14 #ifndef _OLIGOSTRINGKERNEL_H_
15 #define _OLIGOSTRINGKERNEL_H_
86 virtual const char*
get_name()
const {
return "OligoStringKernel"; }
110 const std::string& sequence, uint32_t k_mer_length,
111 const std::string& allowed_characters,
112 std::vector< std::pair<int32_t, float64_t> >& values);
122 const std::vector<std::string>& sequences,
123 uint32_t k_mer_length,
const std::string& allowed_characters,
124 std::vector< std::vector< std::pair<int32_t, float64_t> > >& encoded_sequences);
142 const std::vector< std::pair<int32_t, float64_t> >& x,
143 const std::vector< std::pair<int32_t, float64_t> >& y,
144 int32_t max_distance = -1);
154 const std::vector< std::pair<int32_t, float64_t> >& x,
155 const std::vector< std::pair<int32_t, float64_t> >& y);
169 void getExpFunctionCache(uint32_t sequence_length);
171 static inline bool cmpOligos_(std::pair<int32_t, float64_t> a,
172 std::pair<int32_t, float64_t> b )
174 return (a.second < b.second);
188 #endif // _OLIGOSTRINGKERNEL_H_