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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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Interface functions for banded local alignment.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, Align]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec, typename TTag>
TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TTag const & tag)
{
typedef Align<TSequence, TAlignSpec> TAlign;
typedef typename Size<TAlign>::Type TSize;
typedef typename Position<TAlign>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
SEQAN_ASSERT_EQ(length(rows(align)), 2u);
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
scoringScheme, TAlignConfig2(lowerDiag, upperDiag), tag);
_adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
return res;
}
template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec>
TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
SEQAN_ASSERT(length(rows(align)) == 2u);
if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1))))
return localAlignment(align, scoringScheme, lowerDiag, upperDiag, AffineGaps());
else
return localAlignment(align, scoringScheme, lowerDiag, upperDiag, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, Gaps]
// ----------------------------------------------------------------------------
template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec, typename TTag>
TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TTag const & tag)
{
typedef typename Size<TSequenceH>::Type TSize;
typedef typename Position<TSequenceH>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), tag);
_adaptTraceSegmentsTo(gapsH, gapsV, trace);
return res;
}
template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec>
TScoreValue localAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV)))
return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, AffineGaps());
else
return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, Graph<Alignment<> >]
// ----------------------------------------------------------------------------
template <typename TStringSet, typename TCargo, typename TGraphSpec, typename TScoreValue, typename TScoreSpec,
typename TTag>
TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TTag const & tag)
{
typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
typedef typename Size<TGraph>::Type TSize;
typedef typename Position<TGraph>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
value(stringSet(alignmentGraph), 1), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), tag);
_adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
positionToId(stringSet(alignmentGraph), 1), trace);
return res;
}
template <typename TStringSet, typename TCargo, typename TGraphSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue localAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u);
if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1]))
return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, AffineGaps());
else
return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, String<Fragment<> >]
// ----------------------------------------------------------------------------
// Full interface.
template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec, typename TTag>
TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TTag const & tag)
{
typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
typedef typename Position<TFragments>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), tag);
_adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
return res;
}
template <typename TSize, typename TFragmentSpec, typename TStringSpec,
typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
SEQAN_ASSERT(length(strings) == 2u);
if (_usesAffineGaps(scoringScheme, strings[0], strings[1]))
return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, AffineGaps());
else
return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, LinearGaps());
}
// ============================================================================
// Many-vs-Many align interfaces.
// ============================================================================
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, SIMD version, GapsH, GapsV]
// ----------------------------------------------------------------------------
template <typename TGapSequenceH, typename TSetSpecH,
typename TGapSequenceV, typename TSetSpecV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
inline auto
localAlignment(StringSet<TGapSequenceH, TSetSpecH> & gapSeqSetH,
StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<> > TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [banded, SIMD version, StringSet<Align>]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec, typename TSetSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
inline String<TScoreValue>
localAlignment(StringSet<Align<TSequence, TAlignSpec>, TSetSpec> & alignSet,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & algoTag)
{
typedef Align<TSequence, TAlignSpec> TAlign;
typedef typename Row<TAlign>::Type TGapSequence;
StringSet<TGapSequence, Dependent<> > gapSetH;
StringSet<TGapSequence, Dependent<> > gapSetV;
reserve(gapSetH, length(alignSet));
reserve(gapSetV, length(alignSet));
for (auto & align : alignSet)
{
appendValue(gapSetH, row(align, 0));
appendValue(gapSetV, row(align, 1));
}
return localAlignment(gapSetH, gapSetV, scoringScheme, lowerDiag, upperDiag, algoTag);
}
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec>
String<TScoreValue> localAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag, int upperDiag)
{
if (_usesAffineGaps(scoringScheme, source(row(align[0], 0)), source(row(align[0], 1))))
return localAlignment(align, scoringScheme, lowerDiag, upperDiag, AffineGaps());
else
return localAlignment(align, scoringScheme, lowerDiag, upperDiag, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignmentScore() [banded, no-simd, TSequence]
// ----------------------------------------------------------------------------
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
SEQAN_FUNC_DISABLE_IF(And<And<Is<ContainerConcept<TSequenceH>>, Is<ContainerConcept<typename Value<TSequenceH>::Type>>>,
And<Is<ContainerConcept<TSequenceV>>, Is<ContainerConcept<typename Value<TSequenceV>::Type>>>
>, TScoreValue)
localAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<>, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
DPScoutState_<Default> dpScoutState;
String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments.
return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme,
TAlignConfig2{lowerDiag, upperDiag}, TGapModel{});
}
// ----------------------------------------------------------------------------
// Function localAlignmentScore() [banded, Simd, TSequence]
// ----------------------------------------------------------------------------
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
inline
SEQAN_FUNC_ENABLE_IF(And<And<Is<ContainerConcept<TSeqH>>, Is<ContainerConcept<typename Value<TSeqH>::Type>>>,
And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>>
>, String<TScoreValue>)
localAlignmentScore(TSeqH const & stringsH,
TSeqV const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig2<DPLocal, DPBandConfig<BandOn>, FreeEndGaps_<>, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
SEQAN_ASSERT_EQ(length(stringsH), length(stringsV));
return _alignWrapper(stringsH, stringsV, scoringScheme, TAlignConfig2{lowerDiag, upperDiag}, TGapModel());
}
// Interface without algorithm tag.
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec>
auto localAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return localAlignmentScore(seqH, seqV, scoringScheme, lowerDiag, upperDiag, NeedlemanWunsch());
else
return localAlignmentScore(seqH, seqV, scoringScheme, lowerDiag, upperDiag, Gotoh());
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_
|
