// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
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// modification, are permitted provided that the following conditions are met:
//
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// ==========================================================================
// 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&lt;false, false, false, false&gt;</tt></dt>
 *   <dd>ordinary global alignment</dd>
 *   <dt><tt>AlignConfig&lt;true, false, false, true&gt;</tt></dt>
 *   <dd>semiglobal alignment, free begin and end gaps in second/vertical sequence</dd>
 *   <dt><tt>AlignConfig&lt;false, true, true, false&gt;</tt></dt>
 *   <dd>semiglobal alignment, free begin and end gaps in first/horizontal sequence</dd>
 *   <dt><tt>AlignConfig&lt;false, true, false, true&gt;</tt></dt>
 *   <dd>overlap alignment with second/vertical sequence overhanging to the left of first/horizontal</dd>
 *   <dt><tt>AlignConfig&lt;true, false, true, false&gt;</tt></dt>
 *   <dd>overlap alignment with first/horizontal sequence overhanging to the left of second/vertical</dd>
 *   <dt><tt>AlignConfig&lt;false, true, false, false&gt;</tt></dt>
 *   <dd>free begin gaps in second/vertical sequence only</dd>
 *   <dt><tt>AlignConfig&lt;false, false, true, false&gt;</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_
