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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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>
// ==========================================================================
// Global alignment interface for the banded Needleman-Wunsch and Gotoh
// algorithms.
//
// We define the interface functions pretty explicitely (versus just TAlign,
// TFragments etc.) so the candidates the compiler gives when resolution to
// the globalFunction() fails is actually meaningful.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
template <typename TScoreValue, typename TSpec>
class Score;
template <typename TSpec>
class Graph;
template <typename TStringSet, typename TCargo, typename TGraphSpec>
struct Alignment;
template <typename TSize, typename TFragmentSpec>
class Fragment;
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, Align]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef Align<TSequence, TAlignSpec> TAlign;
typedef typename Size<TAlign>::Type TSize;
typedef typename Position<TAlign>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
_adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
return res;
}
// Interface without AlignConfig<>.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, LinearGaps());
else
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, AffineGaps());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, Gaps]
// ----------------------------------------------------------------------------
template <typename TSequenceH, typename TGapsSpecH,
typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef typename Size<TSequenceH>::Type TSize;
typedef typename Position<TSequenceH>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), TGapModel());
_adaptTraceSegmentsTo(gapsH, gapsV, trace);
return res;
}
// Interface without AlignConfig<>.
template <typename TSequenceH, typename TGapsSpecH,
typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSequenceH, typename TGapsSpecH,
typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSequenceH, typename TGapsSpecH,
typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec>
TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, Graph<Alignment<> >]
// ----------------------------------------------------------------------------
// Full interface.
template <typename TStringSet, typename TCargo, typename TGraphSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
typedef typename Position<TGraph>::Type TPosition;
typedef typename Size<TGraph>::Type TSize;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
value(stringSet(alignmentGraph), 1), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), TGapModel());
_adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
positionToId(stringSet(alignmentGraph), 1), trace);
return res;
}
// Interface without AlignConfig<>.
template <typename TStringSet, typename TCargo, typename TGraphSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TStringSet, typename TCargo, typename TGraphSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TStringSet, typename TCargo, typename TGraphSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, String<Fragment<> >]
// ----------------------------------------------------------------------------
// Full interface.
template <typename TSize, typename TFragmentSpec, typename TStringSpec,
typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
typedef typename Position<TFragments>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), TGapModel());
_adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
return res;
}
// Interface without AlignConfig<>.
template <typename TSize, typename TFragmentSpec, typename TStringSpec,
typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSize, typename TFragmentSpec, typename TStringSpec,
typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSize, typename TFragmentSpec, typename TStringSpec,
typename TSequence, typename TStringSetSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
StringSet<TSequence, TStringSetSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignmentScore() [banded, 2 Strings]
// ----------------------------------------------------------------------------
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
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<TSequenceH>::Type>>>
>,
TScoreValue)
globalAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, 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());
}
// Interface without AlignConfig<>.
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
auto globalAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
auto globalAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSequenceH,
typename TSequenceV,
typename TScoreValue, typename TScoreSpec>
auto globalAlignmentScore(TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignmentScore() [banded, StringSet]
// ----------------------------------------------------------------------------
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
SEQAN_ASSERT_EQ(length(strings), 2u);
DPScoutState_<Default> dpScoutState;
String<TraceSegment_<unsigned, unsigned> > traceSegments; // Dummy segments.
return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme,
TAlignConfig2(lowerDiag, upperDiag), TGapModel());
}
// Interface without AlignConfig<>.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
SEQAN_ASSERT_EQ(length(strings), 2u);
AlignConfig<> alignConfig;
return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
SEQAN_ASSERT_EQ(length(strings), 2u);
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec>
TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
SEQAN_ASSERT_EQ(length(strings), 2u);
AlignConfig<> alignConfig;
return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ============================================================================
// Many-vs-Many align interfaces.
// ============================================================================
// ----------------------------------------------------------------------------
// Function globalAlignmentScore() [banded, SIMD version, 2x StringSet]
// ----------------------------------------------------------------------------
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
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>)
globalAlignmentScore(TSeqH const & stringsH,
TSeqV const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
SEQAN_ASSERT_EQ(length(stringsH), length(stringsV));
return _alignWrapper(stringsH, stringsV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
}
// ----------------------------------------------------------------------------
// Function globalAlignmentScore() [banded, SIMD version, String vs StringSet]
// ----------------------------------------------------------------------------
template <typename TStringH,
typename TStringV, typename TSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
String<TScoreValue> globalAlignmentScore(TStringH const & stringH,
StringSet<TStringV, TSpec> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int lowerDiag,
int upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
return _alignWrapper(stringH, stringsV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
}
// Interface without AlignConfig<>.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
String<TScoreValue> globalAlignmentScore(TString const & stringH,
StringSet<TString, TSpec> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
String<TScoreValue> globalAlignmentScore(TString const & stringH,
StringSet<TString, TSpec> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag,
int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TString, typename TSpec,
typename TScoreValue, typename TScoreSpec>
String<TScoreValue> globalAlignmentScore(TString const & stringH,
StringSet<TString, TSpec> const & stringsV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag,
int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, SIMD version, GapsH, GapsV]
// ----------------------------------------------------------------------------
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
typename TAlgoTag>
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>)
globalAlignment(TSeqH & gapSeqSetH,
TSeqV & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
}
// Interface without AlignConfig<>.
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
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>)
globalAlignment(TSeqH & gapSeqSetH,
TSeqV & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
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>)
globalAlignment(TSeqH & gapSeqSetH,
TSeqV & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int const lowerDiag,
int const upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
{
return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, lowerDiag, upperDiag,
NeedlemanWunsch());
}
else
{
return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSeqH,
typename TSeqV,
typename TScoreValue, typename TScoreSpec>
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>)
globalAlignment(TSeqH & gapSeqSetH,
TSeqV & gapSeqSetV,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int const lowerDiag,
int const upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
// ----------------------------------------------------------------------------
// Function globalAlignment() [banded, SIMD version, StringSet<Align>]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec, typename TAlgoTag>
String<TScoreValue> globalAlignment(StringSet<Align<TSequence, TAlignSpec> > & alignSet,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
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 globalAlignment(gapSetH, gapSetV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without AlignConfig<>.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
String<TScoreValue> globalAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag, int upperDiag,
TAlgoTag const & algoTag)
{
AlignConfig<> alignConfig;
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
}
// Interface without algorithm tag.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
String<TScoreValue> globalAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
int lowerDiag, int upperDiag)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
else
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
}
// Interface without AlignConfig<> and algorithm tag.
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec>
String<TScoreValue> globalAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
int lowerDiag, int upperDiag)
{
AlignConfig<> alignConfig;
return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag);
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
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