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|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
// This file contains the DbFinder class.
// ==========================================================================
#ifndef SANDBOX_ESIRAGUSA_APPS_SEARCHJOIN_DBFINDER_H_
#define SANDBOX_ESIRAGUSA_APPS_SEARCHJOIN_DBFINDER_H_
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/index.h>
#include <seqan/parallel.h>
#include "verifier.h"
using namespace seqan;
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Tag Online
// ----------------------------------------------------------------------------
struct Online_;
typedef Tag<Online_> Online;
// ----------------------------------------------------------------------------
// Tag Top
// ----------------------------------------------------------------------------
struct Top_;
typedef Tag<Top_> Top;
// ----------------------------------------------------------------------------
// Tag Bottom
// ----------------------------------------------------------------------------
struct Bottom_;
typedef Tag<Bottom_> Bottom;
// ----------------------------------------------------------------------------
// Class DbFinder
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec = void>
struct DbFinder
{
typedef Db<TText> TDb;
typedef Db<TText, TDbQuerySpec> TDbQuery;
typedef DbIndex<TIndex> TDbIndex;
typedef DbIndex<TIndex, Query> TDbQueryIndex;
typedef Verifier<TText, TDbQuerySpec> TVerifier;
typedef typename Size<TText>::Type TTextSize;
TDb /* const */ & db;
TDbIndex dbIndex;
Holder<TDbQuery> query;
TDbQueryIndex queryIndex;
TDelegate & delegate;
TVerifier verifier;
TTextSize minSeedLength;
DbFinder(TDb /* const */ & db, TDelegate & delegate) :
db(db),
dbIndex(),
delegate(delegate),
verifier(db),
minSeedLength(0)
{}
template <typename TFinder>
void operator()(TFinder const & finder)
{
onFind(*this, finder);
}
};
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
struct DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Parallel>
{
typedef Db<TText> TDb;
typedef Db<TText, TDbQuerySpec> TDbQuery;
typedef DbIndex<TIndex> TDbIndex;
typedef DbIndex<TIndex, Query> TDbQueryIndex;
typedef Verifier<TText, TDbQuerySpec> TVerifier;
typedef typename Size<TText>::Type TTextSize;
typedef typename Size<TIndex>::Type TDepth;
typedef Backtracking<HammingDistance, Bottom> TBacktrackingExt;
typedef Backtracking<EditDistance, Bottom> TBacktrackingApx;
typedef Finder_<TIndex, TIndex, TBacktrackingExt> TFinderExt;
typedef Finder_<TIndex, TIndex, TBacktrackingApx> TFinderApx;
typedef String<TFinderApx> TFindersApx;
typedef String<TFinderExt> TFindersExt;
TDb /* const */ & db;
TDbIndex dbIndex;
Holder<TDbQuery> query;
TDbQueryIndex queryIndex;
TDelegate & delegate;
TVerifier verifier;
TTextSize minSeedLength;
TDepth parallelDepth;
TFindersExt findersExt;
TFindersApx findersApx;
DbFinder(TDb /* const */ & db, TDelegate & delegate) :
db(db),
dbIndex(),
delegate(delegate),
verifier(db),
minSeedLength(0),
parallelDepth(2)
{}
template <typename TFinder>
void operator()(TFinder const & finder)
{
onFind(*this, finder);
}
};
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
struct DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Online>
{
typedef Db<TText> TDb;
typedef Db<TText, TDbQuerySpec> TDbQuery;
typedef Verifier<TText, TDbQuerySpec> TVerifier;
typedef typename Size<TText>::Type TTextSize;
TDb /* const */ & db;
Holder<TDbQuery> query;
TDelegate & delegate;
TVerifier verifier;
DbFinder(TDb /* const */ & db, TDelegate & delegate) :
db(db),
delegate(delegate),
verifier(db)
{}
};
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
struct DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact>
{
typedef Db<TText> TDb;
typedef Db<TText, TDbQuerySpec> TDbQuery;
typedef DbIndex<TIndex> TDbIndex;
TDb /* const */ & db;
TDbIndex dbIndex;
TDelegate & delegate;
DbFinder(TDb /* const */ & db, TDelegate & delegate) :
db(db),
delegate(delegate)
{}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction PatternIterator_
// ----------------------------------------------------------------------------
namespace seqan {
template <typename TDistance, typename TSpec>
struct PatternIterator_<TDbDnaSaSmall, TDbDnaSaSmall, Backtracking<TDistance, TSpec> >
{
typedef typename Iterator<TDbDnaSaSmall, TopDown<Truncated<Preorder> > >::Type Type;
};
template <typename TDistance, typename TSpec>
struct PatternIterator_<TDbGeoSaSmall, TDbGeoSaSmall, Backtracking<TDistance, TSpec> >
{
typedef typename Iterator<TDbGeoSaSmall, TopDown<Truncated<Preorder> > >::Type Type;
};
template <typename TDistance, typename TSpec>
struct PatternIterator_<TDbDnaSaHuge, TDbDnaSaHuge, Backtracking<TDistance, TSpec> >
{
