OligoStringKernel.h
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00013 #ifndef _OLIGOSTRINGKERNEL_H_
00014 #define _OLIGOSTRINGKERNEL_H_
00015
00016 #include "kernel/StringKernel.h"
00017
00018 #include <vector>
00019 #include <string>
00020
00039 class COligoStringKernel : public CStringKernel<char>
00040 {
00041 public:
00047 COligoStringKernel(int32_t cache_size, int32_t k, float64_t width);
00048
00050 virtual ~COligoStringKernel();
00051
00058 virtual bool init(CFeatures* l, CFeatures* r);
00059
00064 virtual bool load_init(FILE*)
00065 {
00066 return false;
00067 }
00068
00073 virtual bool save_init(FILE*)
00074 {
00075 return false;
00076 }
00077
00082 virtual EKernelType get_kernel_type() { return K_OLIGO; }
00083
00088 virtual const char* get_name() const { return "Oligo"; }
00089
00090
00091 virtual float64_t compute(int32_t x, int32_t y);
00092
00095 virtual void cleanup();
00096
00097 protected:
00111 static void encodeOligo(
00112 const std::string& sequence, uint32_t k_mer_length,
00113 const std::string& allowed_characters,
00114 std::vector< std::pair<int32_t, float64_t> >& values);
00115
00123 static void getSequences(
00124 const std::vector<std::string>& sequences,
00125 uint32_t k_mer_length, const std::string& allowed_characters,
00126 std::vector< std::vector< std::pair<int32_t, float64_t> > >& encoded_sequences);
00127
00143 float64_t kernelOligoFast(
00144 const std::vector< std::pair<int32_t, float64_t> >& x,
00145 const std::vector< std::pair<int32_t, float64_t> >& y,
00146 int32_t max_distance = -1);
00147
00148 private:
00159 void getExpFunctionCache(uint32_t sequence_length);
00160
00161 static inline bool cmpOligos_(std::pair<int32_t, float64_t> a,
00162 std::pair<int32_t, float64_t> b )
00163 {
00164 return (a.second < b.second);
00165 }
00166
00167 protected:
00169 int32_t k;
00171 float64_t width;
00173 float64_t* gauss_table;
00174 };
00175 #endif // _OLIGOSTRINGKERNEL_H_