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// Author: David Alexander, Lance Hepler
#pragma once
#include <ConsensusCore/Mutation.hpp>
#include <ConsensusCore/Types.hpp>
#include <ConsensusCore/Utils.hpp>
#include <string>
#include <vector>
namespace ConsensusCore {
namespace detail {
struct AbstractMutationEnumerator
{
explicit AbstractMutationEnumerator(const std::string& tpl);
virtual ~AbstractMutationEnumerator();
virtual std::vector<Mutation> Mutations() const = 0;
virtual std::vector<Mutation> Mutations(int beginPos, int endPos) const = 0;
protected:
const std::string tpl_;
};
} // detail
struct AllSingleBaseMutationEnumerator : detail::AbstractMutationEnumerator
{
explicit AllSingleBaseMutationEnumerator(const std::string& tpl);
std::vector<Mutation> Mutations() const;
std::vector<Mutation> Mutations(int beginPos, int endPos) const;
};
struct UniqueSingleBaseMutationEnumerator : detail::AbstractMutationEnumerator
{
explicit UniqueSingleBaseMutationEnumerator(const std::string& tpl);
std::vector<Mutation> Mutations() const;
std::vector<Mutation> Mutations(int beginPos, int endPos) const;
};
struct DinucleotideRepeatMutationEnumerator : detail::AbstractMutationEnumerator
{
DinucleotideRepeatMutationEnumerator(const std::string& tpl, int minDinucRepeatElements = 3);
std::vector<Mutation> Mutations() const;
std::vector<Mutation> Mutations(int beginPos, int endPos) const;
private:
int minDinucRepeatElements_;
};
template <typename T>
std::vector<Mutation> UniqueNearbyMutations(const T& mutationEnumerator,
const std::vector<Mutation>& centers,
int neighborhoodSize);
}
#include <ConsensusCore/Quiver/MutationEnumerator-inl.hpp>
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