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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
  // ==========================================================================
  
  // TODO(holtgrew): Should the public interface for the class Score not be defined here?
  
  #ifndef SEQAN_SSCORE_BASE_H_
  #define SEQAN_SSCORE_BASE_H_
  
  namespace seqan {
  
  /*!
   * @class Score
   * @headerfile <seqan/score.h>
   * @brief Scoring scheme.
   *
   * The Score class uses <b>similarity</b> scores, i.e. the greater the score value, the greater the similarity.
   * Depending on the exact score, the scores can also be negative for dissimilarity.  This choice blends in naturally
   * with the BLOSUM and PAM matrices, for examples.  For the edit distance common in computer science, this corresponds
   * to match scores of 0, mismatch and gap scores of -1.
   *
   * @signature template <[typename TValue[, typename TSpec]]>
   *            class Score;
   *
   * @tparam TValue The scoring value, defaults to <tt>int</tt>.
   * @tparam TSpec  The specialization type, defaults to <tt>Simple</tt>.
   *
   * @section Examples
   *
   * @include demos/dox/score/score.cpp
   *
   * The output is as follows:
   *
   * @include demos/dox/score/score.cpp.stdout
   */
  
  template <typename TValue = int, typename TSpec = Simple>
  class Score;
  
  /*!
   * @mfn Score#Value
   * @brief Return the value type of the scoring scheme.
   *
   * @signature Value<TScore>::Type;
   *
   * @tparam TScore The Score specialization.
   *
   * @return Type The score value type of the scoring scheme.
   */
  
  template <typename TValue, typename TSpec>
  struct Value<Score<TValue, TSpec> > {
      typedef TValue Type;
  };
  
  // --------------------------------------------------------------------------
  // Metafunction ConsensusScoreSequenceEntry
  // --------------------------------------------------------------------------
  
  /*!
   * @mfn Score#SequenceEntryForScore
   * @headerfile <seqan/score.h>
   *
   * @note This is used for unified interfaces for position dependent and independent scores.
   * @brief Returns representation type for a character of a position in a sequence.
   *
   * @signature SequenceEntryForScore<TScore, TSequence>::Type;
   *
   * @tparam TScore    The score type to use. Types: Score
   * @tparam TSequence The underlying sequence of the alignments or gaps. Types: ContainerConcept
   *
   * @return Type The type to use for representing a character in a sequence over its position.
   *
   *
   * @see Score#SequenceEntryForScore
   * @see Score#sequenceEntryForScore
   * @see ConsensusScoreSequenceEntry
   */
  
  template <typename TScore, typename TSequence>
  struct SequenceEntryForScore
  {
      typedef typename Value<TSequence>::Type Type;
  };
  
  // --------------------------------------------------------------------------
  // Function sequenceEntryForScore
  // --------------------------------------------------------------------------
  
  /*!
   * @fn Score#sequenceEntryForScore
   * @brief Helper function for element access, depending on score type.
   *
   * @signature TAlphabet sequenceEntryForScore(scoringScheme, seq, pos);
   *
   * @param[in] scoringScheme The Score to get the representation for.
   * @param[in] pos           The position of the character.
   * @param[in] seq           The sequence to get the representation for.
   *
   * @return TAlphabet The value of <tt>seq</tt> at <tt>pos</tt>.
   */
  
  // TODO(rmaerker): Check if using iterator instead would be more efficient than subscript operator.
  template <typename TScore, typename TSequence, typename TPosition>
  inline typename Value<TSequence>::Type
  sequenceEntryForScore(TScore const & /*scoringScheme*/, TSequence const & seq, TPosition pos)
  {
      return seq[pos];
  }
  
  /*!
   * @fn Score#scoreGapOpenHorizontal
   * @brief Returns the score for opening a gap in horizontal direction.
   *
   * @signature TValue scoreGapOpenHorizontal(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score open cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapOpenHorizontal(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGapOpen(me);
  }
  
  /*!
   * @fn Score#scoreGapOpenVertical
   * @brief Returns the score for opening a gap in vertical direction.
   *
   * @signature TValue scoreGapOpenVertical(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score open cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapOpenVertical(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGapOpen(me);
  }
  
  /*!
   * @fn Score#scoreGapExtendHorizontal
   * @brief Returns the score for extending a gap in horizontal direction.
   *
   * @signature TValue scoreGapExtendHorizontal(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score extension cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapExtendHorizontal(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGapExtend(me);
  }
  
  /*!
   * @fn Score#scoreGapExtendVertical
   * @brief Returns the score for extending a gap in vertical direction.
   *
   * @signature TValue scoreGapExtendVertical(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score extension cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence one and an insertion event in sequence two, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapExtendVertical(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGapExtend(me);
  }
  
  /*!
   * @fn Score#scoreGapHorizontal
   * @brief Returns the score for a gap in horizontal direction.
   *
   * @signature TValue scoreGapHorizontal(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score gap cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapHorizontal(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGap(me);
  }
  
  /*!
   * @fn Score#scoreGapVertical
   * @brief Returns the score for a gap in vertical direction.
   *
   * @signature TValue scoreGapVertical(score, entryH, entryV);
   *
   * @param[in] score  The Score to query.
   * @param[in] entryH Entry in sequence one (horizontal), type from Score#SequenceEntryForScore.
   * @param[in] entryV Entry in sequence two (vertical), type from Score#SequenceEntryForScore.
   *
   * @return TValue The score gap cost for gaps at the given position/entry.  TValue is the value type of score.
   *
   * @section Remarks
   *
   * Corresponds to a deletion event in sequence two and an insertion event in sequence one, respectively.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHValue, typename TSeqVValue>
  inline TValue
  scoreGapVertical(
      Score<TValue, TSpec> const & me,
      TSeqHValue const & /*seqHVal*/,
      TSeqVValue const & /*seqHVal*/)
  {
      return scoreGap(me);
  }
  
  /*!
   * @fn Score#score
   * @brief Returns similarity score for two sequence entries.
   *
   * @signature TValue score(score, entryH, entryV);
   *
   * @param[in] score  The Score to use for comparing the two sequence entries.
   * @param[in] entryH The entry in the first/horizontal sequence.
   * @param[in] entryV The entry in the second/vertical sequence.
   *
   * @return TValue The score similarity cost for gaps at the given position/entry.  TValue is the value type of
   *                score.
   */
  
  template <typename TValue, typename TSpec, typename TSeqHVal, typename TSeqVVal>
  inline TValue
  score(Score<TValue, TSpec> const & me, TSeqHVal valH, TSeqVVal valV) {
      if (valH == valV)
          return scoreMatch(me);
      else
          return scoreMismatch(me);
  }
  
  }  // namespace seqan
  
  #endif  // SEQAN_SSCORE_BASE_H_
  