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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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_PIPE_SAMPLER_H
#define SEQAN_HEADER_PIPE_SAMPLER_H
namespace seqan2
{
//namespace seqan2_NAMESPACE_PIPELINING
//{
template <int I, typename T = void>
struct SkewDC_;
//////////////////////////////////////////////////////////////////////////////
template < unsigned m, typename TPack = Pack >
struct Sampler;
template < typename TInput, unsigned m, typename TPack >
struct Value< Pipe< TInput, Sampler<m, TPack> > >
{
typedef Tuple<typename Value<TInput>::Type, m, TPack> mTuple;
typedef Pair<typename Size<TInput>::Type, mTuple, Pack> Type;
};
//////////////////////////////////////////////////////////////////////////////
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
struct Value< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >
{
typedef Tuple<typename Value<TInput>::Type, m, TPack> mTuple;
typedef Pair<TPair, mTuple, Pack> Type;
};
//////////////////////////////////////////////////////////////////////////////
// TODO(holtgrew): Documentation bug with DC!
/*!
* @class Sampler
* @extends Pipe
* @headerfile <seqan/pipe.h>
* @brief Outputs m-tuples beginning at a position of difference cover DC.
*
* @signature template <typename TInput, unsigned M[, typename TPack]>
* class Pipe<TInput, Sampler<M, TPack> >;
*
* @tparam TInput The type of the pipeline module this module reads from.
* @tparam m The tuple size.
* @tparam TPack Specifies the packing method of the tuples (<tt>void</tt> = no packing), default is <tt>Pack</tt>.
*
* The output type is a Pair of size type and Tuple of input elements and length m (i.e. <tt>Pair<Size<TInput>::Type,
* Tuple<Value<TInput>::Type, m, TPack> ></tt>).
*
* The first output field contains the number of remaining pipe elements. The m-tuple in the second field contains the
* first m elements of them. The m-tuples are substrings of the input stream beginning at positions <tt>i</tt>, with
* <tt>(n-i) mod m</tt> is element of the set DC (n is the input stream length).
*
* @section Examples
*
* The set <tt>{1,2,4}</tt> is represented by <tt>int DC[] = { 3, 1, 2, 4 }</tt>.
*
* @see BitPackedTuple
*/
//////////////////////////////////////////////////////////////////////////////
// sampler class
template < typename TInput, unsigned m, typename TPack >
struct Pipe< TInput, Sampler<m, TPack> >
{
typedef typename Value<Pipe>::Type TOutValue;
typedef typename Size<Pipe>::Type TSize;
TInput ∈
bool filter[m];
TSize idx, _size, _rest;
unsigned idxMod;
TOutValue tmp1, tmp2;
TOutValue *outRef, *tmpRef;
bool last;
Pipe(TInput& _in):
in(_in),
outRef(&tmp1),
tmpRef(&tmp2) {}
inline void prepare()
{
for (unsigned i = 0; i < m; ++i)
filter[i] = 0;
for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
filter[SkewDC_<m>::VALUE[i]] = true;
idx = length(in);
idxMod = idx % m;
while (!filter[idxMod] && !eof(in))
{
++in;
if (idxMod == 0) idxMod = m;
--idxMod; --idx;
}
_rest = length(*this);
fill();
swap();
}
inline void fill()
{
unsigned i;
for(i = 0; i < m && !eof(in); ++i, ++in)
tmpRef->i2.i[i] = *in;
last = eof(in);
for(; i < m; ++i)
tmpRef->i2.i[i] = 0;
tmpRef->i1 = idx;
}
inline void rotate(unsigned r)
{
for(unsigned i = 0; i < m; ++i, ++r)
{
if (r == m) r = 0;
tmpRef->i2.i[i] = outRef->i2.i[r];
}
}
inline void swap()
{
TOutValue *newOutRef = tmpRef;
tmpRef = outRef;
outRef = newOutRef;
}
inline TOutValue const& operator*()
{
return *outRef;
}
Pipe& operator++()
{
unsigned skipped = 0;
if (--_rest)
{
if (!last)
{
do
{
#if defined(__GNUC__) && !defined(__llvm__) && !defined(__INTEL_COMPILER) && (__GNUC__ >= 12)
# pragma GCC diagnostic push
# pragma GCC diagnostic ignored "-Wstringop-overflow="
#endif
outRef->i2.i[skipped++] = *in;
#if defined(__GNUC__) && !defined(__llvm__) && !defined(__INTEL_COMPILER) && (__GNUC__ >= 12)
# pragma GCC diagnostic pop
#endif
++in;
if (idxMod == 0) idxMod = m;
--idxMod; --idx;
if (eof(in))
{
last = true;
while (!filter[idxMod])
{
outRef->i2.i[skipped++] = 0;
if (idxMod == 0) idxMod = m;
--idxMod; --idx;
}
break;
}
