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00011 #ifndef _EXPLICITSPECFEATURES_H___
00012 #define _EXPLICITSPECFEATURES_H___
00013
00014 #include "lib/common.h"
00015 #include "lib/io.h"
00016 #include "features/DotFeatures.h"
00017 #include "features/StringFeatures.h"
00018
00019 namespace shogun
00020 {
00021 template <class ST> class CStringFeatures;
00022
00027 class CExplicitSpecFeatures : public CDotFeatures
00028 {
00029 public:
00030
00036 CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true);
00037
00039 CExplicitSpecFeatures(const CExplicitSpecFeatures & orig);
00040
00042 virtual ~CExplicitSpecFeatures();
00043
00048 virtual CFeatures* duplicate() const;
00049
00057 inline virtual int32_t get_dim_feature_space()
00058 {
00059 return spec_size;
00060 }
00061
00068 virtual float64_t dot(int32_t vec_idx1, int32_t vec_idx2);
00069
00076 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
00077
00086 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false);
00087
00089 struct explicit_spec_feature_iterator
00090 {
00092 uint16_t* vec;
00094 int32_t vidx;
00096 int32_t vlen;
00098 bool vfree;
00099
00101 int32_t index;
00102
00103 };
00104
00114 virtual void* get_feature_iterator(int32_t vector_index)
00115 {
00116 SG_NOTIMPLEMENTED;
00117 return NULL;
00118 }
00119
00130 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator)
00131 {
00132 SG_NOTIMPLEMENTED;
00133 return NULL;
00134 }
00135
00141 virtual void free_feature_iterator(void* iterator)
00142 {
00143 SG_NOTIMPLEMENTED;
00144 }
00145
00151 virtual inline int32_t get_nnz_features_for_vector(int32_t num)
00152 {
00153 SG_NOTIMPLEMENTED;
00154 return 0;
00155 }
00156
00161 inline virtual EFeatureType get_feature_type()
00162 {
00163 return F_UNKNOWN;
00164 }
00165
00170 inline virtual EFeatureClass get_feature_class()
00171 {
00172 return C_SPEC;
00173 }
00174
00179 inline virtual int32_t get_num_vectors()
00180 {
00181 return num_strings;
00182 }
00183
00188 inline virtual int32_t get_size()
00189 {
00190 return sizeof(float64_t);
00191 }
00192
00194 inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; }
00195
00196 protected:
00201 void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str);
00202
00204 void delete_kmer_spectrum();
00205
00206 protected:
00208 bool use_normalization;
00210 int32_t num_strings;
00212 int32_t alphabet_size;
00213
00215 int32_t spec_size;
00217 float64_t** k_spectrum;
00218 };
00219 }
00220 #endif // _EXPLICITSPECFEATURES_H___