// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
// All rights reserved.
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// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_HEADER_STORE_MATEPAIR_H
#define SEQAN_HEADER_STORE_MATEPAIR_H

namespace seqan
{

//////////////////////////////////////////////////////////////////////////////
// Mate Store
//////////////////////////////////////////////////////////////////////////////

/*!
 * @class MatePairStoreElement
 * @brief Represents a mate pair.
 *
 * @signature template <[typename TSpec]>
 *            struct MatePairStoreElement;
 *
 * @tparam TSpec The specializing type.
 *
 * A mate pair consists of two reads sequences from opposite ends of the same fragment.  The insert size of a mate pair
 * is the inferred size of the fragment.
 *
 *
 * @fn MatePairStoreElement::MatePairStoreElement
 * @brief Constructor.
 *
 * @signature MatePairStoreElement::MatePairStoreElement();
 *
 * Initialize all member values to INVALID_ID.
 */

/*!
 * @var TId MatePairStoreElement::INVALID_ID;
 * @brief Constant to represent an invalid id.
 *
 * @var TId MatePairStoreElement::libId;
 * @brief Refers to a library in the @link FragmentStore::libraryStore @endlink or is INVALID_ID if the mate pair
 *        has no library.
 *
 * @var TId[2] MatePairStoreElement::readId;
 * @brief Refers to two paried reads in @link FragmentStore::readStore @endlink or is INVALID_ID values.
 */

template <typename TSpec = void>
struct MatePairStoreElement
{
    typedef typename Id<MatePairStoreElement>::Type TId;

    static const TId INVALID_ID;

    TId        readId[2];    // refers to the two reads of a mate-pair, INVALID_ID if this is a singleton fragment (e.g. in afg: reads refer to fragments (mate pairs) and these refer to libraries, singletons refer to an empty fragment)
    TId        libId;

    MatePairStoreElement() : libId(INVALID_ID)
    {
        readId[0] = INVALID_ID;
        readId[1] = INVALID_ID;
    }

    inline bool operator==(MatePairStoreElement const & other) const
    {
        return readId[0] == other.readId[0] &&
                readId[1] == other.readId[1] &&
                libId == other.libId;
    }
};

//////////////////////////////////////////////////////////////////////////////

/*!
 * @mfn MatePairStoreElement#Id
 * @headerfile <seqan/store.h>
 * @brief Returns the id type to use for <tt>MatePairStoreElement</tt>.
 *
 * @signature Id<TMatePairStoreElement>::Type;
 *
 * @tparam TMatePairStoreElement The MatePairStoreElement specialization to get the id type for.
 *
 * @return Type The resulting id type.
 */

template <typename TSpec>
const typename Id<MatePairStoreElement<TSpec> >::Type
MatePairStoreElement<TSpec>::INVALID_ID = std::numeric_limits<typename Id<MatePairStoreElement<TSpec> >::Type>::max();

//////////////////////////////////////////////////////////////////////////////

}// namespace seqan

#endif //#ifndef SEQAN_HEADER_...
