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00011 #ifndef _REGULATORYMODULESSTRINGKERNEL_H___
00012 #define _REGULATORYMODULESSTRINGKERNEL_H___
00013
00014 #include "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 #include "features/SimpleFeatures.h"
00017
00018 namespace shogun
00019 {
00025 class CRegulatoryModulesStringKernel: public CStringKernel<char>
00026 {
00027 public:
00029 CRegulatoryModulesStringKernel(void);
00030
00039 CRegulatoryModulesStringKernel(int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window);
00040
00053 CRegulatoryModulesStringKernel(CStringFeatures<char>* lstr, CStringFeatures<char>* rstr,
00054 CSimpleFeatures<uint16_t>* lpos, CSimpleFeatures<uint16_t>* rpos,
00055 float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10);
00056
00058 virtual ~CRegulatoryModulesStringKernel();
00059
00066 virtual bool init(CFeatures* l, CFeatures* r);
00067
00072 virtual EKernelType get_kernel_type() { return K_REGULATORYMODULES; }
00073
00078 inline virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; }
00079
00085 void set_motif_positions(
00086 CSimpleFeatures<uint16_t>* positions_lhs, CSimpleFeatures<uint16_t>* positions_rhs);
00087
00088 protected:
00097 virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00098
00106 float64_t compute_wds(char* avec, char* bvec, int32_t len);
00107
00108
00110 void set_wd_weights();
00111
00112 protected:
00114 float64_t width;
00115
00117 int32_t degree;
00119 int32_t shift;
00120
00122 int32_t window;
00123
00125 CSimpleFeatures<uint16_t>* motif_positions_lhs;
00126
00128 CSimpleFeatures<uint16_t>* motif_positions_rhs;
00129
00131 float64_t* position_weights;
00132
00134 float64_t* weights;
00135 };
00136 }
00137 #endif