typedef typename Iterator<TDbDnaSaHuge, TopDown<Truncated<Preorder> > >::Type Type;
};
template <typename TDistance, typename TSpec>
struct PatternIterator_<TDbGeoSaHuge, TDbGeoSaHuge, Backtracking<TDistance, TSpec> >
{
typedef typename Iterator<TDbGeoSaHuge, TopDown<Truncated<Preorder> > >::Type Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _inTerminalState() [Finder_<Backtracking>]
// ----------------------------------------------------------------------------
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, Top> > const & finder,
StageFinal_ const & /* tag */)
{
return _inActiveState(finder, StageFinal_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_inTerminalState(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & finder,
StageLower_ const & /* tag */)
{
return _inActiveState(finder, StageLower_());
}
// ----------------------------------------------------------------------------
// Function _moveToNextStage() [Finder_<Backtracking>]
// ----------------------------------------------------------------------------
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_moveToNextStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & /* finder */,
StageLower_ const & /* tag */)
{
return false;
}
// ----------------------------------------------------------------------------
// Function _stayInCurrentStage() [Finder_<Backtracking>]
// ----------------------------------------------------------------------------
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, Top> > const & finder,
StageInitial_ const & /* tag */)
{
return !_moveToNextStage(finder, StageInitial_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<HammingDistance, Top> > const & finder,
StageExact_ const & /* tag */)
{
return !_moveToNextStage(finder, StageExact_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & finder,
StageInitial_ const & /* tag */)
{
return !_moveToNextStage(finder, StageInitial_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & finder,
StageUpper_ const & /* tag */)
{
return !_moveToNextStage(finder, StageUpper_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & finder,
StageDiagonal_ const & /* tag */)
{
return !_moveToNextStage(finder, StageDiagonal_());
}
template <typename TText, typename TTextIndexSpec, typename TPattern, typename TPatternIndexSpec>
inline bool
_stayInCurrentStage(Finder_<Index<TText, TTextIndexSpec>, Index<TPattern, TPatternIndexSpec>, Backtracking<EditDistance, Top> > const & /* finder */,
StageLower_ const & /* tag */)
{
return true;
}
} // namespace seqan
// ----------------------------------------------------------------------------
// Function setMinSeedLength() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec, typename TSeedLength>
void setMinSeedLength(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> & dbFinder, TSeedLength minSeedLength)
{
dbFinder.minSeedLength = minSeedLength;
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSeedLength>
void setMinSeedLength(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Online> & /* dbFinder */, TSeedLength /* minSeedLength */)
{}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSeedLength>
void setMinSeedLength(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact> & /* dbFinder */, TSeedLength /* minSeedLength */)
{}
// ----------------------------------------------------------------------------
// Function index() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec>
void index(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> & dbFinder)
{
// Build database index.
build(dbFinder.dbIndex, dbFinder.db, Default());
// Free some memory if we don't need a q-gram directory
clear(dbFinder.dbIndex.dir);
shrinkToFit(dbFinder.dbIndex.dir);
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void index(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact> & dbFinder)
{
// Build database index.
build(dbFinder.dbIndex, dbFinder.db, seqan::Exact());
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void index(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Online> & /* dbFinder */)
{}
// ----------------------------------------------------------------------------
// Function prepare() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec>
void prepare(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> & dbFinder, Db<TText, TDbQuerySpec> & query)
{
// Set query.
setValue(dbFinder.query, query);
setValue(dbFinder.verifier.query, query);
// Build query index.
buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength);
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void prepare(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Online> & dbFinder, Db<TText, TDbQuerySpec> & query)
{
// Set query.
