// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
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// ==========================================================================
// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
// ==========================================================================
// Reduced Versions of the 24-letter amino acid alphabet
// ==========================================================================

#ifndef SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_
#define SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_

namespace seqan2 {

// ============================================================================
// Forwards
// ============================================================================

// ============================================================================
// Tags, Classes, Enums
// ============================================================================

// -----------------------------------------------------------------------
// Tag ClusterReduction
// -----------------------------------------------------------------------

/*
 * @class ClusterReduction
 * @brief Specialization for @link ReducedAminoAcid @endlink
 * @headerfile seqan/reduced_aminoacid.h
 *
 * @signature template <unsigned char n, unsigned char m = 24, typename TMatrix = Blosum62>
 * struct ClusterReduction;
 *
 * @tparam n the size of the reduced alphabet (between 2 and m-1)
 * @tparam m size to truncate alphabet to, <b>before</b> clustering
 * (one of 20, 22, 24; default 24)
 * @tparam TMatrix Matrix used for clustering (default @link Blosum62 @endlink,
 * none other supported right now)
 *
 * @section WhenToUse
 *
 * Use m = 24 when you expect 'X' and '*' in the dataset you reduce
 * from. This is especially the case on translated genomic reads.
 *
 * If you have validated protein sequences, you can use can use m = 20 or
 * m = 22, which will not include special characters (see
 * @link AminoAcid @endlink for details).
 *
 * @section Background
 *
 * The method employed for reducing the alphabet is similar to Murphy et al,
 * 2000, <a href="https://www.ncbi.nlm.nih.gov/pubmed/10775656">https://www.ncbi.nlm.nih.gov/pubmed/10775656</a>
 *
 * Correlation coefficients for the Blosum62 scores of all pairs of amino
 * acids in the alphabet were computed and clustered with WPGMA (using
 * UPGMA as second criterium when WPGMA yields the same
 * distance between two clusters).
 *
 * <img src="ClusterReduction.png">
 *
 * The exact clustering for m = 24.
 *
 */

template <unsigned char n, unsigned char m = 24, typename TMatrix = Blosum62>
struct ClusterReduction;

// ============================================================================
// Metafunctions
// ============================================================================

// -----------------------------------------------------------------------
// Metafunction ValueSize
// -----------------------------------------------------------------------

template <unsigned char n, unsigned char m, typename TMatrix>
struct ValueSize<
        SimpleType<unsigned char,
                   ReducedAminoAcid_<ClusterReduction<n, m, TMatrix> > > >
{
    typedef uint8_t Type;
    static const Type VALUE = n;
};

// -----------------------------------------------------------------------
// Metafunction BitPerValue
// -----------------------------------------------------------------------

template <unsigned char n, unsigned char m, typename TMatrix>
struct BitsPerValue<
         SimpleType<unsigned char,
                    ReducedAminoAcid_<ClusterReduction<n, m, TMatrix> > > >
{
    typedef uint8_t Type;
    static const Type VALUE = Log2<n>::VALUE;
};

// -----------------------------------------------------------------------
// Translation Tables (implementations see extra files)
// -----------------------------------------------------------------------

// ============================================================================
// Functions
// ============================================================================

}
#endif // def SEQAN_REDUCED_AMINOACID_CLUSTER_RED_BASE_H_
