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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#ifndef INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_
#define INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_
namespace seqan
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _alignWrapperSequential(); Score; StringSet vs. StringSet
// ----------------------------------------------------------------------------
template <typename TString1, typename TSpec1,
typename TString2, typename TSpec2,
typename TScoreValue, typename TScoreSpec,
typename TAlignConfig,
typename TGapModel>
inline auto
_alignWrapperSequential(StringSet<TString1, TSpec1> const & stringsH,
StringSet<TString2, TSpec2> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
TAlignConfig const & config,
TGapModel const & /*gaps*/)
{
String<TScoreValue> results;
resize(results, length(stringsV));
auto zipCont = makeZipView(results, stringsH, stringsV);
forEach(zipCont,
[&] (auto tuple)
{
using namespace seqan;
DPScoutState_<Default> dpScoutState;
String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments.
std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState,
std::get<1>(tuple), std::get<2>(tuple), scoringScheme,
config, TGapModel());
});
return results;
}
// ----------------------------------------------------------------------------
// Function _alignWrapperSequential(); Score; String vs. StringSet
// ----------------------------------------------------------------------------
template <typename TString1,
typename TString2, typename TSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlignConfig,
typename TGapModel>
inline auto
_alignWrapperSequential(TString1 const & stringH,
StringSet<TString2, TSpec> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
TAlignConfig const & config,
TGapModel const & /*gaps*/)
{
String<TScoreValue> results;
resize(results, length(stringsV));
auto zipCont = makeZipView(results, stringsV);
forEach(zipCont,
[&] (auto tuple)
{
using namespace seqan;
DPScoutState_<Default> dpScoutState;
String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments.
std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple),
scoringScheme, config, TGapModel());
});
return results;
}
// ----------------------------------------------------------------------------
// Function _alignWrapperSequential(); Gaps
// ----------------------------------------------------------------------------
template <typename TSequenceH, typename TGapsSpecH, typename TSetSpecH,
typename TSequenceV, typename TGapsSpecV, typename TSetSpecV,
typename TScoreValue, typename TScoreSpec,
typename TAlignConfig,
typename TGapModel>
inline auto
_alignWrapperSequential(StringSet<Gaps<TSequenceH, TGapsSpecH>, TSetSpecH> & gapSeqSetH,
StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
TAlignConfig const & config,
TGapModel const & /*gaps*/)
{
typedef typename Size<TSequenceH>::Type TSize;
typedef typename Position<TSequenceH>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
String<TScoreValue> results;
resize(results, length(gapSeqSetH));
auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV);
forEach(zipCont,
[&] (auto tuple)
{
using namespace seqan;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
std::get<0>(tuple) = _setUpAndRunAlignment(trace, dpScoutState, source(std::get<1>(tuple)),
source(std::get<2>(tuple)), scoringScheme, config,
TGapModel());
_adaptTraceSegmentsTo(std::get<1>(tuple), std::get<2>(tuple), trace);
});
return results;
}
// ----------------------------------------------------------------------------
// Function _alignWrapper()
// ----------------------------------------------------------------------------
template <typename... TArgs>
inline auto _alignWrapper(TArgs && ...args)
{
#ifdef SEQAN_SIMD_ENABLED
return _alignWrapperSimd(std::forward<TArgs>(args)...);
#else
return _alignWrapperSequential(std::forward<TArgs>(args)...);
#endif
}
} // namespace seqan
#endif // #ifndef INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_
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