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
00021 namespace shogun
00022 {
00041 class COligoStringKernel : public CStringKernel<char>
00042 {
00043 public:
00049 COligoStringKernel(int32_t cache_size, int32_t k, float64_t width);
00050
00052 virtual ~COligoStringKernel();
00053
00060 virtual bool init(CFeatures* l, CFeatures* r);
00061
00066 virtual EKernelType get_kernel_type() { return K_OLIGO; }
00067
00072 virtual const char* get_name() const { return "Oligo"; }
00073
00074
00075 virtual float64_t compute(int32_t x, int32_t y);
00076
00079 virtual void cleanup();
00080
00081 protected:
00095 static void encodeOligo(
00096 const std::string& sequence, uint32_t k_mer_length,
00097 const std::string& allowed_characters,
00098 std::vector< std::pair<int32_t, float64_t> >& values);
00099
00107 static void getSequences(
00108 const std::vector<std::string>& sequences,
00109 uint32_t k_mer_length, const std::string& allowed_characters,
00110 std::vector< std::vector< std::pair<int32_t, float64_t> > >& encoded_sequences);
00111
00127 float64_t kernelOligoFast(
00128 const std::vector< std::pair<int32_t, float64_t> >& x,
00129 const std::vector< std::pair<int32_t, float64_t> >& y,
00130 int32_t max_distance = -1);
00131
00132 private:
00143 void getExpFunctionCache(uint32_t sequence_length);
00144
00145 static inline bool cmpOligos_(std::pair<int32_t, float64_t> a,
00146 std::pair<int32_t, float64_t> b )
00147 {
00148 return (a.second < b.second);
00149 }
00150
00151 protected:
00153 int32_t k;
00155 float64_t width;
00157 float64_t* gauss_table;
00158 };
00159 }
00160 #endif // _OLIGOSTRINGKERNEL_H_