} while (!filter[idxMod]);
}
else
{
do
{
// Do not go out of bounds
if (skipped < LENGTH<TInput>::VALUE)
outRef->i2.i[skipped] = 0;
// But always increment skipped
skipped += 1;
if (idxMod == 0) idxMod = m;
--idxMod; --idx;
}
while (!filter[idxMod]);
}
}
rotate(skipped);
tmpRef->i1 = idx;
swap();
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// sampler class (uses packing)
template < typename TInput, unsigned m >
struct Pipe< TInput, Sampler<m, BitPacked<> > >
{
typedef typename Value<Pipe>::Type TOutValue;
typedef typename Size<Pipe>::Type TSize;
typedef typename Value<TOutValue, 2>::Type TTuple;
TInput ∈
bool filter[m];
TSize _size, _rest;
unsigned idxMod;
TOutValue tmp;
bool last;
Pipe(TInput & _in) : in(_in), _size(0), _rest(0), idxMod(0), last(false)
{}
inline void prepare()
{
for (unsigned i = 0; i < m; ++i)
filter[i] = 0;
for (unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
filter[SkewDC_<m>::VALUE[i]] = true;
tmp.i1 = length(in);
idxMod = tmp.i1 % m;
while (!filter[idxMod] && !eof(in))
{
++in;
if (idxMod == 0) idxMod = m;
--idxMod; --tmp.i1;
}
_rest = length(*this);
fill();
}
inline void fill()
{
unsigned i;
clear(tmp.i2);
for(i = 0; i < m && !eof(in); ++i, ++in)
{
tmp.i2 <<= 1;
tmp.i2 |= *in;
}
last = eof(in);
tmp.i2 <<= (m - i);
}
inline TOutValue const& operator*()
{
return tmp;
}
Pipe& operator++()
{
if (--_rest)
{
if (!last)
{
do
{
tmp.i2 <<= 1;
tmp.i2 |= *in;
++in;
if (idxMod == 0) idxMod = m;
--idxMod; --tmp.i1;
if (eof(in))
{
last = true;
while (!filter[idxMod])
{
tmp.i2 <<= 1;
if (idxMod == 0) idxMod = m;
--idxMod; --tmp.i1;
}
break;
}
} while (!filter[idxMod]);
}
else
{
do
{
tmp.i2 <<= 1;
if (idxMod == 0) idxMod = m;
--idxMod; --tmp.i1;
}
while (!filter[idxMod]);
}
}
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput, unsigned m, typename TPack >
inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlBeginRead const &command)
{
if (!control(me.in, command)) return false;
me.prepare();
return true;
}
template < typename TInput, unsigned m, typename TPack >
inline bool control(Pipe< TInput, Sampler<m, TPack> > &me, ControlEof const &/*command*/)
{
return me._rest == 0;
}
template < typename TInput, unsigned m, typename TPack >
inline typename Size< Pipe< TInput, Sampler<m, TPack> > >::Type
length(Pipe< TInput, Sampler<m, TPack> > const &me)
{
typedef typename Size< Pipe< TInput, Sampler<m> > >::Type TSize;
TSize sum = 0;
TSize size = length(me.in);
// sum up the number of tuples in each residue class
// for a string of length n there are 1+(n-x)/m suffixes
// whose lengths are in residue class x
for (unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; ++i)
{
sum += (size + m - SkewDC_<m>::VALUE[i]) / m;
if (SkewDC_<m>::VALUE[i] == 0)
--sum; // we don't consider empty suffixes
}
return sum;
}
//////////////////////////////////////////////////////////////////////////////
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
struct Size< Pipe<TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > > :
public Value<TLimitsString> {};
//////////////////////////////////////////////////////////////////////////////
// sampler class
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
struct Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> >
{
typedef typename Value<Pipe>::Type TOutValue;
typedef typename Size<Pipe>::Type TSize;
typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
TInput ∈
bool filter[m];
Decrementer localPos;
TSize _size, _rest;
TOutValue tmp1, tmp2;
TOutValue *outRef, *tmpRef;
bool last;
TLimitsString const &limits;
template <typename TLimitsString_>
Pipe(TInput& _in, TLimitsString_ &_limits): // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
in(_in),
outRef(&tmp1),
tmpRef(&tmp2),
limits(_limits) {}
inline void prepare()
{
for (unsigned i = 0; i < m; ++i)
filter[i] = 0;
for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
filter[SkewDC_<m>::VALUE[i]] = true;
setHost(localPos, limits);
while (!filter[localPos.residue] && !eof(in))
{
++in;
--localPos;
}
_rest = length(*this);
fill();
swap();
}
inline void fill()
{
unsigned i;
for(i = 0; i < m && !eof(in); ++i, ++in)
