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#ifndef _BLASR_GLOBAL_CHAIN_HPP_
#define _BLASR_GLOBAL_CHAIN_HPP_
#include <vector>
// pbdata
#include "../../../pbdata/Types.h"
#include "../../../pbdata/DNASequence.hpp"
#include "PrioritySearchTree.hpp"
template<typename T_Fragment, typename T_Endpoint>
void FragmentSetToEndpoints(T_Fragment* fragments, int nFragments,
std::vector<T_Endpoint> &endpoints);
template<typename T_Fragment>
UInt RestrictedGlobalChain(T_Fragment *fragments,
DNALength nFragments, float maxIndelRate,
std::vector<VectorIndex>& optFragmentChainIndices,
std::vector<UInt>& scores, std::vector<UInt>& prevOpt);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain( T_Fragment *fragments,
DNALength nFragments,
std::vector<VectorIndex> &optFragmentChainIndices,
std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain(std::vector<T_Fragment> &fragments,
std::vector<VectorIndex> &optFragmentChainIndices);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain(std::vector<T_Fragment> &fragments,
DNALength start, DNALength end,
std::vector<VectorIndex> &optFragmentChainIndices,
std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
#include "GlobalChainImpl.hpp"
#endif
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