setValue(dbFinder.query, query);
setValue(dbFinder.verifier.query, query);
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void prepare(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact> &, Db<TText, TDbQuerySpec> &)
{}
// ----------------------------------------------------------------------------
// Function onFind() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec, typename TBacktracking>
inline void
onFind(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> & dbFinder,
Finder_<TIndex, TIndex, TBacktracking> const & finder)
{
typedef typename TextIterator_<TIndex, TIndex, TBacktracking>::Type TTextIterator;
typedef typename PatternIterator_<TIndex, TIndex, TBacktracking>::Type TPatternIterator;
typedef typename Size<TIndex>::Type TSize;
//typedef typename Size<TText>::Type TErrors;
typedef typename Fibre<TIndex, FibreSA>::Type const TSAFibre;
typedef typename Infix<TSAFibre>::Type TOccurrences;
TTextIterator const & textIt = back(finder.textStack);
TPatternIterator const & patternIt = back(finder.patternStack);
TOccurrences textOccurrences = getOccurrences(textIt);
TOccurrences patternOccurrences = getEmptyEdges(patternIt);
TSize textOccurrencesCount = length(textOccurrences);
TSize patternOccurrencesCount = length(patternOccurrences);
for (TSize i = 0; i < textOccurrencesCount; ++i)
for (TSize j = 0; j < patternOccurrencesCount; ++j)
{
TSize dbId1 = getSeqNo(textOccurrences[i]);
TSize dbId2 = getSeqNo(patternOccurrences[j]);
TSize pos1 = getSeqOffset(textOccurrences[i]);
TSize pos2 = getSeqOffset(patternOccurrences[j]);
if (_validHit(dbFinder, dbId1, dbId2, pos1, pos2))
dbFinder.verifier(dbId1, dbId2, dbFinder.delegate);
}
}
// ----------------------------------------------------------------------------
// Function _validHit() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec>
inline bool
_validHit(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> const & dbFinder,
typename Size<TIndex>::Type dbId1,
typename Size<TIndex>::Type dbId2,
typename Size<TIndex>::Type pos1,
typename Size<TIndex>::Type pos2)
{
if (dbId1 >= dbId2)
return false;
int maxErrors = getErrors(value(dbFinder.query), dbId2);
int dbLen1 = length(dbFinder.db.text[dbId1]);
int dbLen2 = length(dbFinder.db.text[dbId2]);
// Check maximal length difference.
if (dbLen1 + maxErrors < dbLen2 || dbLen2 + maxErrors < dbLen1)
return false;
// Check band according to Lemma 1.
int diag = pos1 - pos2;
int leftDiag = -((dbLen2 - dbLen1 + maxErrors) / 2);
int rightDiag = (dbLen1 - dbLen2 + maxErrors) / 2;
return (leftDiag <= diag && diag <= rightDiag);
}
template <typename TText, typename TIndex, typename TDelegate, typename TSpec>
inline bool
_validHit(DbFinder<TText, TIndex, Query, TDelegate, TSpec> const & dbFinder,
typename Size<TIndex>::Type dbId1,
typename Size<TIndex>::Type dbId2,
typename Size<TIndex>::Type pos1,
typename Size<TIndex>::Type pos2)
{
int maxErrors = getErrors(value(dbFinder.query), dbId2);
int dbLen1 = length(dbFinder.db.text[dbId1]);
int dbLen2 = length(value(dbFinder.query).text[dbId2]);
// Check maximal length difference.
if (dbLen1 + maxErrors < dbLen2 || dbLen2 + maxErrors < dbLen1)
return false;
// Check band according to Lemma 1.
