// Copyright 2009, Andreas Biegert #ifndef CS_CONTEXT_LIB_PSEUDOCOUNTS_H_ #define CS_CONTEXT_LIB_PSEUDOCOUNTS_H_ #include "count_profile-inl.h" #include "emission.h" #include "profile-inl.h" #include "pseudocounts.h" #include "sequence-inl.h" #include "context_library-inl.h" namespace cs { // Encapsulation of context-specific pseudocounts calculated from a library // of context profiles. template class LibraryPseudocounts : public Pseudocounts { public: LibraryPseudocounts(const ContextLibrary& lib, double weight_center = 1.6, double weight_decay = 0.85); virtual ~LibraryPseudocounts() {} virtual void AddToSequence(const Sequence& seq, const Admix& pca, Profile& p) const; virtual void AddToProfile(const CountProfile& cp, const Admix& pca, Profile& p) const; private: // Profile library with context profiles. const ContextLibrary& lib_; // Needed to compute emission probabilities of context profiles. const Emission emission_; DISALLOW_COPY_AND_ASSIGN(LibraryPseudocounts); }; // LibraryPseudocounts } // namespace cs #endif // CS_CONTEXT_LIB_PSEUDOCOUNTS_H_