// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
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// modification, are permitted provided that the following conditions are met:
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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_BASE_LATE_H_
#define SEQAN_REDUCED_AMINOACID_BASE_LATE_H_

namespace seqan2 {

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

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

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

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

// -----------------------------------------------------------------------
// Function unknownValueImpl()
// -----------------------------------------------------------------------

template <typename TRedSpec>
inline SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >
unknownValueImpl(SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> > *)
{
    static const SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >
      _result = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >('X');
    return _result;
}

// -----------------------------------------------------------------------
// Function assign()
// -----------------------------------------------------------------------

template <typename TRedSpec>
inline void assign(char & c_target, SimpleType<unsigned char,
                   ReducedAminoAcid_<TRedSpec> > const & source)
{
    c_target = TranslateTableRedAAToChar_<TRedSpec>::VALUE[source.value];
}

template <typename TRedSpec>
inline void assign(SimpleType<unsigned char,
                   ReducedAminoAcid_<TRedSpec> > & target,
                   uint8_t c_source)
{
    target.value = TranslateTableByteToRedAA_<TRedSpec>::VALUE[c_source];
}

template <typename TRedSpec>
inline void assign(SimpleType<unsigned char,
                   ReducedAminoAcid_<TRedSpec> > & target,
                   char c_source)
{
    target.value = TranslateTableCharToRedAA_<TRedSpec>::VALUE[(unsigned char) c_source];
}

template <typename TRedSpec>
inline void assign(SimpleType<unsigned char,
                   ReducedAminoAcid_<TRedSpec> > & target,
                   AminoAcid c_source)
{
    target.value = TranslateTableAAToRedAA_<TRedSpec>::VALUE[c_source.value];
}

}
#endif // def SEQAN_REDUCED_AMINOACID_BASE_LATE_H_
