libopenms-dev 1.11.1-5 / usr / include / OpenMS / FORMAT / GzipIfstream.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: David Wojnar $
// $Authors: David Wojnar $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_GZIPIFSTREAM_H
#define OPENMS_FORMAT_GZIPIFSTREAM_H

#include <OpenMS/config.h>
#include <zlib.h>

namespace OpenMS
{
/**
    @brief Decompresses files which are compressed in the gzip format (*.gzip)
*/
  class OPENMS_DLLAPI GzipIfstream
  {
public:
    ///Default Constructor
    GzipIfstream();
    /// Detailed constructor with filename
    GzipIfstream(const char * filename);
    ///Destructor
    virtual ~GzipIfstream();

    /**
            @brief reads n bytes from the gzip compressed file into buffer s

            @param s will be filled with bytes
            @param n is the size of the buffer s
            @return the number of actually read bytes. If it is 0 the end of the file was reached and the stream is closed

            @exception Exception::ConversionError is thrown if decompression fails
            @exception Exception::IllegalArgument is thrwon if no file for decompression is given. This can happen even happen if a file was already open but read until the end.
    */
    size_t read(char * s, size_t n);

    /**
        @brief indicates whether the read function can be used safely

        @return true if end of file was reached. Otherwise false.
    */
    bool streamEnd() const;

    /**
        @brief returns whether a file is open.
    */
    bool isOpen() const;

    /**
        @brief opens a file for reading (decompression)
        @note any previous open files will be closed first!
    */
    void open(const char * filename);

    /**
        @brief closes current file.
    */
    void close();

    /*
        @brief updates crc32 check sum whether the buffer is corrupted
        @note if this function is used it has to be called after every call of function read
        @param s the buffer which will be checked
        @param n the size of the buffer
    *
    //void updateCRC32(const char* s,const size_t n);

    *
        @brief	checks if data is corrupted after crc32 was computed
        @note   it can only be used if updateCRC32 was called after every call of function read
        @return true if the buffer and hence the file is corrupted; no decompression is possible
    *
    //bool isCorrupted();

    //unsigned long Crc32_ComputeBuf( unsigned long inCrc32, const void *buf,
//                                 size_t bufLen );*/

protected:

    ///a gzFile object(void*) . Necessary for decompression
    gzFile gzfile_;
    ///counts the last read bufffer
    int     n_buffer_;
    ///saves the last returned error by the read function
    int     gzerror_;
    ///true if end of file is reached
    bool stream_at_end_;

    //needed if one wants to know whetther file is okay
    //unsigned long original_crc;
    //needed if one wants to know whetther file is okay
    //unsigned long crc;

    ///not implemented
    GzipIfstream(const GzipIfstream & bzip2);
    GzipIfstream & operator=(const GzipIfstream & bzip2);
  };

  inline bool GzipIfstream::isOpen() const
  {
    return gzfile_ != NULL;
  }

  inline bool GzipIfstream::streamEnd() const
  {
    return stream_at_end_;
  }

/*	inline bool GzipIfstream::isCorrupted()
    {
        std::cout<<"CRC"<<crc<<std::endl;
        return (crc != original_crc);
    }*/

} //namespace OpenMS
#endif //OPENMS_FORMAT_GZIPIFSTREAM_H