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/* $Id: bin-io.hpp,v 1.5 2008/04/28 16:38:45 rotmistr Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* =========================================================================
*
* Author: Kirill Rotmistrovsky
*
* ========================================================================= */
#ifndef EPCR_BIN_IO__HPP
#define EPCR_BIN_IO__HPP
#include <epcr/build_cfg.h>
#include <stdio.h>
#include <errno.h>
#include <stdexcept>
#include <cstring>
#include <string>
#include <vector>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(EPCR_SCOPE)
// This code is being used INTERNALLY by e-PCR library
enum EByteOrder { eHiEndian = 0x78563412, eLoEndian = 0x12345678 };
template <class T>
inline T BoCvt( T x, bool do_swap )
{
if( do_swap ) {
unsigned char * a = (unsigned char*) &x;
unsigned char * b = a + sizeof( x ) - 1;
for( ; a < b ; ++a, --b ) swap( *a, *b );
}
return x;
}
template<class T>
inline void Write( int fd, const T& t, unsigned sz = 1 )
{
if( (size_t) write( fd, &t, sz * sizeof(T) ) != sz * sizeof( T ) )
throw runtime_error( "write failed: " + string( std::strerror( errno ) ) );
}
template<>
inline void Write<string>( int fd, const string& t, unsigned )
{
Write( fd, Uint4( t.length() ) );
if( (size_t)write( fd, t.data(), t.length() ) != t.length() )
throw runtime_error( "write failed: " + string( strerror( errno ) ) );
}
template<class T>
inline void Write( FILE* f, const T& t, unsigned sz = 1 )
{
if( (size_t)fwrite( &t, sizeof( T ), sz, f ) != sz )
throw runtime_error( "write failed: " + string( strerror( errno ) ) );
}
template<>
inline void Write<string>(FILE* f, const string& t, unsigned )
{
Write( f, Uint4( t.length() ) );
if((size_t)fwrite( t.data(), 1, t.length(), f ) != t.length() )
throw runtime_error( "write failed: " + string( strerror( errno ) ) );
}
template<class T>
inline T Read( int fd )
{
T t( -1 );
if( (size_t)read( fd, &t, sizeof( T ) ) != sizeof( T ) && errno )
throw runtime_error( "read failed: " + string( strerror( errno ) ) );
return t;
}
template<>
inline string Read<string>( int fd )
{
vector<char> t( Read<Uint4>( fd ) );
if( t.size() && (size_t)read( fd, &t[0], t.size() ) != t.size() && errno )
throw runtime_error( "read failed: " + string( strerror( errno ) ) );
return string( &t[0], t.size() );
}
inline off64_t SeekAlign( int fd, unsigned page = 4096 )
{
off64_t c = lseek64( fd, 0, SEEK_CUR );
if( c % page ) c = lseek64( fd, page - c % page, SEEK_CUR );
return c;
}
inline off64_t SeekAlign( FILE* f, unsigned page = 4096 )
{
off64_t c = ftello64( f );
if( c % page ) {
fseeko64( f, page - c % page, SEEK_CUR );
c = ftello64( f );
}
return c;
}
END_SCOPE(EPCR_SCOPE)
END_NCBI_SCOPE
#endif
/*
* $Log: bin-io.hpp,v $
* Revision 1.5 2008/04/28 16:38:45 rotmistr
* Applied patch to build with gcc-4.3
*
* Revision 1.4 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.3 2004/04/01 05:57:52 rotmistr
* Compilable with borland C++
*
* Revision 1.2 2004/02/04 21:23:21 rotmistr
* - gcc-3.3.2 compatible
* - better postfiltering for reverse-e-PCR for discontiguos words
* - cgi added, that supports:
* -- contig to chromosome mapping
* -- simple mapviewer links
* -- unists links
* -- discontiguos words
*
* Revision 1.1.1.1 2003/12/23 18:17:27 rotmistr
* Package that includes e-PCR, reverse e-PCR, and sequence data preparation
* program for reverse e-PCR looks ready
*
*/
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