int diag = pos1 - pos2;
int leftDiag = -((dbLen2 - dbLen1 + maxErrors) / 2);
int rightDiag = (dbLen1 - dbLen2 + maxErrors) / 2;
if (!(leftDiag <= diag && diag <= rightDiag))
return false;
return true;
}
// ----------------------------------------------------------------------------
// Function onFind() [DbFinder<Parallel>]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
inline void
onFind(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Parallel> & dbFinder,
Finder_<TIndex, TIndex, Backtracking<EditDistance, Top> > const & finder)
{
typedef Backtracking<EditDistance, Bottom> TBacktracking;
typedef Finder_<TIndex, TIndex, TBacktracking> TFinder;
TFinder finderBottom;
_setScoreThreshold(finderBottom, finder.maxScore);
appendValue(finderBottom.textStack, back(finder.textStack));
appendValue(finderBottom.patternStack, back(finder.patternStack));
appendValue(finderBottom.scoreStack, back(finder.scoreStack));
back(finderBottom.patternStack).depth = dbFinder.queryIndex.seedLength;
appendValue(dbFinder.findersApx, finderBottom);
}
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
inline void
onFind(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Parallel> & dbFinder,
Finder_<TIndex, TIndex, Backtracking<HammingDistance, Top> > const & finder)
{
typedef Backtracking<HammingDistance, Bottom> TBacktracking;
typedef Finder_<TIndex, TIndex, TBacktracking> TFinder;
TFinder finderBottom;
_setScoreThreshold(finderBottom, finder.maxScore);
appendValue(finderBottom.textStack, back(finder.textStack));
appendValue(finderBottom.patternStack, back(finder.patternStack));
appendValue(finderBottom.scoreStack, back(finder.scoreStack));
back(finderBottom.patternStack).depth = dbFinder.queryIndex.seedLength;
appendValue(dbFinder.findersExt, finderBottom);
}
// ----------------------------------------------------------------------------
// Function execute() [DbFinder]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate, typename TSpec>
void execute(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, TSpec> & dbFinder)
{
typedef Backtracking<EditDistance> TBacktrackingApx;
typedef Backtracking<HammingDistance> TBacktrackingExt;
typedef Finder_<TIndex, TIndex, TBacktrackingApx> TFinderApx;
typedef Finder_<TIndex, TIndex, TBacktrackingExt> TFinderExt;
typedef typename TextIterator_<TIndex, TIndex, TBacktrackingApx>::Type TTextIterator;
typedef typename PatternIterator_<TIndex, TIndex, TBacktrackingApx>::Type TPatternIterator;
// Instantiate a finder.
TFinderApx finderApx;
TFinderExt finderExt;
unsigned seedSetsCount = length(dbFinder.queryIndex.errors);
unsigned seedSet = 0;
// Find exactly query index in database index.
if (seedSetsCount > 0 && dbFinder.queryIndex.errors[seedSet] == 0)
{
TTextIterator textIt(dbFinder.dbIndex.index);
TPatternIterator patternIt(dbFinder.queryIndex.index[seedSet]);
patternIt.depth = dbFinder.queryIndex.seedLength;
_setScoreThreshold(finderExt, 0);
_initState(finderExt, textIt, patternIt);
_find(finderExt, dbFinder, StageInitial_());
clear(finderExt);
seedSet++;
}
// Find approximately query index in database index.
for (; seedSet < seedSetsCount; ++seedSet)
{
unsigned seedErrors = dbFinder.queryIndex.errors[seedSet];
TTextIterator textIt(dbFinder.dbIndex.index);
TPatternIterator patternIt(dbFinder.queryIndex.index[seedSet]);
patternIt.depth = dbFinder.queryIndex.seedLength;
_setScoreThreshold(finderApx, seedErrors);
_initState(finderApx, textIt, patternIt);
_find(finderApx, dbFinder, StageInitial_());
clear(finderApx);
}
}
// ----------------------------------------------------------------------------
// Function execute() [DbFinder<Parallel>]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void execute(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Parallel> & dbFinder)
{
typedef Backtracking<EditDistance, Top> TBacktrackingApx;
typedef Backtracking<HammingDistance, Top> TBacktrackingExt;
typedef Backtracking<EditDistance, Bottom> TBacktrackingApxBottom;
typedef Backtracking<HammingDistance, Bottom> TBacktrackingExtBottom;
typedef Finder_<TIndex, TIndex, TBacktrackingApx> TFinderApx;
typedef Finder_<TIndex, TIndex, TBacktrackingExt> TFinderExt;
typedef Finder_<TIndex, TIndex, TBacktrackingApxBottom> TFinderApxBottom;
typedef Finder_<TIndex, TIndex, TBacktrackingExtBottom> TFinderExtBottom;
typedef typename TextIterator_<TIndex, TIndex, TBacktrackingApx>::Type TTextIterator;
typedef typename PatternIterator_<TIndex, TIndex, TBacktrackingApx>::Type TPatternIterator;
// Instantiate a finder.
