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) 2010 Soeren Sonnenburg 00008 * Copyright (C) 2010 Berlin Institute of Technology 00009 */ 00010 00011 #ifndef _SNPFEATURES_H___ 00012 #define _SNPFEATURES_H___ 00013 00014 #include "lib/common.h" 00015 #include "features/DotFeatures.h" 00016 #include "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(void); 00032 00037 CSNPFeatures(CStringFeatures<uint8_t>* str); 00038 00040 CSNPFeatures(const CSNPFeatures & orig); 00041 00043 virtual ~CSNPFeatures(); 00044 00052 inline virtual int32_t get_dim_feature_space() 00053 { 00054 return w_dim; 00055 } 00056 00064 virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2); 00065 00072 virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len); 00073 00082 virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t* vec2, int32_t vec2_len, bool abs_val=false); 00083 00089 virtual inline int32_t get_nnz_features_for_vector(int32_t num) 00090 { 00091 return w_dim/3; 00092 } 00093 00103 virtual void* get_feature_iterator(int32_t vector_index); 00104 00115 virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator); 00116 00122 virtual void free_feature_iterator(void* iterator); 00123 00128 virtual CFeatures* duplicate() const; 00129 00134 inline virtual EFeatureType get_feature_type() 00135 { 00136 return F_UNKNOWN; 00137 } 00138 00143 inline virtual EFeatureClass get_feature_class() 00144 { 00145 return C_WD; 00146 } 00147 00152 inline virtual int32_t get_num_vectors() 00153 { 00154 return num_strings; 00155 } 00156 00161 inline virtual int32_t get_size() 00162 { 00163 return sizeof(float64_t); 00164 } 00165 00168 void set_normalization_const(float64_t n=0); 00169 00171 inline float64_t get_normalization_const() 00172 { 00173 return normalization_const; 00174 } 00175 00180 void set_minor_base_string(const char* str) 00181 { 00182 m_str_min=(uint8_t*) strdup(str); 00183 } 00184 00185 00190 void set_major_base_string(const char* str) 00191 { 00192 m_str_maj=(uint8_t*) strdup(str); 00193 } 00194 00195 00200 char* get_minor_base_string() 00201 { 00202 return (char*) m_str_min; 00203 } 00204 00205 00210 char* get_major_base_string() 00211 { 00212 return (char*) m_str_maj; 00213 } 00214 00216 void obtain_base_strings(); 00217 00218 00220 inline virtual const char* get_name() const { return "SNPFeatures"; } 00221 00222 protected: 00224 CStringFeatures<uint8_t>* strings; 00225 00227 int32_t string_length; 00229 int32_t num_strings; 00231 int32_t w_dim; 00232 00234 float64_t normalization_const; 00235 00237 uint8_t* m_str_min; 00239 uint8_t* m_str_maj; 00240 00241 }; 00242 } 00243 #endif // _SNPFEATURES_H___