/usr/include/seqan/pipe/pipe_tupler.h is in seqan-dev 1.3.1-1.
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// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, 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_TUPLER_H
#define SEQAN_HEADER_PIPE_TUPLER_H
namespace SEQAN_NAMESPACE_MAIN
{
//namespace SEQAN_NAMESPACE_PIPELINING
//{
//////////////////////////////////////////////////////////////////////////////
template < unsigned tupleLen, bool omitLast = false, typename TCompression = void >
struct Tupler;
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
struct Value< Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > > {
typedef Tuple<typename Value<TInput>::Type, tupleLen, TCompression> TTuple;
typedef Pair<typename Size<TInput>::Type, TTuple, Compressed> Type;
};
//////////////////////////////////////////////////////////////////////////////
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
struct Value< Pipe< TInput, Multi< Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString > > > {
typedef Tuple<typename Value<TInput>::Type, tupleLen, TCompression> TTuple;
typedef Pair<TPair, TTuple, Compressed> Type;
};
//////////////////////////////////////////////////////////////////////////////
// output only fully filled tuples
template < typename TTupler >
struct TuplerLastTuples_ {
enum { VALUE = 1 };
};
// output tupleLen-1 half filled tuples at the end
template < typename TInput, unsigned tupleLen, typename TCompression >
struct TuplerLastTuples_< Pipe< TInput, Tupler<tupleLen, false, TCompression> > > {
enum { VALUE = tupleLen };
};
struct ShiftLeftWorker_ {
template <typename Arg>
static inline void body(Arg &arg, unsigned I) {
arg.i2[I-1] = arg.i2[I];
}
};
/**
.Spec.Tupler:
..cat:Pipelining
..general:Class.Pipe
..summary:Outputs tuples of the $tupleLen$ consecutive elements of the input stream.
..signature:Pipe<TInput, Tupler<tupleLen, omitLast> >
..param.TInput:The type of the pipeline module this module reads from.
..param.tupleLen:The tuple length.
...remarks:The tuples contain elements $in[i]in[i+1]...in[i+(tupleLen-1)]$.
..param.omitLast:Omit half filled tuples.
..param.omitLast:If $true$, the output stream is $tupleLen-1$ elements shorter than the input stream.
..param.omitLast:If $false$, the lengths are identical and the last tuples are filled with blanks (default constructed elements) for undefined entries.
..remarks:The output type is a @Class.Tuple@ of input elements and length $tupleLen$ (i.e. $Tuple<Value<TInput>::Type, tupleLen>$).
..remarks:The tuples are sequences of the form $in[i]in[i-1]in[i-2]..in[i-tupleLen+1]$. For $omitLast=false$ $i$ begins with 0 and for $omitLast=true$ $i$ begins with $tupleLen-1$.
..include:seqan/pipe.h
*/
//////////////////////////////////////////////////////////////////////////////
// tupler class
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
struct Pipe< TInput, Tupler<tupleLen, omitLast, TCompression> >
{
typedef typename Value< typename Value<Pipe>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
TInput ∈
typename Value<Pipe>::Type tmp;
typename Size<TInput>::Type lastTuples;
Pipe(TInput& _in):
in(_in) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
if (eof(in)) --lastTuples;
Loop<ShiftLeftWorker_, tupleLen - 1>::run(this->tmp);
++tmp.i1;
if (lastTuples < TuplerLastTuples_<Pipe>::VALUE)
tmp.i2[tupleLen - 1] = TValue();
else {
tmp.i2[tupleLen - 1] = *in;
++in;
}
return *this;
}
inline void fill() {
unsigned i;
for(i = 0; i < tupleLen && !eof(in); ++i, ++in)
tmp.i2.i[i] = *in;
if (TuplerLastTuples_<Pipe>::VALUE > tupleLen - i)
lastTuples = TuplerLastTuples_<Pipe>::VALUE - (tupleLen - i);
else
lastTuples = 0;
for(; i < tupleLen; ++i)
tmp.i2.i[i] = TValue();
tmp.i1 = 0;
}
};
//____________________________________________________________________________
template < typename TInput, unsigned tupleLen, bool omitLast >
struct Pipe< TInput, Tupler<tupleLen, omitLast, Compressed> >
{
TInput ∈
typename Value<Pipe>::Type tmp;
typename Size<TInput>::Type lastTuples;
Pipe(TInput& _in):
in(_in) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
if (eof(in)) --lastTuples;
tmp.i2 <<= 1;
++tmp.i1;
if (lastTuples == TuplerLastTuples_<Pipe>::VALUE) {
tmp.i2 |= *in;
++in;
}
return *this;
}
inline void fill() {
unsigned i;
clear(tmp.i2);
for(i = 0; i < tupleLen && !eof(in); ++i, ++in) {
tmp.i2 <<= 1;
tmp.i2 |= *in;
}
if (TuplerLastTuples_<Pipe>::VALUE > tupleLen - i)
lastTuples = TuplerLastTuples_<Pipe>::VALUE - (tupleLen - i);
else
lastTuples = 0;
tmp.i2 <<= (tupleLen - i);
tmp.i1 = 0;
}
};
//////////////////////////////////////////////////////////////////////////////
// tupler class for multiple sequences
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
struct Pipe< TInput, Multi<Tupler<tupleLen, omitLast, TCompression>, TPair, TLimitsString> >
{
typedef typename Value< typename Value<Pipe>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
typedef PairIncrementer_<TPair, TLimitsString> Incrementer;
TInput ∈
Incrementer localPos;
typename Value<Pipe>::Type tmp;
typename Size<TInput>::Type seqLength, lastTuples;
TLimitsString const &limits;
Pipe(TInput& _in, TLimitsString const &_limits):
in(_in),
limits(_limits) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
// process next sequence
if (eos())
if (--lastTuples == 0) {
assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
fill();