TFinderApx finderApx;
TFinderExt finderExt;
unsigned seedSetsCount = length(dbFinder.queryIndex.errors);
unsigned seedSet = 0;
// Find exactly query index in database index.
if (seedSetsCount > 0 && dbFinder.queryIndex.errors[seedSet] == 0)
{
TTextIterator textIt(dbFinder.dbIndex.index);
TPatternIterator patternIt(dbFinder.queryIndex.index[seedSet]);
patternIt.depth = _min(dbFinder.queryIndex.seedLength, dbFinder.parallelDepth);
_setScoreThreshold(finderExt, 0);
_initState(finderExt, textIt, patternIt);
_find(finderExt, dbFinder, StageInitial_());
clear(finderExt);
seedSet++;
}
// Find approximately query index in database index.
for (; seedSet < seedSetsCount; ++seedSet)
{
unsigned seedErrors = dbFinder.queryIndex.errors[seedSet];
TTextIterator textIt(dbFinder.dbIndex.index);
TPatternIterator patternIt(dbFinder.queryIndex.index[seedSet]);
patternIt.depth = _min(dbFinder.queryIndex.seedLength, dbFinder.parallelDepth);
_setScoreThreshold(finderApx, seedErrors);
_initState(finderApx, textIt, patternIt);
_find(finderApx, dbFinder, StageInitial_());
clear(finderApx);
}
unsigned findersExtCount = length(dbFinder.findersExt);
unsigned findersApxCount = length(dbFinder.findersApx);
std::cout << "Ext jobs count:\t\t\t\t" << findersExtCount << std::endl;
std::cout << "Apx jobs count:\t\t\t\t" << findersApxCount << std::endl;
SEQAN_OMP_PRAGMA(parallel for schedule(dynamic))
for (int finderExt = 0; finderExt < (int)findersExtCount; ++finderExt)
{
TFinderExtBottom & finderBottom = dbFinder.findersExt[finderExt];
_find(finderBottom, dbFinder, StageInitial_());
clear(finderBottom);
}
SEQAN_OMP_PRAGMA(parallel for schedule(dynamic))
for (int finderApx = 0; finderApx < (int)findersApxCount; ++finderApx)
{
TFinderApxBottom & finderBottom = dbFinder.findersApx[finderApx];
_find(finderBottom, dbFinder, StageInitial_());
clear(finderBottom);
}
}
// ----------------------------------------------------------------------------
// Function execute() [DbFinder<Exact>]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void execute(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact> & dbFinder)
{
typedef typename Fibre<TIndex, FibreSA>::Type const TSA;
typedef typename Size<TIndex>::Type TSize;
typedef typename Value<TText const>::Type TString;
typedef typename Iterator<TString const, Standard>::Type TStringIter;
TText const &text = dbFinder.db.text;
TSA const &sa = indexSA(dbFinder.dbIndex.index);
String<TSize> &dir = dbFinder.dbIndex.dir;
TSize sortedPrefix = dbFinder.dbIndex.sortedPrefix;
SEQAN_OMP_PRAGMA(parallel for schedule(dynamic,1))
for (int i = 1; i < (int)length(dir); ++i)
{
size_t bktBegin = dir[i - 1];
size_t bktEnd = dir[i];
// We need at least 2 suffixes.
if (bktBegin + 2 > bktEnd)
continue;
TSize runBegin = bktBegin;
TSize seqNo1 = getSeqNo(sa[runBegin]);
for (size_t i = bktBegin + 1; i < bktEnd; ++i)
{
TSize seqNo2 = getSeqNo(sa[i]);
SEQAN_ASSERT_EQ(getSeqOffset(sa[i]), 0u);
if (length(text[seqNo1]) == length(text[seqNo2]))
{
TStringIter it1Beg = begin(text[seqNo1], Standard()) + sortedPrefix - 1;
TStringIter it1End = end(text[seqNo1], Standard()) - 1;
TStringIter it2End = end(text[seqNo2], Standard()) - 1;
for (; it1End != it1Beg; --it1End, --it2End)
{
if (*it1End != *it2End)
break;
}
if (it1End == it1Beg)
continue;
}
if (runBegin + 1 < i)
{
for (unsigned j = runBegin; j < i; ++j)
for (unsigned k = j + 1; k < i; ++k)
dbFinder.delegate(getSeqNo(sa[j]), getSeqNo(sa[k]));
}
runBegin = i;
seqNo1 = getSeqNo(sa[runBegin]);
}
if (runBegin + 1 < bktEnd)
{
for (unsigned j = runBegin; j < bktEnd; ++j)
for (unsigned k = j + 1; k < bktEnd; ++k)
dbFinder.delegate(getSeqNo(sa[j]), getSeqNo(sa[k]));
}
}
}
// NOTE(esiragusa): This is computing exact join using a dfs traversal.
