// ==========================================================================
//                 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: Jonathan Goeke <goeke@molgen.mpg.de>
// ==========================================================================
// This file contains the function that calls alignment free sequence
// comparisons algorithms (see AFScore):
// alignmentFreeComparison()
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_
#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_

namespace seqan {

/*!
 * @fn alignmentFreeComparison
 * @headerfile <seqan/alignment_free.h>
 * @brief Computes the pairwise similarity scores for a set of sequences.
 *
 * @signature void alignmentFreeComparison(scoreMatrix, sequenceSet, score);
 *
 * @param[out] scoreMatrix A two-dimensional @link Matrix @endlink, used to store all pairwise scores.
 * @param[in]  sequenceSet @link StringSet @endlink containing all sequences for which pairwise scores will be
 *                         computed.
 * @param[in]  score       The @link AFScore @endlink object to be used for computing the alignment.
 *
 * @section Examples
 *
 * Calculate the alignment free sequence similarity of two masked DNA sequences.
 *
 * @code{.cpp}
 * using namespace seqan;
 * StringSet<Dna5String> sequences;
 * Dna5String seq1 =
 *     "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
 *     "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
 *     "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
 *     "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
 *     "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
 *     "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
 *     "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
 * Dna5String seq2 =
 *     "ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA"
 *     "AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC"
 *     "CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA"
 *     "GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT"
 *     "GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA"
 *     "GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT"
 *     "CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG";
 *
 * clear(sequences);
 * appendValue(sequences, seq1);
 * appendValue(sequences, seq2);
 *
 * Matrix<double, 2> myMatrix;
 *
 * unsigned kmerSize = 5;
 * unsigned bgModelOrder = 1;
 * String<char>  revCom = "both_strands";
 * unsigned mismatches = 1;
 * double mismatchWeight = 0.5;
 * AFScore<N2> myScoreN2(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight);
 *
 * alignmentFreeComparison(myMatrix, sequences, myScoreN2);
 * std::cout << myMatrix;
 * @endcode
 */

template <typename TStringSet, typename TValue, typename TComparisonMethod>
void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComparisonMethod const & comparisonMethod)
{
    _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod);
}

}  // namespace seqan

#endif  // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_COMPARISON_H_
