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/* $Id: fast_seqio_write.cpp,v 1.5 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 <string.h>
#include <errno.h>
USING_NCBI_SCOPE;
USING_SCOPE(EPCR_SCOPE);
void CFastaMapPrepare::Open( const string& fname )
{
if( IsOpen() ) Close();
FILE * f = fopen64( fname.c_str(), "w"FILE_BINARY );
if( f == 0 ) throw runtime_error( fname + ": " + strerror( errno ) );
setvbuf( f, 0, _IOFBF, 16192 );
m_Fptr = f;
WritePrologue();
}
void CFastaMapPrepare::Close()
{
if( m_Fptr ) {
WriteEpilogue();
m_Offset.clear();
m_Size.clear();
m_Defline.clear();
m_Ident.clear();
fclose( (FILE*)m_Fptr );
m_Fptr = 0;
}
}
void CFastaMapPrepare::AddFile( const string& fname, const char * cvtTable )
{
if( IsOpen() ) {
CFastaReader reader( fname );
if( cvtTable ) reader.SetCvtTable( cvtTable );
reader.ReadFile( this );
}
}
void CFastaMapPrepare::WritePrologue()
{
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" );
if( fwrite( "FASTAMAP", 1, 8, (FILE*)m_Fptr ) != 8 )
throw runtime_error( strerror( errno ) +
string(" while writing signature") );
Write( (FILE*)m_Fptr, Uint4( eLoEndian ) );
Write( (FILE*)m_Fptr, Uint2( 1 ));
Write( (FILE*)m_Fptr, Uint2( 0 ));
Write( (FILE*)m_Fptr, Uint4( 20 )); // header size
}
void CFastaMapPrepare::WriteEpilogue()
{
TOffset epilogue = SeekAlign( (FILE*)m_Fptr );
fwrite( "EPILOGUE", 1, 8, (FILE*)m_Fptr );
Write( (FILE*)m_Fptr, Uint4( m_Offset.size() ) );
Write( (FILE*)m_Fptr, m_Offset[0], m_Offset.size() );
Write( (FILE*)m_Fptr, m_Size[0], m_Size.size() );
TOffset ident = ftello64( (FILE*)m_Fptr );
for( unsigned i = 0; i < m_Ident.size(); ++i )
Write( (FILE*)m_Fptr, m_Ident[i] );
TOffset defline = ftello64( (FILE*)m_Fptr );
for( unsigned i = 0; i < m_Defline.size(); ++i )
Write( (FILE*)m_Fptr, m_Defline[i] );
TOffset directory = SeekAlign( (FILE*)m_Fptr );
Write( (FILE*)m_Fptr, epilogue );
Write( (FILE*)m_Fptr, ident );
Write( (FILE*)m_Fptr, defline );
Write( (FILE*)m_Fptr, directory );
}
void CFastaMapPrepare::CbkDefline( const char * defline, unsigned length )
{
m_Defline.back().assign( defline, length );
}
void CFastaMapPrepare::CbkIdent( const char * ident, unsigned length )
{
m_Ident.back().assign( ident, length );
}
void CFastaMapPrepare::CbkSeqline( const char * seqline, unsigned length )
{
Write( (FILE*)m_Fptr, *seqline, length );
m_Size.back() += length;
}
void CFastaMapPrepare::CbkEntryBegin()
{
m_Defline.push_back( string("") );
m_Ident.push_back( string("") );
m_Size.push_back( 0 );
m_Offset.push_back( SeekAlign( (FILE*)m_Fptr, 2 ) );
}
void CFastaMapPrepare::CbkEntryEnd()
{
Write( (FILE*)m_Fptr, char(0) );
}
void CFastaMapPrepare::CbkFileBegin()
{}
void CFastaMapPrepare::CbkFileEnd()
{}
/*
* $Log: fast_seqio_write.cpp,v $
* Revision 1.5 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.4 2004/04/06 04:53:17 rotmistr
* All is compileable with BCC5.5 and runnable on WIndows
*
* 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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