// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Interface functions for unbanded local alignment.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function localAlignment()
// ----------------------------------------------------------------------------
/*!
* @fn localAlignment
* @headerfile <seqan/align.h>
* @brief Computes the best pairwise local alignment using the Smith-Waterman algorithm.
*
* @signature TScoreVal localAlignment(align, scoringScheme, [lowerDiag, upperDiag]);
* @signature TScoreVal localAlignment(gapsH, gapsV, scoringScheme, [lowerDiag, upperDiag]);
* @signature TScoreVal localAlignment(fragmentString, scoringScheme, [lowerDiag, upperDiag]);
*
* @param[in,out] gapsH Horizontal gapped sequence in alignment matrix. Types: @link Gaps @endlink
* @param[in,out] gapsV Vertical gapped sequence in alignment matrix. Types: @link Gaps @endlink
* @param[in,out] align An @link Align @endlink object that stores the alignment. The
* number of rows must be 2 and the sequences must have already
* been set. <tt>align[0]</tt> is the horizontal one in the
* alignment matrix alignment, <tt>align[1]</tt> is the vertical
* one.
* @param[in,out] fragmentString
* String of @link Fragment @endlink objects. The sequence
* with id <tt>0</tt> is the horizontal one, the sequence
* with id <tt>1</tt> is the vertical one.
* @param[in] scoringScheme
* The @link Score scoring scheme @endlink to use for the alignment.
* @param[in] lowerDiag Optional lower diagonal (<tt>int</tt>).
* @param[in] upperDiag Optional upper diagonal (<tt>int</tt>).
*
* @return TScoreVal Score value of the resulting alignment (Metafunction @link Score#Value @endlink of the type of
* <tt>scoringScheme</tt>).
*
* The Waterman-Eggert algorithm (local alignment with declumping) is available through the @link
* LocalAlignmentEnumerator @endlink class.
*
* When using @link Gaps @endlink and @link Align @endlink objects, only parts (i.e. one infix) of each sequence will be
* aligned. This will be presented to the user by setting the clipping begin and end position of the gaps (the rows in
* the case of @link Align @endlink objects). When using @link Fragment @endlink strings, these parts of the sequences
* will not appear in any fragment.
*
* There exist multiple overloads for this function with two configuration dimensions.
*
* First, you can select the type of the target storing the alignment. This can be either an @link Align @endlink
* object, two @link Gaps @endlink objects, or a string of @link Fragment @endlink objects. @link Align @endlink objects
* provide an interface to tabular alignments with the restriction of all rows having the same type. Using two @link
* Gaps @endlink objects has the advantage that you an align sequences with different types, for example @link DnaString
* @endlink and @link Dna5String @endlink. Using @link Fragment @endlink strings is useful for collecting many pairwise
* alignments, for example in the construction of @link AlignmentGraph Alignment Graphs @endlink for multiple- sequence
* alignments (MSA).
*
* Second, you can optionally give a band for the alignment using <tt>lowerDiag</tt> and <tt>upperDiag</tt>. The center
* diagonal has index <tt>0</tt>, the <tt>i</tt>th diagonal below has index <tt>-i</tt>, the <tt>i</tt>th above has
* index <tt>i</tt>.
*
* The examples below show some common use cases.
*
* @section Examples
*
* Local alignment of two sequences using an @link Align @endlink object.
*
* @code{.cpp}
* Dna5String seqH = "CGATT";
* Dna5String seqV = "CGAAATT";
*
* Align<Dna5String> align;
* resize(rows(align), 2);
* assignSource(row(align, 0), seqH);
* assignSource(row(align, 0), seqV);
* Score<int, Simple> scoringScheme(2, -1, -2);
*
* int result = localAlignment(align, scoringScheme);
* @endcode
*
* Local banded alignment of two sequences using two @link Gaps @endlink objects.
*
* @code{.cpp}
* Dna5String seqH = "CGATT";
* Gaps<Dna5String, ArrayGaps> gapsH(seqH);
* DnaString seqV = "CGAAATT";
* Gaps<Dna5String, AnchorGaps<> > gapsV(seqV);
*
* Score<int, Simple> scoringScheme(5, -3, -1, -5);
*
* int result = localAlignment(gapsH, gapsV, scoringScheme, -2, 2);
* @endcode
*
* https://seqan.readthedocs.io/en/develop/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.html
*
* @section References
*
* <ul>
* <li>Smith TF, Waterman, MS: Identification of Common Molecular Subsequences. J Mol Biol 1981, 147(1):195-7.</li>
* </ul>
*
* @see globalAlignment
* @see LocalAlignmentEnumerator
* @see PairwiseLocalAlignmentAlgorithms
*/
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, Align]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec, typename TScoreValue, typename TScoreSpec, typename TTag>
TScoreValue localAlignment(Align<TSequence, TAlignSpec> & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
TTag const & tag)
{
SEQAN_ASSERT_EQ(length(rows(align)), 2u);
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<BandOff>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
scoringScheme, TAlignConfig2(), 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)
{
SEQAN_ASSERT(length(rows(align)) == 2u);
if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1))))
return localAlignment(align, scoringScheme, AffineGaps());
else
return localAlignment(align, scoringScheme, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, 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,
TTag const & tag)
{
typedef typename Size<TSequenceH>::Type TSize;
typedef typename Position<TSequenceH>::Type TPosition;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
TAlignConfig2(), 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)
{
if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV)))
return localAlignment(gapsH, gapsV, scoringScheme, AffineGaps());
else
return localAlignment(gapsH, gapsV, scoringScheme, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, Graph<Alignment<>>]
// ----------------------------------------------------------------------------
// Full interface.
