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00011 #ifndef _SNPFEATURES_H___
00012 #define _SNPFEATURES_H___
00013
00014 #include <shogun/lib/common.h>
00015 #include <shogun/features/DotFeatures.h>
00016 #include <shogun/features/StringFeatures.h>
00017
00018 namespace shogun
00019 {
00020 template <class ST> class CStringFeatures;
00021
00027 class CSNPFeatures : public CDotFeatures
00028 {
00029 public:
00031 CSNPFeatures();
00032
00037 CSNPFeatures(CStringFeatures<uint8_t>* str);
00038
00040 CSNPFeatures(const CSNPFeatures & orig);
00041
00043 virtual ~CSNPFeatures();
00044
00052 virtual int32_t get_dim_feature_space() const;
00053
00061 virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2);
00062
00069 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
00070
00079 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1,
00080 float64_t* vec2, int32_t vec2_len, bool abs_val=false);
00081
00087 virtual int32_t get_nnz_features_for_vector(int32_t num);
00088
00098 virtual void* get_feature_iterator(int32_t vector_index);
00099
00110 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator);
00111
00117 virtual void free_feature_iterator(void* iterator);
00118
00123 virtual CFeatures* duplicate() const;
00124
00129 virtual EFeatureType get_feature_type();
00130
00135 virtual EFeatureClass get_feature_class();
00136
00141 virtual int32_t get_num_vectors() const;
00142
00147 virtual int32_t get_size();
00148
00151 void set_normalization_const(float64_t n=0);
00152
00154 float64_t get_normalization_const();
00155
00160 void set_minor_base_string(const char* str);
00161
00166 void set_major_base_string(const char* str);
00167
00172 char* get_minor_base_string();
00173
00178 char* get_major_base_string();
00179
00185 void obtain_base_strings(CSNPFeatures* snp=NULL);
00186
00188 virtual const char* get_name() const { return "SNPFeatures"; }
00189
00192 virtual SGMatrix<float64_t> get_histogram(bool normalize=true);
00193
00197 static SGMatrix<float64_t> get_2x3_table(CSNPFeatures* pos, CSNPFeatures* neg);
00198
00199 private:
00206 void find_minor_major_strings(uint8_t* minor, uint8_t* major);
00207
00208 protected:
00210 CStringFeatures<uint8_t>* strings;
00211
00213 int32_t string_length;
00215 int32_t num_strings;
00217 int32_t w_dim;
00218
00220 float64_t normalization_const;
00221
00223 uint8_t* m_str_min;
00225 uint8_t* m_str_maj;
00226 };
00227 }
00228 #endif // _SNPFEATURES_H___