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/* $Id: fahash_create.cpp,v 1.14 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/fahash.hpp>
#include <epcr/bin-io.hpp>
#include "fahash_defines.h"
#include <stdexcept>
#include <string.h>
#include <errno.h>
#include <assert.h>
USING_NCBI_SCOPE;
USING_SCOPE(EPCR_SCOPE);
#include "fahash_internal.hpp"
////////////////////////////////////////////////////////////////////////
void AFaIndexerBase::AddFile( const string& path )
{
CFastaMap fmap( path );
m_Fapath.push_back( SFileDesc( 0, path ) );
if( m_Cbk ) m_Cbk->CbkFile( path.c_str() );
for( unsigned i = 0; i < fmap.SequenceCount(); ++i ) {
if( m_Cbk ) m_Cbk->CbkSequence( fmap.GetIdent(i).c_str() );
CMmSequence seq( fmap, i );
AddSequence( seq.GetData(), seq.GetSize(), i );
}
}
void AFaIndexerBase::AttachHeaderDefault( const string& path, Uint4 version )
{
m_File = fopen64( path.c_str(), "w" FILE_BINARY );
if( m_File == 0 ) SYSERROR( path );
setvbuf( m_File, 0, _IOFBF, 1024 * 1024 );
if( fwrite( SIGNATURE, 1, 16, m_File ) != 16 ) SYSERROR( path ); // signature
Write( m_File, Uint4( version ) ); // version
Write( m_File, Uint4( BYTE_ORDER_WORD ) ); // architecture
Write( m_File, Uint4( HEADER_SIZE ) ) ; // header size
Write( m_File, Uint4( m_Hash.GetWordSize() ) ); // word size
Write( m_File, Uint4( m_Hash.GetWordCount() ) ); // period
fseeko64( m_File, HEADER_SIZE, SEEK_SET );
m_Count = 0;
}
void AFaIndexerBase::Finish()
{
DumpTables();
off64_t seq_tbl = SeekAlign( m_File );
Write( m_File, Uint4( m_Seqlst.size() ) );
for( unsigned i = 0; i < m_Seqlst.size(); ++i ) {
Write( m_File, m_Seqlst[i].fid );
Write( m_File, m_Seqlst[i].data );
}
off64_t fil_tbl = SeekAlign( m_File );
Write( m_File, Uint4( m_Fapath.size() ) );
for( unsigned i = 0; i < m_Fapath.size(); ++i ) {
Write( m_File, m_Fapath[i].flags );
Write( m_File, m_Fapath[i].path );
}
off64_t off_tbl = SeekAlign( m_File );
Write( m_File, Uint4( m_Tabloc.size() ) );
for( unsigned i = 0; i < m_Tabloc.size(); ++i ) {
Write( m_File, m_Tabloc[i].first );
Write( m_File, m_Tabloc[i].second );
}
off64_t endoffile = SeekAlign( m_File );
Write( m_File, seq_tbl );
Write( m_File, fil_tbl );
Write( m_File, off_tbl );
Write( m_File, endoffile );
fclose( m_File );
m_File = 0;
}
/*
* $Log: fahash_create.cpp,v $
* Revision 1.14 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.13 2004/05/27 20:35:46 rotmistr
* Version 2.1.0 with appropriate changes (see Changes) is ready for tests.
*
* Revision 1.12 2004/04/27 00:01:54 rotmistr
* Second version of reverse hash file started
*
* Revision 1.11 2004/04/06 04:53:17 rotmistr
* All is compileable with BCC5.5 and runnable on WIndows
*
* Revision 1.10 2004/04/01 05:57:52 rotmistr
* Compilable with borland C++
*
* Revision 1.9 2004/03/07 06:35:59 rotmistr
* Many bugfixes and optimisations -- cgi is to go to production
*
* Revision 1.8 2004/02/18 05:44:25 rotmistr
* Changes in CGI: sort order, separate misalignments for l and r primers, reload button
*
* Revision 1.7 2004/02/12 21:38:20 rotmistr
* Fixed typo in seqcmp
* Optimized and fixed lookup
* Better look for reverse.cgi
*
* Revision 1.6 2004/02/11 04:34:55 rotmistr
* Optimised lookup speed and memory usage
* Fixed bug with end of sequence in stsmatch
* Changing CGI look
*
* Revision 1.5 2004/02/05 23:41:21 rotmistr
* Better reload, fixed margin report in commandline, unists tab in CGI form.
*
* Revision 1.4 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 1.3 2004/01/07 16:57:42 rotmistr
* Fragment size is now configurable.
*
* 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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