//namespace seqan
//{
// struct SAInfix;
//
// template <typename TText>
// struct Fibre<Index<TText, IndexSa<SAInfix> >, FibreSA>
// {
// typedef Segment<typename Fibre<Index<TText, IndexSa<> >, FibreSA>::Type const, InfixSegment> Type;
// };
//
//}
//
//template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
//void execute(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Exact> & dbFinder)
//{
// typedef Index<TText, IndexSa<SAInfix> > TSAInfixIndex;
// typedef typename Iterator<TSAInfixIndex, TopDown<ParentLinks<> > >::Type TIter;
//
// TText const &text = dbFinder.db.text;
// TSA const &sa = indexSA(dbFinder.dbIndex.index);
// String<TSize> &dir = dbFinder.dbIndex.dir;
// TSize sortedPrefix = dbFinder.dbIndex.sortedPrefix;
//
// TSAInfixIndex subIndex(text);
// indexSA(subIndex) = infix(sa, bktBegin, bktEnd);
//
// TIter iter(subIndex);
// value(iter).range.i1 = 0;
// _setSizeInval(value(iter).range.i2);
// value(iter).parentRight = value(iter).range.i2;
// value(iter).repLen = sortedPrefix;
// value(iter).lastChar = suffix(text, sa[bktBegin])[sortedPrefix - 1];
//
// while (!atEnd(iter))
// {
// if (isRightTerminal(iter))
// {
// typename Infix<TSA>::Type emptyEdges = getEmptyEdges(iter);
// TSize len = length(emptyEdges);
// if (len < 2)
// continue;
// std::cout << len << '\t' << representative(iter) << std::endl;
// for (unsigned i = 0; i < len; ++i)
// for (unsigned j = i + 1; j < len; ++j)
// dbFinder.delegate(getSeqNo(sa[j]), getSeqNo(sa[k]));
// }
// goNext(iter);
// }
//}
// ----------------------------------------------------------------------------
// Function execute() [DbFinder<Online>]
// ----------------------------------------------------------------------------
template <typename TText, typename TIndex, typename TDbQuerySpec, typename TDelegate>
void execute(DbFinder<TText, TIndex, TDbQuerySpec, TDelegate, Online> & dbFinder)
{
typedef Db<TText> TDb;
typedef typename Size<TDb>::Type TDbSize;
typedef typename MakeSigned<TDbSize>::Type TDbSSize;
TDbSSize dbSize = (TDbSSize)length(dbFinder.db.text) - 1;
TDbSSize dbQuerySize = length(value(dbFinder.query).text);
SEQAN_OMP_PRAGMA(parallel for schedule(dynamic))
for (TDbSSize dbId1 = 0; dbId1 < dbSize; ++dbId1)
for (TDbSSize dbId2 = dbId1 + 1; dbId2 < dbQuerySize; ++dbId2)
dbFinder.verifier(dbId1, dbId2, dbFinder.delegate);
}
template <typename TText, typename TIndex, typename TDelegate>
void execute(DbFinder<TText, TIndex, Query, TDelegate, Online> & dbFinder)
{
typedef Db<TText> TDb;
typedef Db<TText, Query> TDbQuery;
typedef typename Size<TDb>::Type TDbSize;
typedef typename MakeSigned<TDbSize>::Type TDbSSize;
typedef typename Size<TDbQuery>::Type TDbQuerySize;
typedef typename MakeSigned<TDbQuerySize>::Type TDbQuerySSize;
TDbSSize dbSize = length(dbFinder.db.text);
TDbQuerySSize dbQuerySize = length(value(dbFinder.query).text);
SEQAN_OMP_PRAGMA(parallel for schedule(dynamic))
for (TDbSSize dbId = 0; dbId < dbSize; ++dbId)
for (TDbQuerySSize queryId = 0; queryId < dbQuerySize; ++queryId)
dbFinder.verifier(dbId, queryId, dbFinder.delegate);
}
#endif // #ifndef SANDBOX_ESIRAGUSA_APPS_SEARCHJOIN_DBFINDER_H_
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