org.dishevelled.compress.Compress.java Source code

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Here is the source code for org.dishevelled.compress.Compress.java

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/*
    
dsh-compress  Compression utility classes.
Copyright (c) 2014-2017 held jointly by the individual authors.
    
This library 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 3 of the License, or (at
your option) any later version.
    
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out 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 library;  if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
    
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
    
*/
package org.dishevelled.compress;

import static com.google.common.base.Preconditions.checkNotNull;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.IOException;

import javax.annotation.Nullable;

import com.google.common.io.Files;

import htsjdk.samtools.util.BlockCompressedInputStream;

import org.apache.commons.compress.compressors.bzip2.BZip2Utils;

import org.apache.commons.compress.compressors.gzip.GzipUtils;

/**
 * Compression utility methods.
 *
 * @since 1.3
 * @author  Michael Heuer
 */
public final class Compress {

    /**
     * Private no-arg constructor.
     */
    private Compress() {
        // empty
    }

    /**
     * Return true if the specified file is a block compressed gzip (BGZF) file name.
     *
     * @since 1.3
     * @param fileName file name, must not be null
     * @return true if the specified file is a block compressed gzip (BGZF) file name
     */
    public static boolean isBgzfFilename(final String fileName) {
        checkNotNull(fileName);
        return BgzfUtils.isCompressedFilename(fileName);
    }

    /**
     * Return true if the specified file is a block compressed gzip (BGZF) file.
     *
     * @param file file, if any
     * @return true if the specified file is a block compressed gzip (BGZF) file
     */
    public static boolean isBgzfFile(@Nullable final File file) {
        if (file == null) {
            return false;
        }
        if (isBgzfFilename(file.getName())) {
            return true;
        }
        // block compressed gzip files may also have .gz file extension, check the stream
        try (BufferedInputStream inputStream = new BufferedInputStream(new FileInputStream(file))) {
            return isBgzfInputStream(inputStream);
        } catch (IOException e) {
            return false;
        }
    }

    /**
     * Return true if the specified file is a block compressed gzip (BGZF) input stream.
     *
     * @param inputStream input stream, must not be null
     * @return true if the specified file is a block compressed gzip (BGZF) input stream
     */
    public static boolean isBgzfInputStream(final InputStream inputStream) {
        checkNotNull(inputStream);
        BufferedInputStream bufferedInputStream = inputStream instanceof BufferedInputStream
                ? (BufferedInputStream) inputStream
                : new BufferedInputStream(inputStream);
        try {
            return BlockCompressedInputStream.isValidFile(bufferedInputStream);
        } catch (IOException e) {
            return false;
        }
    }

    /**
     * Return true if the specified file is a gzip file name.
     *
     * @since 1.3
     * @param fileName file name, must not be null
     * @return true if the specified file is a gzip file name
     */
    public static boolean isGzipFilename(final String fileName) {
        checkNotNull(fileName);
        return GzipUtils.isCompressedFilename(fileName);
    }

    /**
     * Return true if the specified file is a gzip file.  Block compressed gzip (BGZF)
     * files are also gzip files, so <code>isBgzfFile(File)</code> should be called before
     * this method.
     *
     * @param file file, if any
     * @return true if the specified file is a gzip file
     */
    public static boolean isGzipFile(@Nullable final File file) {
        if (file == null) {
            return false;
        }
        return isGzipFilename(file.getName());
    }

    /**
     * Return true if the specified file is a gzip input stream.
     *
     * @since 1.3
     * @param inputStream input stream, must not be null
     * @return true if the specified file is a gzip input stream
     */
    public static boolean isGzipInputStream(final InputStream inputStream) {
        checkNotNull(inputStream);
        InputStream in = inputStream.markSupported() ? inputStream : new BufferedInputStream(inputStream);
        try {
            in.mark(2);
            return in.read() == 31 && in.read() == 139;
        } catch (IOException e) {
            return false;
        } finally {
            try {
                in.reset();
            } catch (IOException e) {
                // ignore
            }
        }
    }

    /**
     * Return true if the specified file is a bzip2 file name.
     *
     * @since 1.3
     * @param fileName file name, must not be null
     * @return true if the specified file is a bzip2 file name
     */
    public static boolean isBzip2Filename(final String fileName) {
        return BZip2Utils.isCompressedFilename(fileName);
    }

    /**
     * Return true if the specified file is a bzip2 file.
     *
     * @param file file, if any
     * @return true if the specified file is a bzip2 file
     */
    public static boolean isBzip2File(@Nullable final File file) {
        if (file == null) {
            return false;
        }
        return isBzip2Filename(file.getName());
    }

    /**
     * Return true if the specified file is a bzip2 input stream.
     *
     * @since 1.3
     * @param inputStream input stream, must not be null
     * @return true if the specified file is a bzip2 input stream
     */
    public static boolean isBzip2InputStream(final InputStream inputStream) {
        checkNotNull(inputStream);
        InputStream in = inputStream.markSupported() ? inputStream : new BufferedInputStream(inputStream);
        try {
            in.mark(3);
            return in.read() == 'B' && in.read() == 'Z' && in.read() == 'h';
        } catch (IOException e) {
            return false;
        } finally {
            try {
                in.reset();
            } catch (IOException e) {
                // ignore
            }
        }
    }
}