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,
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<BandOff>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
value(stringSet(alignmentGraph), 1), scoringScheme, TAlignConfig2(), 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)
{
SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u);
if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1]))
return localAlignment(alignmentGraph, scoringScheme, AffineGaps());
else
return localAlignment(alignmentGraph, scoringScheme, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, 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,
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<BandOff>, FreeEndGaps_<> > TAlignConfig2;
String<TTraceSegment> trace;
DPScoutState_<Default> dpScoutState;
TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
TAlignConfig2(), 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)
{
SEQAN_ASSERT(length(strings) == 2u);
if (_usesAffineGaps(scoringScheme, strings[0], strings[1]))
return localAlignment(fragmentString, strings, scoringScheme, AffineGaps());
else
return localAlignment(fragmentString, strings, scoringScheme, LinearGaps());
}
// ============================================================================
// Many-vs-Many align interfaces.
// ============================================================================
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, 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,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<> > TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel());
}
// ----------------------------------------------------------------------------
// Function localAlignment() [unbanded, SIMD version, StringSet<Align>]
// ----------------------------------------------------------------------------
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec,
typename TAlgoTag>
inline String<TScoreValue>
localAlignment(StringSet<Align<TSequence, TAlignSpec> > & alignSet,
Score<TScoreValue, TScoreSpec> const & scoringScheme,
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, algoTag);
}
template <typename TSequence, typename TAlignSpec,
typename TScoreValue, typename TScoreSpec>
String<TScoreValue> localAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
Score<TScoreValue, TScoreSpec> const & scoringScheme)
{
if (_usesAffineGaps(scoringScheme, source(row(align[0], 0)), source(row(align[0], 1))))
return localAlignment(align, scoringScheme, AffineGaps());
else
return localAlignment(align, scoringScheme, LinearGaps());
}
// ----------------------------------------------------------------------------
// Function localAlignmentScore() [unbanded, TSequence]
// ----------------------------------------------------------------------------
/*!
* @fn localAlignmentScore
* @headerfile <seqan/align.h>
* @brief Computes the best global pairwise alignment score.
*
* @signature TScoreVal localAlignmentScore([exec,] subject, query, scoringScheme[, lowerDiag, upperDiag]);
*
* @param[in] exec @link ExecutionPolicy Policy@endlink to select execution mode of alignment algorithm.
* @param[in] subject Subject sequence(s) (horizontal in alignment matrix). Must satisfy @link ContainerConcept @endlink or container-of-container concept.
* @param[in] query Query sequence(s) (vertical in alignment matrix). Must satisfy @link ContainerConcept @endlink or container-of-container concept.
* @param[in] scoringScheme The scoring scheme to use for the alignment. Note that the user is responsible for ensuring
* that the scoring scheme is compatible with <tt>algorithmTag</tt>. Type: @link Score @endlink.
* @param[in] lowerDiag Optional lower diagonal. Types: <tt>int</tt>
* @param[in] upperDiag Optional upper diagonal. Types: <tt>int</tt>
*
* @return TScoreVal Score value of the resulting alignment (Metafunction: @link Score#Value @endlink of
* the type of <tt>scoringScheme</tt>). If subject and query are sets the function returns a
* set of scores representing the score for each pairwise alignment (<tt>subject[i]</tt> with <tt>query[i]</tt>).
*
* This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming
* step. Local alignment score can be either used with two sequences or two sets of sequences of equal size.
*
* @section Parallel execution
*
* Some of the local alingment score functions are parallelized and vectorized.
* The parallelization mode can be selected via the @link ExecutionPolicy @endlink as first argument.
* Following execution modes are possible: <i>sequential</i>, <i>parallel</i>, <i>wave-front</i>, <i>vectorized</i>,
* <i>parallel+vectorized</i> and <i>wave-front+vectorized</i>.
*
* The wave-front execution can be selected via the @link WavefrontExecutionPolicy @endlink, which can also be combined
* with a vectorized execution. In addition the wave-front execution parallelizes a single pairwise alignment, while the
* standard @link ParallelismTags#Parallel @endlink specialization does only parallelizes the sequence set via chunking.
* Note, the banded version is at the moment only supported for the following execution modes: <i>sequential</i>,
* <i>parallel</i>, <i>vectorized</i> and <i>parallel+vectorized</i>. At the moment the vectorized version only works
* reliable if all subject sequences and respectively all query sequences have the same length.
*
* @see https://seqan.readthedocs.io/en/develop/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.html
* @see localAlignment
*
* @datarace thread-safe. No shared state is modified during the execution and concurrent invocations of this function
* on the same data does not cause any race conditions.
*/
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,
TAlgoTag const & /*algoTag*/)
{
typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, 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{}, TGapModel{});
}
// ----------------------------------------------------------------------------
// Function localAlignmentScore() [unbanded, 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,
TAlgoTag const & /*algoTag*/)
{
SEQAN_ASSERT_EQ(length(stringsH), length(stringsV));
typedef AlignConfig2<DPLocal, DPBandConfig<BandOff>, FreeEndGaps_<>, TracebackOff> TAlignConfig2;
typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
return _alignWrapper(stringsH, stringsV, scoringScheme, TAlignConfig2(), 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)
{
if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
return localAlignmentScore(seqH, seqV, scoringScheme, NeedlemanWunsch());
else
return localAlignmentScore(seqH, seqV, scoringScheme, Gotoh());
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_
