/usr/include/seqan/index/pipe_merger7.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_INDEX_MERGER7_H
#define SEQAN_HEADER_INDEX_MERGER7_H
namespace SEQAN_NAMESPACE_MAIN
{
//namespace SEQAN_NAMESPACE_PIPELINING
//{
template <int I, typename T = void>
struct SkewShift_;
template <int I, typename T = void>
struct SkewNIndex_;
template <typename T>
struct SkewShift_<7, T> {
static const unsigned VALUE[7][7];
};
template <typename T>
struct SkewNIndex_<7, T> {
static const unsigned VALUE[7][7];
};
template <typename T>
const unsigned SkewShift_<7, T>::VALUE[7][7] =
{{0,6,5,6,3,3,5},
{6,0,0,6,0,4,4},
{5,0,0,1,0,1,5},
{6,6,1,0,2,1,2},
{3,0,0,2,0,3,2},
{3,4,1,1,3,0,4},
{5,4,5,2,2,4,0}};
template <typename T>
const unsigned SkewNIndex_<7, T>::VALUE[7][7] =
{{0,0,0,0,0,1,2},
{0,0,0,0,1,1,2},
{0,1,1,1,1,2,2},
{0,0,1,1,1,1,2},
{0,0,1,2,2,2,2},
{0,0,0,1,2,2,2},
{0,0,0,0,1,2,2}};
template <typename TValue>
struct SkewDCStream {
TValue i;
unsigned stream;
};
template <typename TValue>
std::ostream& operator<<(std::ostream &out, const SkewDCStream<TValue> &s) {
out << "< " << s.i.i1 << " , [ ";
for(unsigned i = 0; i < 3; ++i)
out << s.i.i2[i] << " ";
out << "] , [ ";
for(unsigned i = 0; i < 6; ++i)
out << s.i.i3[i] << " ";
out << "] , " << s.stream << " >";
return out;
}
// greater-operator for two SkewDCStreams
template <typename TValue>
struct CompareSkewDCStream :
public ::std::binary_function < SkewDCStream<TValue>,
SkewDCStream<TValue>,
bool >
{
inline bool operator()(const SkewDCStream<TValue> &a,
const SkewDCStream<TValue> &b) const
{
typedef typename TValue::T2::T SizeType;
int shft = SkewShift_<7>::VALUE[a.stream][b.stream];
for(int i = 0; i < shft; ++i) {
if (a.i.i3[i] < b.i.i3[i]) return false;
if (a.i.i3[i] > b.i.i3[i]) return true;
}
SizeType na = a.i.i2[SkewNIndex_<7>::VALUE[a.stream][shft]];
SizeType nb = b.i.i2[SkewNIndex_<7>::VALUE[b.stream][shft]];
if (na < nb) return false;
if (na > nb) return true;
// we get here, only if a septet crosses the border of
// the single text or a sequence in a multiple sequence text
return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
}
};
// greater-operator for two SkewDCStreams (optimized for bit-compressed character tuples)
template <typename T1, typename T2, typename T, unsigned _size>
struct CompareSkewDCStream< Triple<T1,T2,Tuple<T,_size,Compressed>, Compressed> > :
public ::std::binary_function < SkewDCStream<Triple<T1,T2,Tuple<T,_size,Compressed>,Compressed> >,
SkewDCStream<Triple<T1,T2,Tuple<T,_size,Compressed>,Compressed> >,
bool >
{
typedef Tuple<T,_size,Compressed> T3;
inline bool operator()(const SkewDCStream<Triple<T1,T2,T3,Compressed> > &a,
const SkewDCStream<Triple<T1,T2,T3,Compressed> > &b) const
{
typedef typename T2::T SizeType;
int shft = SkewShift_<7>::VALUE[a.stream][b.stream];
typename T3::CT mask = ~((1 << ((_size - shft) * T3::bitSize)) - 1);
if ((a.i.i3.i & mask) < (b.i.i3.i & mask)) return false;
if ((a.i.i3.i & mask) > (b.i.i3.i & mask)) return true;
SizeType na = a.i.i2[SkewNIndex_<7>::VALUE[a.stream][shft]];
SizeType nb = b.i.i2[SkewNIndex_<7>::VALUE[b.stream][shft]];
if (na < nb) return false;
if (na > nb) return true;
// we get here, only if a septet crosses the border of
// the single text or a sequence in a multiple sequence text
return a.stream - 1 > b.stream - 1; // this is NOT the same as a.stream > b.stream, 0 should be bigger than 6
}
};
struct Merger7;
template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124 >
struct Value< Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7 > > {
typedef typename Value<TInput0>::Type::T1 Type;
};
template <typename TLimitsString>
struct Merger7Multi;
template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124, typename TLimitsString >
struct Value< Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7Multi<TLimitsString> > > {
