/usr/include/OpenMS/FORMAT/Bzip2Ifstream.h is in libopenms-dev 1.11.1-5.
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// 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_BZIP2IFSTREAM_H
#define OPENMS_FORMAT_BZIP2IFSTREAM_H
#include <OpenMS/config.h>
#include <bzlib.h>
#include <istream>
namespace OpenMS
{
/**
@brief Decompresses files which are compressed in the bzip2 format (*.bz2)
*/
class OPENMS_DLLAPI Bzip2Ifstream
{
public:
///Default Constructor
Bzip2Ifstream();
/// Detailed constructor with filename
Bzip2Ifstream(const char * filename);
///Destructor
virtual ~Bzip2Ifstream();
/**
@brief reads n bytes from the bzip2 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 thrown if no file for decompression is given. This can happen even happen if a file was already open but read until the end.
@note it is undefined what will happen if parameter n is bigger than the length of the buffer
*/
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();
protected:
/// pointer to a FILE object. Necessary for opening the file
FILE * file_;
/// a pointer to a BZFILE object. Necessary for decompression
BZFILE * bzip2file_;
///counts the last read buffer
size_t n_buffer_;
///saves the last returned error by the read function
int bzerror_;
///true if end of file is reached
bool stream_at_end_;
//not implemented
Bzip2Ifstream(const Bzip2Ifstream & bzip2);
Bzip2Ifstream & operator=(const Bzip2Ifstream & bzip2);
};
//return bzip2file???!!!!????
inline bool Bzip2Ifstream::isOpen() const
{
return file_ != NULL;
}
inline bool Bzip2Ifstream::streamEnd() const
{
return stream_at_end_;
}
} //namespace OpenMS
#endif //OPENMS_FORMAT_BZIP2IFSTREAM_H
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