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/* $Id: fast_seqio_read.cpp,v 1.6 2007/07/11 20:49:29 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
*
* ========================================================================= */
#include <epcr/fast_seqio.hpp>
#include <epcr/bin-io.hpp>
#include <stdexcept>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <string.h>
#include <errno.h>
USING_NCBI_SCOPE;
USING_SCOPE(EPCR_SCOPE);
CFastaMap::~CFastaMap() throw()
{
Close();
}
CFastaMap::CFastaMap():m_Fd(-1)
{}
CFastaMap::CFastaMap(const string& path):m_Fd(-1)
{
Open(path);
}
void CFastaMap::Open(const string& path)
{
if(m_Fd!=-1) Close();
int fd=open(path.c_str(),O_RDONLY|O_LARGEFILE);
if(fd==-1) throw runtime_error(path+": "+strerror(errno));
m_Fd=fd;
ReadPrologue();
ReadEpilogue();
}
void CFastaMap::Close()
{
if(m_Fd!=-1) {
m_Size.clear();
m_Offset.clear();
m_Defline.clear();
m_Ident.clear();
close(m_Fd);
}
}
void CFastaMap::ReadPrologue()
{
if( sizeof( Int2 ) != 2 ) throw logic_error( "Bad compile options: sizeof( Int2 ) != 2" );
if( sizeof( Int4 ) != 4 ) throw logic_error( "Bad compile options: sizeof( Int4 ) != 4" );
if( sizeof( Int8 ) != 8 ) throw logic_error( "Bad compile options: sizeof( Int8 ) != 8" );
char buff[128];
if(read(m_Fd,buff,8) != 8) throw runtime_error(strerror(errno));
if(memcmp(buff,"FASTAMAP",8))
throw runtime_error("FastaMap Signature is not found");
switch(Read<unsigned>(m_Fd)){
case eHiEndian: m_SwapBytes=true; break;
case eLoEndian: m_SwapBytes=false; break;
default: throw runtime_error("Bad format: wrong byteorder signature");
}
// if(m_SwapBytes) fprintf(stderr,"* FaMap: Swapping bytes\n");
short ver=BoCvt(Read<short>(m_Fd),m_SwapBytes);
short rev=BoCvt(Read<short>(m_Fd),m_SwapBytes);
if(ver!=1 && rev!=0) throw runtime_error("Wrong FastaMap file version");
}
void CFastaMap::ReadEpilogue()
{
/*TOffset filesize=*/lseek64(m_Fd,0,SEEK_END);
TOffset directory_pos=lseek64(m_Fd,-(TOffset)sizeof(TOffset),SEEK_CUR);
TOffset directory=BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
if(TOffset(directory+3*sizeof(TOffset)) != directory_pos)
throw runtime_error("Wrong directory record");
lseek64(m_Fd,directory,SEEK_SET);
TOffset epilogue=BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
TOffset ident =BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
TOffset defline =BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
lseek64(m_Fd,epilogue,SEEK_SET);
char buff[128];
if(read(m_Fd,buff,8)!=8) throw runtime_error("read failed");
if(memcmp(buff,"EPILOGUE",8))
throw runtime_error("epilogue is not found!");
unsigned sz=BoCvt(Read<unsigned>(m_Fd),m_SwapBytes);
m_Size.resize(sz);
m_Offset.resize(sz);
m_Defline.resize(sz);
m_Ident.resize(sz);
for(unsigned i=0; i<sz; ++i) {
m_Offset[i]=BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
}
for(unsigned i=0; i<sz; ++i) {
m_Size[i]=BoCvt(Read<TOffset>(m_Fd),m_SwapBytes);
}
lseek64(m_Fd,ident,SEEK_SET);
for(unsigned i=0; i<sz; ++i) m_Ident[i]=Read<string>(m_Fd);
lseek64(m_Fd,defline,SEEK_SET);
for(unsigned i=0; i<sz; ++i) m_Defline[i]=Read<string>(m_Fd);
}
CMmSequence::CMmSequence(CFastaMap& fm, unsigned i):
CIndexAssert(i,fm.GetCount()),
CMMap(fm.m_Size[i]+1,CMMap::fProtRead,CMMap::fMapPrivate,fm.m_Fd,fm.m_Offset[i])
{ if(m_Size>1) m_Size--; }
CMmSequence::~CMmSequence() throw ()
{ if(m_Size) ++m_Size; }
/*
* $Log: fast_seqio_read.cpp,v $
* Revision 1.6 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.5 2004/04/01 16:37:41 rotmistr
* Cleaned after adding windows capabilities
*
* Revision 1.4 2004/04/01 05:57:53 rotmistr
* Compilable with borland C++
*
* Revision 1.3 2004/02/04 21:23:22 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 1.2 2003/12/30 15:27:22 rotmistr
* Fixed bug with sequence end
*
* Revision 1.1.1.1 2003/12/23 18:17:28 rotmistr
* Package that includes e-PCR, reverse e-PCR, and sequence data preparation
* program for reverse e-PCR looks ready
*
*/
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