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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: Tobias Rausch <rausch@embl.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class AlignConfig
// ----------------------------------------------------------------------------
/*!
* @class AlignConfig
* @headerfile <seqan/align.h>
* @brief Indication of whether begin/end gaps are free for DP alignment algorithms.
*
* @signature template <bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TSpec>
* struct AlignConfig;
*
* @tparam TOP Whether or not the begin gaps in the vertical sequence are free.
* @tparam LEFT Whether or not the begin gaps in the horizontal sequence are free.
* @tparam RIGHT Whether or not the end gaps in the horizontal sequence are free.
* @tparam BOTTOM Whether or not the end gap sin the vertical sequence are free.
* @tparam TSpec Tag for specializing the AlignConfig object (default: <tt>Default</tt>).
*
* Used in the DP alignment algorithms to configure the begin/end gap free-nes.
*
* @see globalAlignment
*
* @section Specialization List
*
* The following gives an (incomplete) list of useful AlignConfig specializations.
*
* <dl>
* <dt><tt>AlignConfig<false, false, false, false></tt></dt>
* <dd>ordinary global alignment</dd>
* <dt><tt>AlignConfig<true, false, false, true></tt></dt>
* <dd>semiglobal alignment, free begin and end gaps in second/vertical sequence</dd>
* <dt><tt>AlignConfig<false, true, true, false></tt></dt>
* <dd>semiglobal alignment, free begin and end gaps in first/horizontal sequence</dd>
* <dt><tt>AlignConfig<false, true, false, true></tt></dt>
* <dd>overlap alignment with second/vertical sequence overhanging to the left of first/horizontal</dd>
* <dt><tt>AlignConfig<true, false, true, false></tt></dt>
* <dd>overlap alignment with first/horizontal sequence overhanging to the left of second/vertical</dd>
* <dt><tt>AlignConfig<false, true, false, false></tt></dt>
* <dd>free begin gaps in second/vertical sequence only</dd>
* <dt><tt>AlignConfig<false, false, true, false></tt></dt>
* <dd>free end gaps in second/vertical sequence only</dd>
* </dl>
*/
template <bool TOP = false, bool LEFT = false, bool RIGHT = false, bool BOTTOM = false, typename TSpec = Default>
class AlignConfig
{};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// TODO(holtgrew): Make this follow the header structure.
template<bool TTop, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
inline void
_initFirstColumn(AlignConfig<TTop, false, TRight, TBottom, TSpec> const,
TElement& element,
TCost const cost)
{
element = cost;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
inline void
_initFirstColumn(AlignConfig<TTop, true, TRight, TBottom, TSpec> const,
TElement& element,
TCost const)
{
element = 0;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TLeft, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
inline void
_initFirstRow(AlignConfig<false, TLeft, TRight, TBottom, TSpec> const,
TElement& element,
TCost const cost)
{
element = cost;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TLeft, bool TRight, bool TBottom, typename TSpec, typename TElement, typename TCost>
inline void
_initFirstRow(AlignConfig<true, TLeft, TRight, TBottom, TSpec> const,
TElement& element,
TCost const)
{
element = 0;
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
TValue1&,
TIndex1&,
TValue2 const,
TIndex2 const)
{
// Nop
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastRow(AlignConfig<TTop, TLeft, TRight, true, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TValue2 const val,
TIndex2 const index)
{
if (val > maxValue[0]) {
maxValue[0] = val;
maxIndex[0] = index;
}
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TColumn>
inline void
_lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
TValue1& maxValue,
TIndex1&,
TColumn const& column)
{
maxValue[1] = column[length(column) - 1];
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TColumn>
inline void
_lastColumn(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TColumn const& column)
{
typedef typename Size<TColumn>::Type TSize;
typedef typename Iterator<TColumn, Standard>::Type TColIter;
TSize limit = length(column) - 1;
maxValue[1] = column[limit];
TColIter itCol = begin(column, Standard());
TColIter itColEnd = end(column, Standard());
