org.helm.notation2.tools.MolfileEncoder.java Source code

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Here is the source code for org.helm.notation2.tools.MolfileEncoder.java

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/*******************************************************************************
 * Copyright C 2012, The Pistoia Alliance
 *
 * 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 org.helm.notation2.tools;

import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.zip.GZIPInputStream;

import org.apache.commons.io.IOUtils;
import org.helm.notation2.exception.EncoderException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class MolfileEncoder {

    private static final Logger LOG = LoggerFactory.getLogger(MolfileEncoder.class);

    public static String encode(String string) throws EncoderException {
        String result = null;
        if (null != string) {
            result = compress(string);
            return result;
        } else {
            return null;
        }
    }

    public static String decode(String encodedString) throws EncoderException {
        String result = null;
        if (null != encodedString) {
            result = decompress(encodedString);
            return result;
        } else {
            return null;
        }
    }

    /**
     * method to compress the given molfile in a Base64 string
     *
     * @param str given molfile
     */
    private static String compress(String str) {
        return Base64.encodeToString(str.getBytes(), false);
    }

    /**
     * method to decompress the givenmolfile input
     *
     * @param str the molefile input can be in base64 format or in the gzipped
     *          Base64 format
     * @return molfile
     * @throws EncoderException
     */
    private static String decompress(String str) throws EncoderException {
        /* First base64 decode the string */
        String result = null;
        byte[] bytes = Base64.decode(str);
        GZIPInputStream zi = null;
        try {
            zi = new GZIPInputStream(new ByteArrayInputStream(bytes));
            InputStreamReader reader = new InputStreamReader(zi);
            BufferedReader in = new BufferedReader(reader);
            StringBuilder sb = new StringBuilder();
            String read;
            while ((read = in.readLine()) != null) {
                sb.append(read + "\n");
            }

            String molfile = sb.toString();
            if (molfile.endsWith("\n$$$$\n")) {
                molfile = molfile.replace("\n$$$$\n", "");
            }
            reader.close();
            in.close();
            zi.close();
            return molfile;

        } catch (IOException e) {
            LOG.info("Molfile was not in gzipped");
            result = new String(bytes);
        } finally {
            IOUtils.closeQuietly(zi);
        }
        return result;

    }
}