text: // ==========================================================================
  //                 SeqAn - The Library for Sequence Analysis
  // ==========================================================================
  // Copyright (c) 2006-2013, 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>
  // ==========================================================================
  // Global alignment interface for the banded Needleman-Wunsch and Gotoh
  // algorithms.
  //
  // We define the interface functions pretty explicitely (versus just TAlign,
  // TFragments etc.) so the candidates the compiler gives when resolution to
  // the globalFunction() fails is actually meaningful.
  // ==========================================================================
  
  #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
  #define SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
  
  namespace seqan {
  
  // ============================================================================
  // Forwards
  // ============================================================================
  
  template <typename TScoreValue, typename TSpec>
  class Score;
  template <typename TSpec>
  class Graph;
  template <typename TStringSet, typename TCargo, typename TGraphSpec>
  struct Alignment;
  template <typename TSize, typename TFragmentSpec>
  class Fragment;
  
  // ============================================================================
  // Tags, Classes, Enums
  // ============================================================================
  
  // ============================================================================
  // Metafunctions
  // ============================================================================
  
  // ============================================================================
  // Functions
  // ============================================================================
  
  // ----------------------------------------------------------------------------
  // Function globalAlignment()                                   [banded, Align]
  // ----------------------------------------------------------------------------
  
  template <typename TSequence, typename TAlignSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & /*algoTag*/)
  {
      typedef Align<TSequence, TAlignSpec> TAlign;
      typedef typename Size<TAlign>::Type  TSize;
      typedef typename Position<TAlign>::Type TPosition;
      typedef TraceSegment_<TPosition, TSize> TTraceSegment;
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      String<TTraceSegment> trace;
  
      DPScoutState_<Default> dpScoutState;
      TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)),
                                              scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel());
  
      _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace);
      return res;
  }
  
  // Interface without AlignConfig<>.
  template <typename TSequence, typename TAlignSpec,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & algoTag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TSequence, typename TAlignSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                              int lowerDiag,
                              int upperDiag)
  {
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, LinearGaps());
      else
          return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, AffineGaps());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TSequence, typename TAlignSpec,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignment(Align<TSequence, TAlignSpec> & align,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  // ----------------------------------------------------------------------------
  // Function globalAlignment()                                    [banded, Gaps]
  // ----------------------------------------------------------------------------
  
  template <typename TSequenceH, typename TGapsSpecH,
            typename TSequenceV, typename TGapsSpecV,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                              Gaps<TSequenceV, TGapsSpecV> & gapsV,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & /*algoTag*/)
  {
      typedef typename Size<TSequenceH>::Type TSize;
      typedef typename Position<TSequenceH>::Type TPosition;
      typedef TraceSegment_<TPosition, TSize> TTraceSegment;
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      String<TTraceSegment> trace;
  
      DPScoutState_<Default> dpScoutState;
      TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme,
                                              TAlignConfig2(lowerDiag, upperDiag), TGapModel());
      _adaptTraceSegmentsTo(gapsH, gapsV, trace);
      return res;
  }
  
  // Interface without AlignConfig<>.
  template <typename TSequenceH, typename TGapsSpecH,
            typename TSequenceV, typename TGapsSpecV,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                              Gaps<TSequenceV, TGapsSpecV> & gapsV,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & algoTag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TSequenceH, typename TGapsSpecH,
            typename TSequenceV, typename TGapsSpecV,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                              Gaps<TSequenceV, TGapsSpecV> & gapsV,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                              int lowerDiag,
                              int upperDiag)
  {
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
      else
          return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TSequenceH, typename TGapsSpecH,
            typename TSequenceV, typename TGapsSpecV,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
                              Gaps<TSequenceV, TGapsSpecV> & gapsV,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  // ----------------------------------------------------------------------------
  // Function globalAlignment()                     [banded, Graph<Alignment<> >]
  // ----------------------------------------------------------------------------
  
  // Full interface.
  template <typename TStringSet, typename TCargo, typename TGraphSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & /*algoTag*/)
  {
      typedef Graph<Alignment<TStringSet, TCargo, TGraphSpec> > TGraph;
      typedef typename Position<TGraph>::Type TPosition;
      typedef typename Size<TGraph>::Type TSize;
      typedef TraceSegment_<TPosition, TSize> TTraceSegment;
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      String<TTraceSegment> trace;
  
      DPScoutState_<Default> dpScoutState;
      TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0),
                                              value(stringSet(alignmentGraph), 1), scoringScheme,
                                              TAlignConfig2(lowerDiag, upperDiag), TGapModel());
  
      _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0),
                            positionToId(stringSet(alignmentGraph), 1), trace);
      return res;
  }
  
  // Interface without AlignConfig<>.
  template <typename TStringSet, typename TCargo, typename TGraphSpec,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & algoTag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TStringSet, typename TCargo, typename TGraphSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                              int lowerDiag,
                              int upperDiag)
  {
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
      else
          return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TStringSet, typename TCargo, typename TGraphSpec,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignment(Graph<Alignment<TStringSet, TCargo, TGraphSpec> > & alignmentGraph,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  // ----------------------------------------------------------------------------
  // Function globalAlignment()                     [banded, String<Fragment<> >]
  // ----------------------------------------------------------------------------
  
