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#ifndef _BLASR_LISPVALUE_WEIGHTOR_HPP_
#define _BLASR_LISPVALUE_WEIGHTOR_HPP_
#include <alignment/algorithms/anchoring/LISPValue.hpp>
#include <alignment/tuples/TupleMetrics.hpp>
template <typename T_RefSequence, typename T_MatchList>
class LISSumOfLogPWeightor
{
public:
DNALength genomeLength;
LISSumOfLogPWeightor(T_RefSequence &targetGenome);
float ComputePValue(T_MatchList &matchList, int &noOvpLisNBases, int &noOvpLisSize);
float operator()(T_MatchList &matchList);
};
template <typename T_RefSequence, typename T_Tuple, typename T_MatchList>
class LISSMatchFrequencyPValueWeightor
{
public:
T_RefSequence target;
LISSMatchFrequencyPValueWeightor(T_RefSequence &_target);
float ComputePValue(T_MatchList &lis, int &noOvpLisNBases, int &noOvpLisSize);
float operator()(T_MatchList &lis);
};
template <typename T_RefSequence, typename T_Tuple, typename T_MatchList>
class LISPValueWeightor
{
public:
//
// All of these must be initialized prior to
// computing weights (running the functor).
//
FASTASequence query;
T_RefSequence target;
TupleMetrics tm;
TupleCountTable<T_RefSequence, T_Tuple> *ct;
LISPValueWeightor(FASTASequence &_query, T_RefSequence &_target, TupleMetrics _tm,
TupleCountTable<T_RefSequence, T_Tuple> *_ct);
float ComputePValue(T_MatchList &matchList, int &noOvpLisNBases, int &noOvpLisSize);
float operator()(T_MatchList &matchList);
};
#include "LISPValueWeightorImpl.hpp"
#endif
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