// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
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// ==========================================================================
// Author: Kristin Knorr <kristin.knorr@fu-berlin.de>
// ==========================================================================
// Buchfink11 reduction of AminoAcid alphabet
// ==========================================================================

#ifndef SEQAN_REDUCED_AMINOACID_BUCHFINK11_BASE_H_
#define SEQAN_REDUCED_AMINOACID_BUCHFINK11_BASE_H_

namespace seqan {

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

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

// -----------------------------------------------------------------------
// Tag Buchfink11
// -----------------------------------------------------------------------

/*!
 * @tag Buchfink11
 * @brief Specialization for @link ReducedAminoAcid @endlink#
 * @headerfile seqan/reduced_aminoacid.h
 *
 * @signature typedef Buchfink11 Tag<Buchfink11_>;
 *
 * This is the 11-character reduction defined by Buchfink et al,
 * 2014, <a href="https://www.ncbi.nlm.nih.gov/pubmed/25402007">https://www.ncbi.nlm.nih.gov/pubmed/25402007</a>
 *
 * This alphabet is used by tool Diamond.
 *
 * Since it was created from the 20-letter alphabet the clusters in SeqAn are
 * not identical (they contain more symbols). This is the clustering:
 * @code{.txt}
 *   'A', // A S T X
 *   'B', // B D E K N O Q R Z
 *   'C', // C U
 *   'F', // F *
 *   'G', // G
 *   'H', // H
 *   'I', // I J L V
 *   'M', // M
 *   'P', // P
 *   'W', // W
 *   'Y'  // Y
 * @endcode
 *
 */

struct Buchfink11_ {};

typedef Tag<Buchfink11_> Buchfink11;

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

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

template <>
struct ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Buchfink11> > >
{
    typedef uint8_t Type;
    static const Type VALUE = 11;
};

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

template <>
struct BitsPerValue<SimpleType<unsigned char, ReducedAminoAcid_<Buchfink11> > >
{
    typedef uint8_t Type;
    static const Type VALUE = 4;
};

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

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

}
#endif // def SEQAN_REDUCED_AMINOACID_BUCHFINK11_BASE_H_
