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/* $Id: fahash_create1.cpp,v 1.2 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 CFaIndexer1::AddSequence( const char * sequence, unsigned len, off64_t pos )
{
Uint8 exp_count = len * m_Hash.GetWordCount();
if( exp_count > m_Hi ) throw runtime_error( "Too large sequence" );
if( ( m_Count + exp_count ) > m_Hi ) DumpTables();
m_Seqlst.push_back( SSeqDesc( m_Fapath.size() - 1, pos ) );
m_Hash.Begin( sequence );
assert( m_Hash.GetWordCount() == m_Data.size() );
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
assert( m_Hash.GetTableSize( wd ) == m_Data[ wd ].size() );
for( unsigned u = 0; u < m_Hash.GetTableSize( wd ); ++u ) {
THashElement sid = ( m_Seqlst.size() - 1 ) | kHighBit;
if( m_Data[ wd ][ u ].size() &&
m_Data[ wd ][ u ][ m_Data[ wd ][ u ].size() - 1 ] & kHighBit )
// subst last sid
m_Data[ wd ][ u ][ m_Data[ wd ][ u ].size() - 1 ] = sid;
else {
m_Data[ wd ][ u ].push_back( sid );
m_Count++;
}
}
}
for( ; m_Hash.GetPosition() < len/*!m_Hash.End()*/; m_Hash.Next() ) {
if( m_Hash.GetPosition() % 100 == 0 && m_Cbk ) m_Cbk->CbkProgress( m_Hash.GetPosition(), len );
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
if( m_Hash.Good(wd) ) {
m_Data[ wd ][ m_Hash.GetValue(wd) ].push_back( THashElement( m_Hash.GetPosition() ) );
m_Count++;
}
}
}
if( m_Count > m_Lo ) DumpTables();
}
void CFaIndexer1::AttachFile( const string& path )
{
AttachHeaderDefault( path, FILE_VERSION );
}
void CFaIndexer1::DumpTables()
{
// INDICATE("DUMPING...");
if( m_Cbk ) m_Cbk->CbkDumpStart();
off64_t start_off = SeekAlign( m_File );
Uint4 pos = 0;
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
pos += m_Hash.GetTableSize(wd) * 2 * sizeof(Uint4);
}
Uint4 cur=pos;
long double avg=0, dev=0;
Uint8 cnt=0;
if( m_Flags & fSkipRepeatitive ) {
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
for( unsigned el = 0; el < m_Hash.GetTableSize( wd ); ++el, ++cnt ) {
avg += m_Data[ wd ][ el ].size();
dev += m_Data[ wd ][ el ].size() * m_Data[ wd ][ el ].size();
}
}
if( cnt ) {
avg /= cnt;
dev /= cnt;
}
dev -= avg;
}
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
for(unsigned el = 0; el < m_Hash.GetTableSize( wd ); ++el ) {
Write<Uint4>( m_File, pos );
if( m_Flags & fSkipRepeatitive && m_Data[wd][el].size() > avg + 3 * dev ) {
Write<Uint4>( m_File, ~0 );
} else {
Write<Uint4>( m_File, m_Data[wd][el].size() );
}
pos += m_Data[wd][el].size() * sizeof( THashElement );
}
}
for( unsigned wd = 0; wd < m_Hash.GetWordCount(); ++wd ) {
for( unsigned el = 0; el < m_Hash.GetTableSize( wd ); ++el ) {
if( m_Cbk ) m_Cbk->CbkDumpProgress( cur, pos );
if( m_Flags & fSkipRepeatitive && m_Data[wd][el].size() > avg + 3 * dev ) {
} else {
if( fwrite( &m_Data[wd][el][0], sizeof(THashElement),
m_Data[wd][el].size(), m_File ) !=
m_Data[wd][el].size() ) SYSERROR( string( "Block write" ) );
cur += m_Data[wd][el].size() * sizeof(THashElement);
}
}
}
off64_t end_off = ftello64(m_File);
if( m_Cbk ) m_Cbk->CbkDumpEnd();
// fprintf(stderr,
// "DUMP: start offset = %lld\n"
// "DUMP: end offset = %lld\n"
// "DUMP: distance = %lld\n"
// "DUMP: pos calculated = %u\n"
// "DUMP: pos accumulated = %u\n",
// start_off, end_off, end_off-start_off,pos, cur);
if( end_off - start_off != pos || pos != cur )
throw runtime_error( "File format error!" );
if( m_Cbk ) m_Cbk->CbkResetStart();
m_Tabloc.push_back( make_pair( start_off, end_off - start_off ) );
// INDICATE("RESETTING...");
for( unsigned i = 0; i < m_Hash.GetWordCount(); ++i ) {
for( unsigned j = 0; j < m_Hash.GetTableSize(i); ++j ) {
m_Data[i][j].clear();
}
}
m_Count = 0;
// SetHash(m_Hash);
if( m_Cbk ) m_Cbk->CbkResetEnd();
// INDICATE("DUMPING...DONE");
}
void CFaIndexer1::SetHash( const CHashSet& hs )
{
// for(unsigned i=0; i<m_data.size();++i) {
// for(unsigned j=0; j<m_data[i].size();++j) {
// m_data[i][j].clear();
// }
// m_data[i].clear();
// }
m_Data.clear();
m_Data.resize(hs.GetWordCount());
for( unsigned i = 0; i < hs.GetWordCount(); ++i ) {
// m_data[i].clear();
m_Data[i].resize( hs.GetTableSize( i ) );
// for(unsigned j=0; j<m_data[i].size();++j) {
// m_data[i][j].clear();
// }
}
m_Hash = hs;
m_Count = 0;
}
/*
* $Log: fahash_create1.cpp,v $
* Revision 1.2 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.1 2004/05/27 20:35:46 rotmistr
* Version 2.1.0 with appropriate changes (see Changes) is ready for tests.
*
*/
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