13 #ifndef _OLIGOSTRINGKERNEL_H_
14 #define _OLIGOSTRINGKERNEL_H_
75 virtual const char*
get_name()
const {
return "OligoStringKernel"; }
99 const std::string& sequence, uint32_t k_mer_length,
100 const std::string& allowed_characters,
101 std::vector< std::pair<int32_t, float64_t> >& values);
111 const std::vector<std::string>& sequences,
112 uint32_t k_mer_length,
const std::string& allowed_characters,
113 std::vector< std::vector< std::pair<int32_t, float64_t> > >& encoded_sequences);
131 const std::vector< std::pair<int32_t, float64_t> >& x,
132 const std::vector< std::pair<int32_t, float64_t> >& y,
133 int32_t max_distance = -1);
146 void getExpFunctionCache(uint32_t sequence_length);
148 static inline bool cmpOligos_(std::pair<int32_t, float64_t> a,
149 std::pair<int32_t, float64_t> b )
151 return (a.second < b.second);
167 #endif // _OLIGOSTRINGKERNEL_H_