typedef typename Value<TInput0>::Type::T1 Type;
};
//////////////////////////////////////////////////////////////////////////////
// merger7 class
template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124 >
struct Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7 >
{
typedef typename Value<TInput0>::Type InType0;
typedef typename Value<TInput3>::Type InType3;
typedef typename Value<TInput5>::Type InType5;
typedef typename Value<TInput6>::Type InType6;
typedef typename Value<TInput124>::Type InType124;
typedef typename Size<Pipe>::Type SizeType;
typedef typename InType0::T3::T Type;
typedef SkewDCStream<InType0> TSkewDCStream;
TSkewDCStream inValue[7];
unsigned rank[5];
unsigned first;
CompareSkewDCStream<InType0> streamGreater;
Bundle5 <
TInput0,
TInput3,
TInput5,
TInput6,
TInput124 > in;
SizeType N;
Pipe(Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 > _in):
in(_in) {}
template <typename T1, typename T2, typename T3>
inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,T3,Compressed> const &src) {
memcpy(&dst.i.i2, &src.i2, sizeof(T2));
memcpy(&dst.i.i3, &src.i3, sizeof(T3));
}
template <typename T1, typename T2, typename T, unsigned _size>
inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,Tuple<T,_size,Compressed>,Compressed> const &src)
{
typedef typename InType0::T3 CharTuple;
memcpy(&dst.i.i2, &src.i2, sizeof(T2));
dst.i.i3 = src.i3;
dst.i.i3 <<= CharTuple::size - _size;
}
inline typename Value<Pipe>::Type const operator*() {
return getValueI1(inValue[rank[first]].i);
}
inline void insertStream(unsigned stream) {
switch (stream) {
case 0:
if (eof(in.in1)) {
++first;
return;
}
inValue[0].i.i1 = N - (*in.in1).i1;
_copy(inValue[0], *in.in1);
++in.in1;
break;
case 3:
if (eof(in.in2)) {
++first;
return;
}
inValue[3].i.i1 = N - (*in.in2).i1;
_copy(inValue[3], *in.in2);
++in.in2;
break;
case 5:
if (eof(in.in3)) {
++first;
return;
}
inValue[5].i.i1 = N - (*in.in3).i1;
_copy(inValue[5], *in.in3);
++in.in3;
break;
case 6:
if (eof(in.in4)) {
++first;
return;
}
inValue[6].i.i1 = N - (*in.in4).i1;
_copy(inValue[6], *in.in4);
++in.in4;
break;
default: // case 1, 2, or 4
if (eof(in.in5)) {
++first;
return;
}
// calculate residue class from the suffix length
inValue[1].stream = (*in.in5).i1 % 7;
inValue[1].i.i1 = N - (*in.in5).i1;
_copy(inValue[1], *in.in5);
++in.in5;
}
// linear search
int right;
for(right = first + 1; right < 5; ++right)
if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
// remove the least suffix ...
for(int i = first + 1; i < right; ++i)
rank[i-1] = rank[i];
// ... and insert the new one
rank[right-1] = stream;
}
Pipe& operator++() {
insertStream(rank[first]);
return *this;
}
void fill() {
inValue[0].stream = 0;
inValue[3].stream = 3;
inValue[5].stream = 5;
inValue[6].stream = 6;
first = 4; insertStream(0);
--first; insertStream(3);
--first; insertStream(5);
--first; insertStream(6);
--first; insertStream(1);
}
};
//////////////////////////////////////////////////////////////////////////////
// merger7 class for multiple sequences
template < typename TInput0, typename TInput3, typename TInput5, typename TInput6, typename TInput124, typename TLimitsString >
struct Pipe< Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 >, Merger7Multi<TLimitsString> >
{
typedef typename Value<TInput0>::Type InType0;
typedef typename Value<TInput3>::Type InType3;
typedef typename Value<TInput5>::Type InType5;
typedef typename Value<TInput6>::Type InType6;
typedef typename Value<TInput124>::Type InType124;
typedef typename Size<Pipe>::Type SizeType;
typedef typename InType0::T3::T Type;
typedef SkewDCStream<InType0> TSkewDCStream;
TSkewDCStream inValue[7];
unsigned rank[5];
unsigned first;
CompareSkewDCStream<InType0> streamGreater;
Bundle5 <
TInput0,
TInput3,
TInput5,
TInput6,
TInput124 > in;
TLimitsString const &limits;