tmpRef->i2.i[i] = *in;
last = eof(in);
for(; i < m; ++i)
tmpRef->i2.i[i] = 0;
tmpRef->i1 = localPos;
}
inline void rotate(unsigned r)
{
for(unsigned i = 0; i < m; ++i, ++r)
{
if (r == m) r = 0;
tmpRef->i2.i[i] = outRef->i2.i[r];
}
}
inline void swap()
{
TOutValue *newOutRef = tmpRef;
tmpRef = outRef;
outRef = newOutRef;
}
inline TOutValue const& operator*()
{
return *outRef;
}
Pipe& operator++()
{
unsigned skipped = 0;
if (--_rest)
{
if (!last)
{
do
{
outRef->i2.i[skipped++] = *in;
++in;
--localPos;
if (eof(in))
{
last = true;
while (!filter[localPos.residue])
{
outRef->i2.i[skipped++] = 0;
--localPos;
}
break;
}
}
while (!filter[localPos.residue]);
}
else
{
do
{
// Do not go out of bounds
if (skipped < LENGTH<TInput>::VALUE)
outRef->i2.i[skipped] = 0;
// But always increment skipped
skipped += 1;
--localPos;
}
while (!filter[localPos.residue]);
}
rotate(skipped);
tmpRef->i1 = localPos;
swap();
}
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// sampler class (uses bit-packing)
template < typename TInput, unsigned m, typename TPair, typename TLimitsString >
struct Pipe< TInput, Multi<Sampler<m, BitPacked<> >, TPair, TLimitsString> >
{
typedef typename Value<Pipe>::Type TOutValue;
typedef typename Size<Pipe>::Type TSize;
typedef typename Value<TOutValue, 2>::Type TTuple;
typedef PairDecrementer_<TPair, TLimitsString, m> Decrementer;
TInput ∈
bool filter[m];
TSize _size, _rest;
Decrementer localPos;
TOutValue tmp;
bool last;
TLimitsString const &limits;
template <typename TLimitsString_>
Pipe(TInput& _in, TLimitsString_ &_limits): // const &_limits is intentionally omitted to suppress implicit casts (if types mismatch) and taking refs of them
in(_in),
limits(_limits) {}
inline void prepare()
{
for (unsigned i = 0; i < m; ++i)
filter[i] = 0;
for(unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; i++)
filter[SkewDC_<m>::VALUE[i]] = true;
setHost(localPos, limits);
while (!filter[localPos.residue] && !eof(in)) {
++in;
--localPos;
}
_rest = length(*this);
fill();
}
inline void fill()
{
unsigned i;
clear(tmp.i2);
for(i = 0; i < m && !eof(in); ++i, ++in) {
tmp.i2 <<= 1;
tmp.i2 |= *in;
}
last = eof(in);
tmp.i2 <<= (m - i);
tmp.i1 = localPos;
}
inline TOutValue const& operator*()
{
return tmp;
}
Pipe& operator++()
{
if (--_rest)
{
if (!last)
{
do
{
tmp.i2 <<= 1;
tmp.i2 |= *in;
++in;
--localPos;
if (eof(in))
{
last = true;
while (!filter[localPos.residue])
{
tmp.i2 <<= 1;
--localPos;
}
break;
}
}
while (!filter[localPos.residue]);
}
else
{
do
{
tmp.i2 <<= 1;
--localPos;
} while (!filter[localPos.residue]);
}
}
tmp.i1 = localPos;
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlBeginRead const &command)
{
if (!control(me.in, command))
return false;
me.prepare();
return true;
}
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEof const &/*command*/)
{
return me._rest == 0;
}
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
inline bool control(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > &me, ControlEos const &/*command*/)
{
return control(me, ControlEof());
}
template < typename TInput, unsigned m, typename TPack, typename TPair, typename TLimitsString >
inline typename Size< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >::Type
length(Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > const &me)
{
typedef typename Size< Pipe< TInput, Multi<Sampler<m, TPack>, TPair, TLimitsString> > >::Type TSize;
if (empty(me.limits))
return 0;
TSize sum = 0;
TLimitsString const &limits = me.limits;
int64_t seqCountPlusOne = length(me.limits);
SEQAN_OMP_PRAGMA(parallel for reduction(+:sum) if (seqCountPlusOne > 99))
for (int64_t i = 1; i < seqCountPlusOne; ++i)
{
TSize prev = limits[i - 1];
TSize cur = limits[i];
SEQAN_ASSERT_LEQ(prev, cur);
TSize size = cur - prev;
// sum up the number of tuples in each residue class
// for a string of length n there are 1+(n-x)/m suffixes
// whose lengths are in residue class x
for (unsigned i = 1; i <= SkewDC_<m>::VALUE[0]; ++i)
{
sum += (size + m - SkewDC_<m>::VALUE[i]) / m;
if (SkewDC_<m>::VALUE[i] == 0)
--sum; // we don't consider empty suffixes
}
}
return sum;
}
//}
}
#endif
|
