/usr/include/seqan/index/pipe_merger3.h is in seqan-dev 1.3.1-1.
This file is owned by root:root, with mode 0o644.
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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_MERGER3_H
#define SEQAN_HEADER_INDEX_MERGER3_H
namespace SEQAN_NAMESPACE_MAIN
{
//namespace SEQAN_NAMESPACE_PIPELINING
//{
struct Merger3;
template < typename TInput0, typename TInput12 >
struct Value< Pipe< Bundle2< TInput0, TInput12 >, Merger3 > > {
typedef typename Size<TInput0>::Type Type;
};
//////////////////////////////////////////////////////////////////////////////
// merger3 class
template < typename TInput0, typename TInput12 >
struct Pipe< Bundle2< TInput0, TInput12 >, Merger3 >
{
typedef typename Value<TInput0>::Type InType0;
typedef typename Value<TInput12>::Type InType12;
typedef typename Size<Pipe>::Type SizeType;
Bundle2 <
TInput0,
TInput12 > in;
SizeType N, tmp;
int minStream;
bool twoStreams;
Pipe(Bundle2< TInput0, TInput12 > _in):
in(_in) {}
static inline bool less1(const InType0& i0, const InType12& i12)
{ // lexic. order for pairs
return (i0.i3[0] < i12.i3[0] ||
(i0.i3[0] == i12.i3[0] && i0.i2[0] < i12.i2[1]));
}
static inline bool less2(const InType0& i0, const InType12& i12)
{ // and triples
if (i0.i3[0] < i12.i3[0]) return true;
if (i0.i3[0] > i12.i3[0]) return false;
if (i0.i3[1] < i12.i3[1]) return true;
if (i0.i3[1] > i12.i3[1]) return false;
if (i0.i2[1] < i12.i2[1]) return true;
return false; // is also false if the names are equal (cross-border compare)
}
inline void getMin() {
if (twoStreams)
if ((*in.in2).i1 % 3 == 2 ? less1(*in.in1, *in.in2): less2(*in.in1, *in.in2)) {
minStream = 0;
tmp = N - (*in.in1).i1;
} else {
minStream = 1;
tmp = N - (*in.in2).i1;
}
else
if (minStream >= 0)
tmp = minStream? N - (*in.in2).i1: N - (*in.in1).i1;
}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
if (minStream) {
#ifdef SEQAN_TEST_SKEW3
InType12 a = *in.in2;
#endif
++in.in2;
if (eof(in.in2)) {
minStream = (twoStreams)? 0: -1;
twoStreams = false;
}
#ifdef SEQAN_TEST_SKEW3
else {
InType12 b = *in.in2;
SEQAN_ASSERT((a.i3[0] < b.i3[0]) || (a.i3[0] == b.i3[0] && a.i3[1] <= b.i3[1]));
SEQAN_ASSERT(a.i2[0] < b.i2[0]);
}
#endif
} else {
#ifdef SEQAN_TEST_SKEW3
InType0 a = *in.in1;
#endif
++in.in1;
if (eof(in.in1)) {
minStream = (twoStreams)? 1: -1;
twoStreams = false;
}
#ifdef SEQAN_TEST_SKEW3
else {
InType0 b = *in.in1;
SEQAN_ASSERT((a.i3[0] < b.i3[0]) || (a.i3[0] == b.i3[0] && a.i3[1] <= b.i3[1]));
SEQAN_ASSERT((a.i3[0] < b.i3[0]) || (a.i3[0] == b.i3[0] && a.i2[0] < b.i2[0]));
}
#endif
}
getMin();
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput >
inline bool control(Pipe< TInput, Merger3 > &me, ControlBeginRead const &command) {
if (!control(me.in, command)) return false;
me.twoStreams = !eof(me.in.in1);
me.minStream = eof(me.in.in2)? -1: 1;
me.N = length(me);
me.getMin();
return true;
}
template < typename TInput >
inline typename Size< Pipe< TInput, Merger3 > >::Type
length(Pipe< TInput, Merger3 > const &me) {
return length(me.in.in1) + length(me.in.in2);
}
//}
}
#endif
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