/*
 * MX Cheminformatics Tools for Java
 *
 * Copyright (c) 2007-2009 Metamolecular, LLC
 *
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.metamolecular.mx.test;

import junit.framework.TestCase;
import com.metamolecular.mx.model.*;
import com.metamolecular.mx.io.Molecules;
import com.metamolecular.mx.io.mdl.MolfileReader;

import java.io.*;

/**
 * @author Duan Lian
 */
public class MolfileWriterTest extends TestCase
{
    public void testWriterOutputsSubstructure()
    {
        Molecule ethylbenzene = Molecules.createEthylbenzeneWithSubstructure();

        String molfile = MoleculeKit.writeMolfile(ethylbenzene);
        Molecule molecule = MoleculeKit.readMolfile(molfile);
        assertEquals(1, molecule.countSubstructures());
    }
    public void testWriterOutputReaderInput() throws FileNotFoundException {
        File[] molfiles = new File("../resources/molfiles").listFiles();
        for (File molfile : molfiles)
        {
            String content = null;
            try {
                content = getFileContent(molfile);
            } catch (IOException e) {
                e.printStackTrace();
                fail("File reading failed");
            }
            Molecule molecule1 = MoleculeKit.readMolfile(content);
            String molfile1 = MoleculeKit.writeMolfile(molecule1);
            Molecule molecule2 = MoleculeKit.readMolfile(molfile1);
            String molfile2 = MoleculeKit.writeMolfile(molecule2);
            assertEquals(molfile1,molfile2);
        }
    }
    private String getFileContent(File file) throws IOException {
        StringBuffer stringBuffer = new StringBuffer();
        BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        String line;
        while ((line = bufferedReader.readLine()) != null) {
            stringBuffer.append(line+"\n");
        }
        return stringBuffer.toString();
    }
}

/*
 * MX Cheminformatics Tools for Java
 *
 * Copyright (c) 2007-2009 Metamolecular, LLC
 *
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.metamolecular.mx.test;

import junit.framework.TestCase;
import com.metamolecular.mx.model.*;
import com.metamolecular.mx.io.Molecules;
import com.metamolecular.mx.io.mdl.MolfileReader;

import java.io.*;

/**
 * @author Duan Lian
 */
public class MolfileWriterTest extends TestCase
{
    public void testWriterOutputsSubstructure()
    {
        Molecule ethylbenzene = Molecules.createEthylbenzeneWithSubstructure();

        String molfile = MoleculeKit.writeMolfile(ethylbenzene);
        Molecule molecule = MoleculeKit.readMolfile(molfile);
        assertEquals(1, molecule.countSubstructures());
    }
    public void testWriterOutputReaderInput() throws IOException {
        File[] molfiles = new File("../resources/molfiles").listFiles();
        for (File molfile : molfiles)
        {
            String content = null;
            content = getFileContent(molfile);
            Molecule molecule1 = MoleculeKit.readMolfile(content);
            String molfile1 = MoleculeKit.writeMolfile(molecule1);
            Molecule molecule2 = MoleculeKit.readMolfile(molfile1);
            String molfile2 = MoleculeKit.writeMolfile(molecule2);
            assertEquals(molfile1,molfile2);
        }
    }
    private String getFileContent(File file) throws IOException {
        StringBuffer stringBuffer = new StringBuffer();
        BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        String line;
        while ((line = bufferedReader.readLine()) != null) {
            stringBuffer.append(line+"\n");
        }
        return stringBuffer.toString();
    }
}

change Exception handling