-standard
 */
public class MorganNumbersToolsTest extends CDKTestCase {

    public MorganNumbersToolsTest() {
        super();
    }

    @Test
    public void testGetMorganNumbers_IAtomContainer() {
        // This is an array with the expected Morgan Numbers for a-pinene
        long[] reference = {28776, 17899, 23549, 34598, 31846, 36393, 9847, 45904, 15669, 15669};

        IAtomContainer mol = TestMoleculeFactory.makeAlphaPinene();
        long[] morganNumbers = MorganNumbersTools.getMorganNumbers(mol);
        Assert.assertEquals(reference.length, morganNumbers.length);
        for (int f = 0; f < morganNumbers.length; f++) {
            //logger.debug(morganNumbers[f]);
            Assert.assertEquals(reference[f], morganNumbers[f]);
        }
    }

    @Test
    public void testPhenylamine() {
        // This is an array with the expected Morgan Numbers for a-pinene
        String[] reference = {"C-457", "C-428", "C-325", "C-354", "C-325", "C-428", "N-251"};

        IAtomContainer mol = TestMoleculeFactory.makePhenylAmine();
        String[] morganNumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(mol);
        Assert.assertEquals(reference.length, morganNumbers.length);
        for (int f = 0; f < morganNumbers.length; f++) {
            //logger.debug(morganNumbers[f]);
            Assert.assertEquals(reference[f], morganNumbers[f]);
        }
    }

    /**
     * @cdk.bug 2846213
     */
    @Test
    public void testBug2846213() throws CDKException {
        String filename = "data/mdl/bug2846213.mol";
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
        ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
        IAtomContainer ac = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
        long[] morganNumbers = MorganNumbersTools.getMorganNumbers(ac);
        Assert.assertFalse(morganNumbers[7] == morganNumbers[8]);
    }

}
