com.progressiveaccess.cmlspeech.base.FileHandler.java Source code

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Here is the source code for com.progressiveaccess.cmlspeech.base.FileHandler.java

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// Copyright 2015 Volker Sorge
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//      http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

/**
 * @file   FileHandler.java
 * @author Volker Sorge
 *         <a href="mailto:V.Sorge@progressiveaccess.com">Volker Sorge</a>
 * @date   Thu Feb 26 19:06:25 2015
 *
 * @brief  File handler utility functions.
 *
 *
 */

//

package com.progressiveaccess.cmlspeech.base;

import nu.xom.Builder;
import nu.xom.Document;
import nu.xom.ParsingException;
import nux.xom.pool.XOMUtil;

import org.apache.commons.io.FilenameUtils;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.io.CMLWriter;
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.xmlcml.cml.base.CMLBuilder;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;

/**
 * Utility class for handling CML files and other chem file formats.
 */

public final class FileHandler {

    /** Dummy constructor. */
    private FileHandler() {
        throw new AssertionError("Instantiating utility class...");
    }

    /**
     * Loads current file into the molecule IAtomContainer.
     *
     * @param fileName
     *          File to load.
     *
     * @return The molecule loaded.
     *
     * @throws IOException
     *           Problems with loading file.
     * @throws CDKException
     *           Problems with input file format.
     */
    public static IAtomContainer readFile(final String fileName) throws IOException, CDKException {
        final InputStream file = new BufferedInputStream(new FileInputStream(fileName));
        final ISimpleChemObjectReader reader = new ReaderFactory().createReader(file);
        IChemFile cmlFile = null;
        cmlFile = reader.read(SilentChemObjectBuilder.getInstance().newInstance(IChemFile.class));
        reader.close();
        final IAtomContainer molecule = ChemFileManipulator.getAllAtomContainers(cmlFile).get(0);
        Logger.logging(molecule);
        return molecule;
    }

    /**
     * Builds the CML XOM element.
     *
     * @param molecule
     *          The molecule to rewritten.
     *
     * @return The CML document.
     *
     * @throws IOException
     *           Problems with StringWriter
     * @throws CDKException
     *           Problems with CMLWriter
     * @throws ParsingException
     *           Problems with building CML XOM.
     */
    public static Document buildXom(final IAtomContainer molecule)
            throws IOException, CDKException, ParsingException {
        final StringWriter outStr = new StringWriter();
        final CMLWriter cmlwriter = new CMLWriter(outStr);
        cmlwriter.write(molecule);
        cmlwriter.close();
        final String cmlcode = outStr.toString();

        final Builder builder = new CMLBuilder();
        // this.doc.getRootElement().addNamespaceDeclaration
        // ("cml", "http://www.xml-cml.org/schema");
        final Document doc = builder.build(cmlcode, "");
        Logger.logging(doc.toXML());
        return doc;
    }

    /**
     * Writes a document to a CML file.
     *
     * @param doc
     *          The output document.
     * @param fileName
     *          The base filename.
     * @param extension
     *          The additional extension.
     *
     * @throws IOException
     *           Problems with opening output file.
     * @throws CDKException
     *           Problems with writing the CML XOM.
     */
    public static void writeFile(final Document doc, final String fileName, final String extension)
            throws IOException, CDKException {
        final String basename = FilenameUtils.getBaseName(fileName);
        final OutputStream outFile = new BufferedOutputStream(
                new FileOutputStream(basename + "-" + extension + ".cml"));
        final PrintWriter output = new PrintWriter(outFile);
        output.write(XOMUtil.toPrettyXML(doc));
        output.flush();
        output.close();
    }

}