text: // ==========================================================================
  //                 SeqAn - The Library for Sequence Analysis
  // ==========================================================================
  // Copyright (c) 2006-2016, 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 seqan {
  
  // ============================================================================
  // 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 seqan
  
  #endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_
  