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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _KmerInit_
#define _KmerInit_
#include "LargeInt.hpp"
#include <boost/variant.hpp>
#include <unordered_map>
/******************
This is the only place where we manipulate boost::variant directly. The rest of the code MUST use these definitions and boost::visitor
*******************/
using namespace std;
namespace DeBruijn {
#define MaxPrec 16 // kmer up to 512
template<template<int, typename...> class BoundedType, typename... V>
using BoostVariant = boost::variant<BoundedType<1,V...>, BoundedType<2,V...>, BoundedType<3,V...>, BoundedType<4,V...>,
BoundedType<5,V...>, BoundedType<6,V...>, BoundedType<7,V...>, BoundedType<8,V...>,
BoundedType<9,V...>, BoundedType<10,V...>, BoundedType<11,V...>, BoundedType<12,V...>,
BoundedType<13,V...>, BoundedType<14,V...>, BoundedType<15,V...>, BoundedType<16,V...>>;
// for TKmer
typedef BoostVariant<LargeInt> TLargeIntN;
// for TKmerCount
template<int N> using TLargeIntVec = vector<pair<LargeInt<N>,size_t>>;
typedef BoostVariant<TLargeIntVec> TKmerCountN;
// for TKmerMap
struct SKmerHash {
template<typename T>
size_t operator() (const T& kmer) const { return kmer.oahash(); }
};
template<int N, class V> using TLargeIntMap = unordered_map<LargeInt<N>,V,SKmerHash>;
template<class V> using TKmerMapN = BoostVariant<TLargeIntMap, V>;
// This variadic template could be used in construsctors of all boost::variants used in this code
template<typename Variant, template<int, typename...> class BoundedType, typename... Params>
Variant CreateVariant(int p) {
switch(p) {
case 1 : return BoundedType<1, Params...>();
case 2 : return BoundedType<2, Params...>();
case 3 : return BoundedType<3, Params...>();
case 4 : return BoundedType<4, Params...>();
case 5 : return BoundedType<5, Params...>();
case 6 : return BoundedType<6, Params...>();
case 7 : return BoundedType<7, Params...>();
case 8 : return BoundedType<8, Params...>();
case 9 : return BoundedType<9, Params...>();
case 10 : return BoundedType<10, Params...>();
case 11 : return BoundedType<11, Params...>();
case 12 : return BoundedType<12, Params...>();
case 13 : return BoundedType<13, Params...>();
case 14 : return BoundedType<14, Params...>();
case 15 : return BoundedType<15, Params...>();
case 16 : return BoundedType<16, Params...>();
default : throw runtime_error("Not supported kmer length");
}
}
}; // namespace
#endif /* _KmerInit_ */
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