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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_PUMP_EXTENDER3_H
#define SEQAN_HEADER_PUMP_EXTENDER3_H
namespace seqan2
{
//namespace seqan2_NAMESPACE_PIPELINING
//{
struct Extender3;
template < typename TTextInput, typename TNameInput >
struct Pipe< Bundle2< TTextInput, TNameInput >, Extender3 >
{
enum { maxShift = 2 };
typedef typename Size<Pipe>::Type TSize;
typedef typename Value<TTextInput>::Type TValue;
typedef typename Value<TNameInput>::Type TNameInputValue;
typedef typename Value<TNameInputValue, 2>::Type TName;
typedef Tuple<TValue, maxShift> XTuple;
typedef Tuple<TName, maxShift> NTuple;
typedef Triple<TSize, NTuple, XTuple, Pack> OutType0;
typedef Triple<TSize, NTuple, XTuple, Pack> OutType12;
// pipeline interfaces to ease specialization
typedef Pipe< void, AbstractSource< OutType0, TSize > > Out0;
typedef Pipe< void, AbstractSource< OutType12, TSize > > Out12;
};
template < typename TTextInput, typename TNameInput, typename TOut0, typename TOut12 >
static bool _skew3Extend(TTextInput &textIn, TNameInput &nameIn, TOut0 &out0, TOut12 &out12)
{
resize(out0, length(textIn) / 3);
resize(out12, length(nameIn));
if (!(
beginRead(textIn) &&
beginRead(nameIn) &&
beginWrite(out0) &&
beginWrite(out12))) return false;
typename Value<TOut0>::Type o0 = typename Value<TOut0>::Type();
typename Value<TOut12>::Type o1 = typename Value<TOut12>::Type();
typename Value<TOut12>::Type o2 = typename Value<TOut12>::Type();
unsigned r = (unsigned)(length(textIn) % 3);
bool filled = (r != 0);
if (r == 2)
{
o2.i1 = (*nameIn).i1;
o2.i2[0] = (*nameIn).i2; ++nameIn;
o2.i3[0] = *textIn; ++textIn;
}
if (r >= 1)
{
o1.i1 = (*nameIn).i1;
o1.i2[0] = (*nameIn).i2; ++nameIn;
o1.i3[0] = *textIn; ++textIn;
}
if (r == 2)
{
o2.i2[1] = o1.i2[0];
o2.i3[1] = o1.i3[0];
push(out12, o2);
}
while (!eof(nameIn))
{
o1.i3[1] = o0.i3[0] = *textIn; ++textIn;
o2.i3[0] = o0.i3[1] = *textIn; ++textIn;
o2.i1 = (*nameIn).i1;
o0.i2[0] = o2.i2[0] = o1.i2[1] = (*nameIn).i2; ++nameIn;
o2.i3[1] = *textIn; ++textIn;
if (filled)
push(out12, o1);
else
filled = true;
o1.i1 = (*nameIn).i1;
o0.i2[1] = o2.i2[1] = o1.i2[0] = (*nameIn).i2; ++nameIn;
o1.i3[0] = o2.i3[1];
push(out12, o2);
o0.i1 = o2.i1 + 1;
push(out0, o0);
}
o1.i2[1] = 0;
o1.i3[1] = 0;
if (filled) push(out12, o1);
endWrite(out12);
endWrite(out0);
endRead(nameIn);
endRead(textIn);
return true;
}
//}
}
#endif
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