for(TSize i = 0;itCol != itColEnd; ++i, ++itCol) {
if (*itCol > maxValue[1]) {
maxValue[1] = *itCol;
maxIndex[1] = i;
}
}
}
//////////////////////////////////////////////////////////////////////////////
template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
inline TScoreValue
_maxOfAlignment(AlignConfig<TTop, TLeft, false, false, TSpec> const,
TValue& maxValue,
TIndex&,
TSize const,
TSize const)
{
return maxValue[1];
}
//////////////////////////////////////////////////////////////////////////////
template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
inline TScoreValue
_maxOfAlignment(AlignConfig<TTop, TLeft, true, false, TSpec> const,
TValue& maxValue,
TIndex& maxIndex,
TSize const len1,
TSize const)
{
maxIndex[0] = len1;
return maxValue[1];
}
//////////////////////////////////////////////////////////////////////////////
template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
inline TScoreValue
_maxOfAlignment(AlignConfig<TTop, TLeft, false, true, TSpec> const,
TValue& maxValue,
TIndex& maxIndex,
TSize const,
TSize const len2)
{
maxIndex[1] = len2;
return maxValue[0];
}
//////////////////////////////////////////////////////////////////////////////
template<typename TScoreValue, bool TTop, bool TLeft, typename TSpec, typename TValue, typename TIndex, typename TSize>
inline TScoreValue
_maxOfAlignment(AlignConfig<TTop, TLeft, true, true, TSpec> const,
TValue& maxValue,
TIndex& maxIndex,
TSize const len1,
TSize const len2)
{
// Find the maximum
if (maxValue[1] > maxValue[0]) maxIndex[0] = len1;
else maxIndex[1] = len2;
return (maxValue[0] > maxValue[1]) ? maxValue[0] : maxValue[1];
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastColumn(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TValue2 const val,
TIndex2 const row,
TIndex2 const col)
{
maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TBottom, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastColumn(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TValue2 const val,
TIndex2 const row,
TIndex2 const col)
{
if (val > maxValue[1]) {maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; }
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastRow(AlignConfig<TTop, TLeft, TRight, false, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TValue2 const val,
TIndex2 const row,
TIndex2 const col)
{
maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TRight, typename TSpec, typename TValue1, typename TIndex1, typename TValue2, typename TIndex2>
inline void
_lastRow(AlignConfig<TTop, TLeft, TRight, true, TSpec> const,
TValue1& maxValue,
TIndex1& maxIndex,
TValue2 const val,
TIndex2 const row,
TIndex2 const col)
{
if (val > maxValue[0]) {maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; }
}
//////////////////////////////////////////////////////////////////////////////
template<bool TLeft, bool TRight, bool TBottom, typename TSpec>
inline bool
_configValueTop(AlignConfig<true, TLeft, TRight, TBottom, TSpec> const)
{
return true;
}
template<bool TLeft, bool TRight, bool TBottom, typename TSpec>
inline bool
_configValueTop(AlignConfig<false, TLeft, TRight, TBottom, TSpec> const)
{
return false;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TRight, bool TBottom, typename TSpec>
inline bool
_configValueLeft(AlignConfig<TTop, true, TRight, TBottom, TSpec> const)
{
return true;
}
template<bool TTop, bool TRight, bool TBottom, typename TSpec>
inline bool
_configValueLeft(AlignConfig<TTop, false, TRight, TBottom, TSpec> const)
{
return false;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TBottom, typename TSpec>
inline bool
_configValueRight(AlignConfig<TTop, TLeft, true, TBottom, TSpec> const)
{
return true;
}
template<bool TTop, bool TLeft, bool TBottom, typename TSpec>
inline bool
_configValueRight(AlignConfig<TTop, TLeft, false, TBottom, TSpec> const)
{
return false;
}
//////////////////////////////////////////////////////////////////////////////
template<bool TTop, bool TLeft, bool TRight, typename TSpec>
inline bool
_configValueBottom(AlignConfig<TTop, TLeft, TRight, true, TSpec> const)
{
return true;
}
template<bool TTop, bool TLeft, bool TRight, typename TSpec>
inline bool
_configValueBottom(AlignConfig<TTop, TLeft, TRight, false, TSpec> const)
{
return false;
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
|
