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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// Author: Tobias Rausch <rausch@embl.de>
// ==========================================================================
// AlignTraceback object for storing the alignment traceback results.
//
// The _pump* functions for converting from AlignTrace to Gaps and Fragment
// String objects are defined where Gaps / the Alignment Graph spec is
// defined.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Specialization TraceBack
// ----------------------------------------------------------------------------
// TODO(holtgrew): Mark as internal with underscore?
/*!
* @typedef TraceBack
* @headerfile <seqan/align.h>
* @brief Traceback value.
*
* @signature struct TraceBack_;
* @signature typedef SimpleType<unsigned char, TraceBack_> TraceBack.
*
* The ValueSize of <tt>TraceBack</tt> is 3. The values are defined in the following way:
*
* <ul>
* <li>0 - Diagonal Move</li>
* <li>1 - Horizontal Move</li>
* <li>2 - Vertical Move</li>
* </ul>
*/
struct TraceBack_ {};
typedef SimpleType<unsigned char, TraceBack_> TraceBack;
template <> struct ValueSize<TraceBack>
{
typedef uint8_t Type;
static const Type VALUE = 3;
};
template <> struct BitsPerValue<TraceBack>
{
typedef uint8_t Type;
static const Type VALUE = 2;
};
// ----------------------------------------------------------------------------
// Helper Class AlignTraceback
// ----------------------------------------------------------------------------
// TODO(holtgrew): Mark as internal with underscore?
/*!
* @class AlignTraceback
* @headerfile <seqan/align.h>
* @brief Data structure for storing alignment traceback.
*
* @signature template <typename TSize>
* struct AlignTraceback;
*
* @tparam TSize Size type to use in the traceback.
*/
/*!
* @var TSizes AlignTraceback::sizes
* @brief The traceback lengths.
*/
/*!
* @var TLengths AlignTraceback::tsv
* @brief The traceback lengths.
*/
template <typename TSize>
struct AlignTraceback
{
// Run lengths in the align matrix.
String<TSize> sizes;
// Trace values: 0 = diagonal, 1 = horizontal, 2 = vertical.
String<TraceBack> tvs;
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _alignTracePrint()
// ----------------------------------------------------------------------------
// _alignTracePrint: this function is called by various alignment algorithm to build up the alignment during traceback
template <typename TSize, typename TSequenceH, typename TSequenceV, typename TId, typename TPos, typename TTraceValue>
inline void
_alignTracePrint(AlignTraceback<TSize> & tb,
TSequenceH const &,
TSequenceV const &,
TId const,
TPos const,
TId const,
TPos const,
TPos const segLen,
TTraceValue const tv)
{
appendValue(tb.sizes, segLen);
appendValue(tb.tvs, tv);
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_
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