Pipe(Bundle5< TInput0, TInput3, TInput5, TInput6, TInput124 > _in, TLimitsString const &_limits):
in(_in),
limits(_limits) {}
template <typename T1, typename T2, typename T3>
inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,T3,Compressed> const &src) {
memcpy(&dst.i.i1, &src.i1, sizeof(T1));
memcpy(&dst.i.i2, &src.i2, sizeof(T2));
memcpy(&dst.i.i3, &src.i3, sizeof(T3));
}
template <typename T1, typename T2, typename T, unsigned _size>
inline static void _copy(TSkewDCStream &dst, Triple<T1,T2,Tuple<T,_size,Compressed>,Compressed> const &src)
{
typedef typename InType0::T3 CharTuple;
memcpy(&dst.i.i1, &src.i1, sizeof(T1));
memcpy(&dst.i.i2, &src.i2, sizeof(T2));
dst.i.i3 = src.i3;
dst.i.i3 <<= CharTuple::size - _size;
}
inline typename Value<Pipe>::Type const operator*() {
return getValueI1(inValue[rank[first]].i);
}
inline void insertStream(unsigned stream) {
switch (stream) {
case 0:
if (eof(in.in1)) {
++first;
return;
}
_copy(inValue[0], *in.in1);
++in.in1;
break;
case 3:
if (eof(in.in2)) {
++first;
return;
}
_copy(inValue[3], *in.in2);
++in.in2;
break;
case 5:
if (eof(in.in3)) {
++first;
return;
}
_copy(inValue[5], *in.in3);
++in.in3;
break;
case 6:
if (eof(in.in4)) {
++first;
return;
}
_copy(inValue[6], *in.in4);
++in.in4;
break;
default: // case 1, 2, or 4
if (eof(in.in5)) {
++first;
return;
}
// calculate residue class from the suffix length
typename Value<InType124,1>::Type in_in5_i1 = getValueI1(*in.in5);
unsigned seqNo = getValueI1(in_in5_i1);
inValue[1].stream = ((limits[seqNo + 1] - limits[seqNo]) - getValueI2(in_in5_i1)) % 7;
_copy(inValue[1], *in.in5);
++in.in5;
}
// linear search
int right;
for(right = first + 1; right < 5; ++right)
if (!streamGreater(inValue[stream],inValue[rank[right]])) break;
// remove the least suffix ...
for(int i = first + 1; i < right; ++i)
rank[i-1] = rank[i];
// ... and insert the new one
rank[right-1] = stream;
}
Pipe& operator++() {
insertStream(rank[first]);
return *this;
}
void fill() {
inValue[0].stream = 0;
inValue[3].stream = 3;
inValue[5].stream = 5;
inValue[6].stream = 6;
first = 4; insertStream(0);
--first; insertStream(3);
--first; insertStream(5);
--first; insertStream(6);
--first; insertStream(1);
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput >
inline bool control(Pipe< TInput, Merger7 > &me, ControlBeginRead const &command) {
if (!control(me.in, command)) return false;
me.N = length(me);
me.fill();
return true;
}
template < typename TInput >
inline bool control(Pipe< TInput, Merger7 > &me, ControlEof const &) {
return me.first == 5;
}
template < typename TInput >
inline bool control(Pipe< TInput, Merger7 > &me, ControlEos const &) {
return control(me, ControlEof());
}
template < typename TInput >
inline typename Size< Pipe< TInput, Merger7 > >::Type
length(Pipe< TInput, Merger7 > const &me) {
return length(me.in.in1) +
length(me.in.in2) +
length(me.in.in3) +
length(me.in.in4) +
length(me.in.in5);
}
template < typename TInput, typename TLimitsString >
inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlBeginRead const &command) {
if (!control(me.in, command)) return false;
me.fill();
return true;
}
template < typename TInput, typename TLimitsString >
inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEof const &) {
return me.first == 5;
}
template < typename TInput, typename TLimitsString >
inline bool control(Pipe< TInput, Merger7Multi<TLimitsString> > &me, ControlEos const &) {
return control(me, ControlEof());
}
template < typename TInput, typename TLimitsString >
inline typename Size< Pipe< TInput, Merger7Multi<TLimitsString> > >::Type
length(Pipe< TInput, Merger7Multi<TLimitsString> > const &me) {
return length(me.in.in1) +
length(me.in.in2) +
length(me.in.in3) +
length(me.in.in4) +
length(me.in.in5);
}
//}
}
#endif
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