/usr/include/blasr/algorithms/anchoring/LISPValueWeightor.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | #ifndef _BLASR_LISPVALUE_WEIGHTOR_HPP_
#define _BLASR_LISPVALUE_WEIGHTOR_HPP_
#include "algorithms/anchoring/LISPValue.hpp"
#include "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 "algorithms/anchoring/LISPValueWeightorImpl.hpp"
#endif
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