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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.
//
// ==========================================================================
#ifndef SEQAN_HEADER_SHAPE_MINIMIZER_H
#define SEQAN_HEADER_SHAPE_MINIMIZER_H
namespace seqan2
{
struct ReverseComplementTag_;
typedef Tag<ReverseComplementTag_> const ReverseComplement;
// ----------------------------------------------------------------------------
// Struct MinimizerShape
// ----------------------------------------------------------------------------
template <unsigned TSPAN, unsigned TWEIGHT, typename TSpec = void>
struct MinimizerShape;
// ----------------------------------------------------------------------------
// Class Shape<MinimizerShape>
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
class Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> >
{
public:
typedef typename Value<Shape>::Type THashValue;
unsigned span;
unsigned weight;
THashValue hValue; //current minimizer hash
Shape():
span(TSPAN),
weight(TWEIGHT)
{}
};
// ----------------------------------------------------------------------------
// Metafunction LENGTH
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
struct LENGTH<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >
{
enum { VALUE = TSPAN };
};
// ----------------------------------------------------------------------------
// Metafunction WEIGHT
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
struct WEIGHT<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >
{
enum { VALUE = TWEIGHT };
};
// ----------------------------------------------------------------------------
// Function weight()
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec>
inline
typename Size< Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
weight(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > const &me)
{
return me.weight;
}
// ----------------------------------------------------------------------------
// Function _minHash()
// ----------------------------------------------------------------------------
// return lexicographically smaller hash as the minimizer
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TString>
inline typename Value< Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
_minHash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TString const & str)
{
typedef typename Iterator<TString const, Standard>::Type TIter;
typedef typename Value<Shape<TValue, UngappedShape<TWEIGHT> > >::Type THValue;
SEQAN_ASSERT_GT((unsigned)me.span, 0u);
SEQAN_ASSERT_GT((unsigned)me.span, (unsigned)me.weight);
Shape<TValue, UngappedShape<TWEIGHT> > tmpShape;
TIter strIt = begin(str, Standard());
TIter strEnd = end(str, Standard()) - weight(me) + 1;
THValue miniTmp = hash(tmpShape, strIt);
for (strIt++; strIt != strEnd; strIt++)
miniTmp = _min(miniTmp, hashNext(tmpShape, strIt));
return miniTmp;
}
// ----------------------------------------------------------------------------
// Function hash()
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TIter>
inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
hash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TIter const &it)
{
Range<TIter> range(it, it + length(me));
me.hValue = _minHash(me, range);
return me.hValue;
}
// ----------------------------------------------------------------------------
// Function hash(); ReverseComplement
// ----------------------------------------------------------------------------
// Uses the lexicographically smaller of S and the reverse complement of S as the minimizer
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TIter>
inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, ReverseComplement> > >::Type
hash(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, ReverseComplement> > &me, TIter const &it)
{
typedef Range<TIter> TContainer;
typedef typename Value<TContainer>::Type TAlphabet;
typedef typename RemoveConst<TAlphabet>::Type TNCAlphabet;
typedef ModifiedString<TContainer, ModView<FunctorComplement<TNCAlphabet> > > TComplement;
typedef ModifiedString<TComplement, ModReverse> TRC;
Range<TIter> range(it, it + length(me));
TRC revComplRange(range);
me.hValue = _min(_minHash(me, range), _minHash(me, revComplRange));
return me.hValue;
}
// ----------------------------------------------------------------------------
// Function hashNext()
// ----------------------------------------------------------------------------
template <typename TValue, unsigned TSPAN, unsigned TWEIGHT, typename TSpec, typename TIter>
inline typename Value<Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > >::Type
hashNext(Shape<TValue, MinimizerShape<TSPAN, TWEIGHT, TSpec> > &me, TIter const &it)
{
return hash(me, it);
}
} // namespace seqan2
#endif
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