SHOGUN v0.9.0
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00001 /* 00002 * This program is free software; you can redistribute it and/or modify 00003 * it under the terms of the GNU General Public License as published by 00004 * the Free Software Foundation; either version 3 of the License, or 00005 * (at your option) any later version. 00006 * 00007 * Written (W) 2009 Soeren Sonnenburg 00008 * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society 00009 */ 00010 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: 00031 CExplicitSpecFeatures(void); 00032 00038 CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true); 00039 00041 CExplicitSpecFeatures(const CExplicitSpecFeatures & orig); 00042 00044 virtual ~CExplicitSpecFeatures(); 00045 00050 virtual CFeatures* duplicate() const; 00051 00059 inline virtual int32_t get_dim_feature_space() 00060 { 00061 return spec_size; 00062 } 00063 00071 virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2); 00072 00079 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len); 00080 00089 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false); 00090 00092 struct explicit_spec_feature_iterator 00093 { 00095 uint16_t* vec; 00097 int32_t vidx; 00099 int32_t vlen; 00101 bool vfree; 00102 00104 int32_t index; 00105 00106 }; 00107 00117 virtual void* get_feature_iterator(int32_t vector_index) 00118 { 00119 SG_NOTIMPLEMENTED; 00120 return NULL; 00121 } 00122 00133 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator) 00134 { 00135 SG_NOTIMPLEMENTED; 00136 return NULL; 00137 } 00138 00144 virtual void free_feature_iterator(void* iterator) 00145 { 00146 SG_NOTIMPLEMENTED; 00147 } 00148 00154 virtual inline int32_t get_nnz_features_for_vector(int32_t num) 00155 { 00156 SG_NOTIMPLEMENTED; 00157 return 0; 00158 } 00159 00164 inline virtual EFeatureType get_feature_type() 00165 { 00166 return F_UNKNOWN; 00167 } 00168 00173 inline virtual EFeatureClass get_feature_class() 00174 { 00175 return C_SPEC; 00176 } 00177 00182 inline virtual int32_t get_num_vectors() 00183 { 00184 return num_strings; 00185 } 00186 00191 inline virtual int32_t get_size() 00192 { 00193 return sizeof(float64_t); 00194 } 00195 00197 inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; } 00198 00199 protected: 00204 void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str); 00205 00207 void delete_kmer_spectrum(); 00208 00209 protected: 00211 bool use_normalization; 00213 int32_t num_strings; 00215 int32_t alphabet_size; 00216 00218 int32_t spec_size; 00220 float64_t** k_spectrum; 00221 }; 00222 } 00223 #endif // _EXPLICITSPECFEATURES_H___