  // Full interface.
  template <typename TSize, typename TFragmentSpec, typename TStringSpec,
            typename TSequence, typename TStringSetSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                              StringSet<TSequence, TStringSetSpec> const & strings,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & /*algoTag*/)
  {
      typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments;
      typedef typename Position<TFragments>::Type TPosition;
      typedef TraceSegment_<TPosition, TSize> TTraceSegment;
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      String<TTraceSegment> trace;
  
      DPScoutState_<Default> dpScoutState;
      TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme,
                                              TAlignConfig2(lowerDiag, upperDiag), TGapModel());
  
      _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace);
      return res;
  }
  
  // Interface without AlignConfig<>.
  template <typename TSize, typename TFragmentSpec, typename TStringSpec,
            typename TSequence, typename TStringSetSpec,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                              StringSet<TSequence, TStringSetSpec> const & strings,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag,
                              TAlgoTag const & algoTag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TSize, typename TFragmentSpec, typename TStringSpec,
            typename TSequence, typename TStringSetSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                              StringSet<TSequence, TStringSetSpec> const & strings,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                              int lowerDiag,
                              int upperDiag)
  {
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
      else
          return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TSize, typename TFragmentSpec, typename TStringSpec,
            typename TSequence, typename TStringSetSpec,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
                              StringSet<TSequence, TStringSetSpec> const & strings,
                              Score<TScoreValue, TScoreSpec> const & scoringScheme,
                              int lowerDiag,
                              int upperDiag)
  {
      AlignConfig<> alignConfig;
      return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  // ----------------------------------------------------------------------------
  // Function globalAlignmentScore()                        [banded, 2 Strings]
  // ----------------------------------------------------------------------------
  
  template <typename TSequenceH,
            typename TSequenceV,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                   TSequenceV const & seqV,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                                   int lowerDiag,
                                   int upperDiag,
                                   TAlgoTag const & /*algoTag*/)
  {
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      DPScoutState_<Default> dpScoutState;
      String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
      return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme,
                                   TAlignConfig2(lowerDiag, upperDiag), TGapModel());
  }
  
  // Interface without AlignConfig<>.
  template <typename TSequenceH,
            typename TSequenceV,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                   TSequenceV const & seqV,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   int lowerDiag,
                                   int upperDiag,
                                   TAlgoTag const & algoTag)
  {
      AlignConfig<> alignConfig;
      return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TSequenceH,
            typename TSequenceV,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                   TSequenceV const & seqV,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                                   int lowerDiag,
                                   int upperDiag)
  {
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
      else
          return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TSequenceH,
            typename TSequenceV,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignmentScore(TSequenceH const & seqH,
                                   TSequenceV const & seqV,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   int lowerDiag,
                                   int upperDiag)
  {
      AlignConfig<> alignConfig;
      return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  // ----------------------------------------------------------------------------
  // Function globalAlignmentScore()                        [banded, StringSet]
  // ----------------------------------------------------------------------------
  
  template <typename TString, typename TSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec,
            typename TAlgoTag>
  TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & /*alignConfig*/,
                                   int lowerDiag,
                                   int upperDiag,
                                   TAlgoTag const & /*algoTag*/)
  {
      typedef AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> TAlignConfig;
      typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps;
      typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2;
      typedef typename SubstituteAlgoTag_<TAlgoTag>::Type TGapModel;
  
      SEQAN_ASSERT_EQ(length(strings), 2u);
  
      DPScoutState_<Default> dpScoutState;
      String<TraceSegment_<unsigned, unsigned> > traceSegments;  // Dummy segments.
      return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme,
                                   TAlignConfig2(lowerDiag, upperDiag), TGapModel());
  }
  
  // Interface without AlignConfig<>.
  template <typename TString, typename TSpec,
            typename TScoreValue, typename TScoreSpec,
            typename TAlgoTag>
  TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   int lowerDiag,
                                   int upperDiag,
                                   TAlgoTag const & algoTag)
  {
      SEQAN_ASSERT_EQ(length(strings), 2u);
  
      AlignConfig<> alignConfig;
      return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag);
  }
  
  // Interface without algorithm tag.
  template <typename TString, typename TSpec,
            typename TScoreValue, typename TScoreSpec,
            bool TOP, bool LEFT, bool RIGHT, bool BOTTOM, typename TACSpec>
  TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec> const & alignConfig,
                                   int lowerDiag,
                                   int upperDiag)
  {
      SEQAN_ASSERT_EQ(length(strings), 2u);
  
      if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme))
          return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch());
      else
          return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh());
  }
  
  // Interface without AlignConfig<> and algorithm tag.
  template <typename TString, typename TSpec,
            typename TScoreValue, typename TScoreSpec>
  TScoreValue globalAlignmentScore(StringSet<TString, TSpec> const & strings,
                                   Score<TScoreValue, TScoreSpec> const & scoringScheme,
                                   int lowerDiag,
                                   int upperDiag)
  {
      SEQAN_ASSERT_EQ(length(strings), 2u);
  
      AlignConfig<> alignConfig;
      return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag);
  }
  
  }  // namespace seqan
  
  #endif  // #ifndef SEQAN_CORE_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_
  