return *this;
}
// shift left 1 character
Loop<ShiftLeftWorker_, tupleLen - 1>::run(this->tmp);
assignValueI2(tmp.i1, getValueI2(tmp.i1) + 1);
if (lastTuples < TuplerLastTuples_<Pipe>::VALUE) {
tmp.i2[tupleLen - 1] = TValue();
} else {
tmp.i2[tupleLen - 1] = *in;
++localPos;
++in;
}
return *this;
}
inline void fill() {
do {
unsigned i = 0;
if (!eof(in))
do {
tmp.i2.i[i] = *in;
++in;
++i;
++localPos;
} while ((i < tupleLen) && !eos());
lastTuples = TuplerLastTuples_<Pipe>::VALUE;
// fill up with null chars
for(; i < tupleLen; ++i)
tmp.i2.i[i] = TValue();
// eventually, reduce the number of half-filled tuples
if (lastTuples <= tupleLen - i)
lastTuples = 0;
else
lastTuples -= tupleLen - i;
if (lastTuples == 0)
assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
} while ((lastTuples == 0) && !eof(in));
assignValueI2(tmp.i1, 0);
}
inline bool eos() {
return (getValueI1(localPos) > 0) && (getValueI2(localPos) == 0);
}
};
//____________________________________________________________________________
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TPair,
typename TLimitsString >
struct Pipe< TInput, Multi<Tupler<tupleLen, omitLast, Compressed>, TPair, TLimitsString> >
{
typedef typename Value< typename Value<Pipe>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
typedef PairIncrementer_<TPair, TLimitsString> Incrementer;
TInput ∈
Incrementer localPos;
typename Value<Pipe>::Type tmp;
typename Size<TInput>::Type seqLength, lastTuples;
TLimitsString const &limits;
Pipe(TInput& _in, TLimitsString const &_limits):
in(_in),
limits(_limits) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
// process next sequence
if (eos())
if (--lastTuples == 0) {
assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
fill();
return *this;
}
// shift left 1 character
tmp.i2 <<= 1;
assignValueI2(tmp.i1, getValueI2(tmp.i1) + 1);
if (lastTuples == TuplerLastTuples_<Pipe>::VALUE) {
tmp.i2 |= *in;
++localPos;
++in;
}
return *this;
}
inline void fill() {
do {
unsigned i = 0;
if (!eof(in))
do {
tmp.i2 <<= 1;
tmp.i2 |= *in;
++in;
++i;
++localPos;
} while ((i < tupleLen) && !eos());
lastTuples = TuplerLastTuples_<Pipe>::VALUE;
// fill up with null chars
tmp.i2 <<= (tupleLen - i);
// eventually, reduce the number of half-filled tuples
if (lastTuples <= tupleLen - i)
lastTuples = 0;
else
lastTuples -= tupleLen - i;
if (lastTuples == 0)
assignValueI1(tmp.i1, getValueI1(tmp.i1) + 1);
} while ((lastTuples == 0) && !eof(in));
assignValueI2(tmp.i1, 0);
}
inline bool eos() {
return (getValueI1(value(localPos)) > 0) && (getValueI2(value(localPos)) == 0);
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
inline bool
control(
Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > &me,
ControlBeginRead const &command)
{
if (!control(me.in, command)) return false;
me.fill();
return true;
}
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
inline bool
control(
Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > &me,
ControlBeginRead const &command)
{
if (!control(me.in, command)) return false;
setHost(me.localPos, me.limits);
assignValueI1(me.tmp.i1, 0);
me.fill();
return true;
}
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
inline bool
control(
Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > &me,
ControlEof const &)
{
return me.lastTuples == 0;
}
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
inline bool
control(
Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > &me,
ControlEof const &)
{
return me.lastTuples == 0;
}
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
inline bool
control(
Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > &me,
ControlEos const &)
{
return control(me, ControlEof());
}
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
inline bool
control(
Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > &me,
ControlEos const &)
{
return (getValueI1(me.tmp.i1) > 0) && (getValueI2(me.tmp.i1) == 0);
}
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
inline typename Size< Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > >::Type
length(Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > const &me)
{
typedef Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > TPipe;
if (length(me.in) >= (tupleLen - TuplerLastTuples_<TPipe>::VALUE))
return length(me.in) - (tupleLen - TuplerLastTuples_<TPipe>::VALUE);
else
return 0;
}
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
inline typename Size< Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > >::Type
length(Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > const &me)
{
typedef Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > TPipe;
unsigned seqs = countSequences(me);
if (length(me.in) >= seqs * (tupleLen - TuplerLastTuples_<TPipe>::VALUE))
return length(me.in) - seqs * (tupleLen - TuplerLastTuples_<TPipe>::VALUE);
else
return 0;
}
template < typename TInput, unsigned tupleLen, bool omitLast, typename TCompression >
inline unsigned
countSequences(Pipe< TInput, Tupler< tupleLen, omitLast, TCompression > > const &) {
return 1;
}
template <
typename TInput,
unsigned tupleLen,
bool omitLast,
typename TCompression,
typename TPair,
typename TLimitsString >
inline unsigned
countSequences(Pipe< TInput, Multi<Tupler< tupleLen, omitLast, TCompression >, TPair, TLimitsString> > const &me) {
return length(me.limits) - 1;
}
//}
}
#endif
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