// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
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// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Definitions for piggybacking qualities in free bits of bytes.
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_

// TODO(holtgrew): Should the documentation be here?

namespace seqan {

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

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

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

// ----------------------------------------------------------------------------
// Metafunction QualityValueSize
// ----------------------------------------------------------------------------

// TODO(holtgrew): Do we want a default specialization? Should it return 0?
template <typename TValue>
struct QualityValueSize
{
    enum { VALUE = ValueSize<TValue>::VALUE };
};

template <typename TValue>
struct QualityValueSize<TValue const> : QualityValueSize<TValue>
{};

// ----------------------------------------------------------------------------
// Metafunction HasQualities
// ----------------------------------------------------------------------------

template <typename TValue>
struct HasQualities
{
    typedef False Type;
    static const bool VALUE = false;
};

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

// ----------------------------------------------------------------------------
// Function assignQualityValue()
// ----------------------------------------------------------------------------

// Documentation is in alphabet_concept.h.

// ----------------------------------------------------------------------------
// Function getQualityValue()
// ----------------------------------------------------------------------------

// Documentation is in alphabet_concept.h.

// ----------------------------------------------------------------------------
// Function convertQuality()
// ----------------------------------------------------------------------------

// TODO(holtgrew): This could use some thought, what about other scales?

/*!
 * @fn convertQuality
 * @headerfile <seqan/basic.h>
 *
 * @brief Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
 *
 * @signature void convertQuality(c, q);
 *
 * @param[in]  q Value of the quality to convert.  The quality value is an integral value between 0 and 62
 *               (inclusive), <tt>int</tt>.
 * @param[out] c Character to store the quality in, <tt>char</tt>.
 *
 * @see AlphabetWithQualitiesConcept#getQualityValue
 * @see AlphabetWithQualitiesConcept#assignQualityValue
 */

inline
void convertQuality(char & c, int q)
{
    c = '!' + char(q);
}

}  // namespace seqan

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
